Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.
Transport proteins that carry specific substances in the blood or across cell membranes.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
Proteins found in any species of bacterium.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
The process by which a DNA molecule is duplicated.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Established cell cultures that have the potential to propagate indefinitely.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Proteins found in any species of virus.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Deoxyribonucleic acid that makes up the genetic material of viruses.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Proteins prepared by recombinant DNA technology.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-
The rate dynamics in chemical or physical systems.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Proteins obtained from ESCHERICHIA COLI.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.
A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)
The sum of the weight of all the atoms in a molecule.
Nucleic acid sequences involved in regulating the expression of genes.
Y-box-binding protein 1 was originally identified as a DNA-binding protein that interacts with Y-box PROMOTER REGIONS of MHC CLASS II GENES. It is a highly conserved transcription factor that regulates expression of a wide variety of GENES.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Proteins found in any species of fungus.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.
A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Proteins that specifically bind to TELOMERES. Proteins in this class include those that perform functions such as telomere capping, telomere maintenance and telomere stabilization.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A family of transcription factors found primarily in PLANTS that bind to the G-box DNA sequence CACGTG or to a consensus sequence CANNTG.
A cellular transcriptional coactivator that was originally identified by its requirement for the stable assembly IMMEDIATE-EARLY PROTEINS of the HERPES SIMPLEX VIRUS. It is a nuclear protein that is a transcriptional coactivator for a number of transcription factors including VP16 PROTEIN; GA-BINDING PROTEIN; EARLY GROWTH RESPONSE PROTEIN 2; and E2F4 TRANSCRIPTION FACTOR. It also interacts with and stabilizes HERPES SIMPLEX VIRUS PROTEIN VMW65 and helps regulate GENETIC TRANSCRIPTION of IMMEDIATE-EARLY GENES in HERPES SIMPLEX VIRUS.
A genus of aerobic, chemolithotrophic, coccoid ARCHAEA whose organisms are thermoacidophilic. Its cells are highly irregular in shape, often lobed, but occasionally spherical. It has worldwide distribution with organisms isolated from hot acidic soils and water. Sulfur is used as an energy source.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
A ubiquitously expressed sequence-specific transcriptional repressor that is normally the target of signaling by NOTCH PROTEINS.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.
A family of low-molecular weight, non-histone proteins found in chromatin.
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
Preparations of cell constituents or subcellular materials, isolates, or substances.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
Species of the genus MASTADENOVIRUS, causing a wide range of diseases in humans. Infections are mostly asymptomatic, but can be associated with diseases of the respiratory, ocular, and gastrointestinal systems. Serotypes (named with Arabic numbers) have been grouped into species designated Human adenovirus A-F.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
A DNA-dependent DNA polymerase characterized in E. coli and other lower organisms but may be present in higher organisms. Use also for a more complex form of DNA polymerase III designated as DNA polymerase III* or pol III* which is 15 times more active biologically than DNA polymerase I in the synthesis of DNA. This polymerase has both 3'-5' and 5'-3' exonuclease activities, is inhibited by sulfhydryl reagents, and has the same template-primer dependence as pol II. EC
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.
Inhibitor of differentiation proteins are negative regulators of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS. They inhibit CELL DIFFERENTIATION and induce CELL PROLIFERATION by modulating different CELL CYCLE regulators.
A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.
A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.
Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
Periplasmic proteins that scavenge or sense diverse nutrients. In the bacterial environment they usually couple to transporters or chemotaxis receptors on the inner bacterial membrane.
Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.
An individual having only one allele at a given locus because of the loss of the other allele through a mutation (e.g., CHROMOSOME DELETION).
A member of the p300-CBP transcription factor family that was initially identified as a binding partner for CAMP RESPONSE ELEMENT-BINDING PROTEIN. Mutations in CREB-binding protein are associated with RUBINSTEIN-TAYBI SYNDROME.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
A 12-KDa tacrolimus binding protein that is found associated with and may modulate the function of calcium release channels. It is a peptidyl-prolyl cis/trans isomerase which is inhibited by both tacrolimus (commonly called FK506) and SIROLIMUS.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
A family of secreted multidomain proteins that were originally identified by their association with the latent form of TRANSFORMING GROWTH FACTORS. They interact with a variety of EXTRACELLULAR MATRIX PROTEINS and may play a role in the regulation of TGB-beta bioavailability.
A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.
Biochemical identification of mutational changes in a nucleotide sequence.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.
Proteins found in any species of archaeon.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A genus of gram-positive aerobic cocci found in the soil, that is highly resistant to radiation, especially ionizing radiation (RADIATION, IONIZING). Deinococcus radiodurans is the type species.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
A family of non-enveloped viruses infecting mammals (MASTADENOVIRUS) and birds (AVIADENOVIRUS) or both (ATADENOVIRUS). Infections may be asymptomatic or result in a variety of diseases.
Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.
A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.
A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.
A highly abundant DNA binding protein whose expression is strongly correlated with the growth phase of bacteria. The protein plays a role in regulating DNA topology and activation of RIBOSOMAL RNA transcription. It was originally identified as a factor required for inversion stimulation by the Hin recombinase of SALMONELLA and Gin site-specific recombinase of BACTERIOPHAGE MU.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
A family of structurally related proteins that were originally discovered for their role in cell-cycle regulation in CAENORHABDITIS ELEGANS. They play important roles in regulation of the CELL CYCLE and as components of UBIQUITIN-PROTEIN LIGASES.
A complex of several closely related glycosidic antibiotics from Streptomyces griseus. The major component, CHROMOMYCIN A3, is used as a fluorescent stain of DNA where it attaches and inhibits RNA synthesis. It is also used as an antineoplastic agent, especially for solid tumors.
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
One of the six homologous proteins that specifically bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions. The function of this protein is not completely defined. However, several studies demonstrate that it inhibits IGF binding to cell surface receptors and thereby inhibits IGF-mediated mitogenic and cell metabolic actions. (Proc Soc Exp Biol Med 1993;204(1):4-29)
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
The functional hereditary units of FUNGI.

The surface ectoderm is essential for nephric duct formation in intermediate mesoderm. (1/69904)

The nephric duct is the first epithelial tubule to differentiate from intermediate mesoderm that is essential for all further urogenital development. In this study we identify the domain of intermediate mesoderm that gives rise to the nephric duct and demonstrate that the surface ectoderm is required for its differentiation. Removal of the surface ectoderm resulted in decreased levels of Sim-1 and Pax-2 mRNA expression in mesenchymal nephric duct progenitors, and caused inhibition of nephric duct formation and subsequent kidney development. The surface ectoderm expresses BMP-4 and we show that it is required for the maintenance of high-level BMP-4 expression in lateral plate mesoderm. Addition of a BMP-4-coated bead to embryos lacking the surface ectoderm restored normal levels of Sim-1 and Pax-2 mRNA expression in nephric duct progenitors, nephric duct formation and the initiation of nephrogenesis. Thus, BMP-4 signaling can substitute for the surface ectoderm in supporting nephric duct morphogenesis. Collectively, these data suggest that inductive interactions between the surface ectoderm, lateral mesoderm and intermediate mesoderm are essential for nephric duct formation and the initiation of urogenital development.  (+info)

Separation of shoot and floral identity in Arabidopsis. (2/69904)

The overall morphology of an Arabidopsis plant depends on the behaviour of its meristems. Meristems derived from the shoot apex can develop into either shoots or flowers. The distinction between these alternative fates requires separation between the function of floral meristem identity genes and the function of an antagonistic group of genes, which includes TERMINAL FLOWER 1. We show that the activities of these genes are restricted to separate domains of the shoot apex by different mechanisms. Meristem identity genes, such as LEAFY, APETALA 1 and CAULIFLOWER, prevent TERMINAL FLOWER 1 transcription in floral meristems on the apex periphery. TERMINAL FLOWER 1, in turn, can inhibit the activity of meristem identity genes at the centre of the shoot apex in two ways; first by delaying their upregulation, and second, by preventing the meristem from responding to LEAFY or APETALA 1. We suggest that the wild-type pattern of TERMINAL FLOWER 1 and floral meristem identity gene expression depends on the relative timing of their upregulation.  (+info)

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (3/69904)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (4/69904)

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3' untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3' untranslated region.  (+info)

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. (5/69904)

Early developmental patterning of the Drosophila embryo is driven by the activities of a diverse set of maternally and zygotically derived transcription factors, including repressors encoded by gap genes such as Kruppel, knirps, giant and the mesoderm-specific snail. The mechanism of repression by gap transcription factors is not well understood at a molecular level. Initial characterization of these transcription factors suggests that they act as short-range repressors, interfering with the activity of enhancer or promoter elements 50 to 100 bp away. To better understand the molecular mechanism of short-range repression, we have investigated the properties of the Giant gap protein. We tested the ability of endogenous Giant to repress when bound close to the transcriptional initiation site and found that Giant effectively represses a heterologous promoter when binding sites are located at -55 bp with respect to the start of transcription. Consistent with its role as a short-range repressor, as the binding sites are moved to more distal locations, repression is diminished. Rather than exhibiting a sharp 'step-function' drop-off in activity, however, repression is progressively restricted to areas of highest Giant concentration. Less than a two-fold difference in Giant protein concentration is sufficient to determine a change in transcriptional status of a target gene. This effect demonstrates that Giant protein gradients can be differentially interpreted by target promoters, depending on the exact location of the Giant binding sites within the gene. Thus, in addition to binding site affinity and number, cis element positioning within a promoter can affect the response of a gene to a repressor gradient. We also demonstrate that a chimeric Gal4-Giant protein lacking the basic/zipper domain can specifically repress reporter genes, suggesting that the Giant effector domain is an autonomous repression domain.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (6/69904)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

Requirement of a novel gene, Xin, in cardiac morphogenesis. (7/69904)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (8/69904)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

TY - JOUR. T1 - Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. AU - Montano, Sherwin P.. AU - Pierce, Michael. AU - Coté, Marie L.. AU - Vershon, Andrew K.. AU - Georgiadis, Millie. PY - 2002/12/1. Y1 - 2002/12/1. N2 - The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Ndt80 is strongly induced during the middle stages of the sporulation pathway and binds specifically to a promoter element called the MSE to activate transcription of genes required for the meiotic divisions. Here, the preliminary structural and functional studies to characterize the DNA-binding activity of this protein are reported. Through deletion analysis and limited proteolysis studies of Ndt80, a novel 32 kDa DNA-binding domain that is sufficient for DNA-binding in vitro has been defined. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been ...
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences (k-mers). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other ...
p53 is an allosterically regulated protein with a latent DNA-binding activity. Posttranslational modification of a carboxy-terminal regulatory site in vitro, by casein kinase II and protein kinase C, can activate the sequence-specific DNA-binding function of the wild-type protein. The latent form of...
DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of
Members of the ARID (AT-rich interaction domain) (see ,PDOC51011,) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. Bright/ARID3a and the other two members (Bdp/ARID3b and Bright-like/ARID3c) have been described as the extended or eARID subfamily, having additional conserved sequences at both the N and C termini of the core ARID domain. In addition to the conserved regions immediately adjacent to the core ARID, the eARID proteins also share a conserved motif C-terminal to the ARID, named the REKLES domain after a conserved amino acid motif. The REKLES domain has not been found in any non-ARID proteins. REKLES consists of two subdomains: a modestly conserved N-terminal REKLESα and a highly conserved C-terminal REKLESβ. REKLES is a multifunctional domain that as co-evolved with and regulates functional properties of the eARID DNA-binding domain. REKLESα and -β are required, respectively, for nuclear entry and export of Bright during its ...
The manipulation of DNA by proteins is central to the life of a cell. It is critical for processes ranging from replication and recombination to transcription and the repair of DNA damage. Introduction to Protein-DNA Interactions, written by Gary Stormo, provides an up-to-date and interdisciplinary perspective on protein-DNA interactions, with an emphasis on DNA-binding proteins…
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. [provided by RefSeq, Jul 2008 ...
XRCC genes (X-ray cross-complementing group) were discovered mainly for their roles in protecting mammalian cells against damage caused by ionizing radiation. Studies determined that these genes are important in the genetic stability of DNA. Although the loss of some of these genes does not necessarily confer high levels of sensitivity to radiation, they have been found to represent ... more ...
IRF-4 binds with LANA through its DNA-binding domain in vitro.(A) IRF-4 binds to C-terminal domain of LANA in vitro. The 35S-radiolabeled in vitro-translated pr
iDNA-Prot,dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid ...
Lachke, Salil A.; OConnell, Daniel J.; Aboukhalil, Anton; Choe, Sung E.; Turbe-Doan, Annick; Robertson, Erin A.; Amendt, Brad A. et al. (PLoS ONE, 2012) Link to Published Version ...
DDB1 was originally identified as a large subunit of damaged DNA-binding protein (DDB), which plays a role in DNA repair. DDB1 also functions as an adaptor molecule of Cul4/DDB1 ubiquitin E3 ligase and participates in various cellular processes. ...
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Fig 5: regulation of transcription : which evidence code should be used? kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b ...
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of
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Looking for online definition of DNA-binding protein RFX8 in the Medical Dictionary? DNA-binding protein RFX8 explanation free. What is DNA-binding protein RFX8? Meaning of DNA-binding protein RFX8 medical term. What does DNA-binding protein RFX8 mean?
Summary Evidence is presented here which indicates that the adenovirus DNA-binding protein (DBP) is phosphorylated at a tyrosine residue early in infection. This was suggested by the discovery that a proportion of the label in 32P-labelled DBP was resistant to alkali, and was substantiated by acid hydrolysis of DBP immunoprecipitates and by immunoblotting with a monoclonal antibody against phosphotyrosine. Treatment of [35S] methionine-labelled DBPs with chymotrypsin produced fragments of apparent M r 45K and 39K whereas digestion of 32P-labelled DBP resulted in fragments of 45K and 26K. Consideration of the distribution of 32P label and its alkali stability in these fragments suggested that chymotrypsin cleaved populations of DBP at different sites depending on their phosphorylation states. The conservation, in all of the seven adenovirus serotypes sequenced, of a tyrosine residue (at amino acid 195 in adenovirus type 2) together with its surrounding residues, suggests that phosphorylation
The human transcription enhancer factor-1 (TEF-1) belongs to a family of evolutionarily conserved proteins that have a DNA binding TEA domain. TEF-1 shares a 98% homology with Drosophila scalloped (sd) in the DNA binding domain and a 50% similarity in the activation domain. We have expressed human TEF-1 in Drosophila under the hsp-70 promoter and find that it can substitute for Sd function. The transformants rescue the wingblade defects as well as the lethality of loss-of-function alleles. Observation of reporter activity in the imaginal wing discs of the enhancer-trap alleles suggests that TEF-1 is capable of promoting sd gene regulation. The functional capability of the TEF-1 product was assessed by comparing the extent of rescue by heat shock (hs)-TEF-1 with that of hs-sd. The finding that TEF-1 can function in vivo during wingblade development offers a potent genetic system for the analysis of its function and in the identification of the molecular partners of TEF-1.. ...
The molecular determinants necessary and sufficient for recognition of its specific DNA target are contained in the C-domain (H-NSctd) of nucleoid-associated protein H-NS. H-NSctd protects from DNaseI cleavage a few short DNA segments of the H-NS-sensitive hns promoter whose sequences closely match the recently identified H-NS consensus motif (tCGt/aTa/tAATT) and, ... read more alone or fused to the protein oligomerization domain of phage λ CI repressor, inhibits transcription from the hns promoter in vitro and in vivo. The importance of H-NS oligomerization is indicated by the fact that with an extended hns promoter construct (400 bp), which allows protein oligomerization, DNA binding and transcriptional repression are highly and almost equally efficient with native H-NS and H-NSctd::λCI and much less effective with the monomeric H-NSctd. With a shorter (110 bp) construct, which does not sustain extensive protein oligomerization, transcriptional repression is less effective, but native H-NS, ...
TY - JOUR. T1 - A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. AU - Bargonetti, Jill. AU - Manfredi, James J.. AU - Chen, Xinbin. AU - Marshak, Daniel R.. AU - Prives, Carol. PY - 1993. Y1 - 1993. N2 - p53 is a sequence-specific DNA-binding oligomeric protein that can activate transcription from promoters bearing p53-binding sites. Whereas the activation region of p53 has been identified within the amino terminus, the location of the specific DNA-binding domain has not been reported. Thermolysin treatment of p53 protein generates a stable protease-resistant fragment that binds with marked specificity to p53 DNA-binding sites. Amino-terminal sequencing of the fragment located the thennolysin cleavage site to residue 91. Because the fragment does not contain the cdc2 phosphorylation site at Ser-315, we conclude that the the site-specific DNA-binding domain of p53 spans ...
TY - JOUR. T1 - Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. AU - Senear, D. F.. AU - Brenowitz, M.. PY - 1991/9/9. Y1 - 1991/9/9. N2 - We have investigated the question of whether the gel mobility-shift assay can provide data that are useful to the demonstration of cooperativity in the site-specific binding of proteins to DNA. Three common patterns of protein-DNA interaction were considered: (i) the cooperative binding of a protein to two sites (illustrated by the Escherichia coli Gal repressor); (ii) the cooperative binding of a bidentate protein to two sites (illustrated by the E. coli Lac repressor); and (iii) the cooperative binding of a protein to three sites (illustrated by the λcI repressor). A simple, rigorous, and easily extendable statistical mechanical approach to the derivation of the binding equations for the different patterns is presented. Both stimulated and experimental data for each case are ...
Naturally elaborated membrane bleb fractions BI and BII of Neisseria gonorrhoeae contain both linear and circular DNAs. Because little is known about the interactions between DNA and blebs, studies were initiated to identify specific proteins that bind DNA in elaborated membrane blebs. Western immunoblots of whole-cell and bleb proteins from transformation-competent and DNA-uptake-deficient (dud) mutants were probed with single- or double-stranded gonococcal DNA, pBR322, or synthetic DNA oligomers containing intact or altered gonococcal transformation uptake sequences. The specificity and sensitivity of a nonradioactive DNA-binding protein assay was evaluated, and the assay was used to visualize DNA-protein complexes on the blots. The complexes were then characterized by molecular mass, DNA-binding specificity, and expression in bleb fractions. The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; unique subsets occurred in BI ...
Purpose To evaluate the prognostic significance of DNA excision repair gene polymorphisms, excision repair cross-complementation group 1 ( ERCC1) and X-ray repair complementing defective repair in...
An inducible program of inflammatory gene expression is a hallmark of antimicrobial defenses. This response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. Here we have identified a highly conserved Zinc finger DNA binding protein CNBP (also called ZNF9) upregulated in myeloid cells exposed to lipopolysaccharide. CNBP resides primarily in the cytosol and upon TLR4 engagement, CNBP translocate to the nucleus. To investigate the functional consequences of these events, we generated mice lacking CNBP and characterized the role of CNBP in controlling the inducible transcriptional program using a combination of RNA-sequencing and multiplex gene expression analysis (Nanostring). In response to an array of signals such as LPS, CNBP-deficient macrophages were impaired in their ability to induce important immune genes including IL12p40 and IL6 amongst others. CNBP-deficient cells showed normal ...
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with a few mutations and that selection on one function will impact the other. This work helps us to better understand the mechanism of transcriptional regulation and its evolution, and
Cervical cancer is a public health problem and the molecular mechanisms underlying radioresistance are still poorly understood. Here, we evaluated the modulation of key molecules involved in cell proliferation, cell cycle and DNA repair in cervical cancer cell lines (CASKI and C33A) and in malignant tissues biopsied from 10 patients before and after radiotherapy. The expression patterns of epidermal growth factor receptor (EGFR), excision repair cross-complementation group 1 (ERCC1) and p53 were evaluated in cancer cell lines by quantitative PCR and western blotting, and in human malignant tissues by immunohistochemistry. The mutation status of TP53 gene was evaluated by direct sequencing. Among cell lines, absent or weak modulations of EGFR, ERCC1 and p53 ...
Genome replication and maintenance occurs through the collective action of proteins that operate on single-stranded DNA (ssDNA). All cells express single-stranded DNA binding proteins (SSBs), which prevent errors by sequestering ssDNA with high-affinity, keeping it free from transient structures and protecting it from unwanted chemical modification. SSBs must be easily repositioned, or else risk stalling DNA replication and repair processes. How does a protein simulataneously bind DNA tightly yet diffuse rapidly?. Through a set of extensive all-atom molecular dynamics (MD) simulations, we have elucidated the molecular mechanism of SSB association with ssDNA. First, we showed that the same SSB-ssDNA complex can both spontaneously rearrange its structure and maintain its stable conformation depending on whether it is surrounded by physiological solution or a protein-crystal environment. Next, we probed the local interaction between ssDNA and SSB through simulations of mechanical unraveling of the ...
XPB antibody (excision repair cross-complementation group 3) for IHC-P, WB. Anti-XPB pAb (GTX55844) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
TY - JOUR. T1 - Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. AU - Kalodimos, Charalampos G.. AU - Biris, Nikolaos. AU - Bonvin, Alexandre M.J.J.. AU - Levandoski, Marc M.. AU - Guennuegues, Marc. AU - Boelens, Rolf. AU - Kaptein, Robert. PY - 2004/7/16. Y1 - 2004/7/16. N2 - Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient ...
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Binding of transcriptional activators to a promoter is a prerequisite process in transcriptional activation. It is well established that the efficiency of activator binding to a promoter is determined by the affinity of direct interactions between the DNA-binding domain of an activator and its specific target sequences. However, I describe here that activator binding to a promoter is augmented in vivo by the effects of two other determinants that have not been generally appreciated: (i) the number of activator binding sites present in a promoter and (ii) the potency of activation domains of activators. Multiple sites within a promoter can cooperatively recruit cognate factors regardless of whether they contain an effective activation domain. This cooperativity can result in the synergistic activation of transcription. The second effect is the enhancement of activator binding to a promoter by the presence of activation domains. In this case, activation domains are not simply tethered to the ...
The hns gene is a member of the cold-shock regulon, indicating that the nucleoid-associated, DNA-binding protein H-NS plays an important role in the adaptation of Escherichia coli to low temperatures. We show here that the ability to cope efficiently with a cold environment (12 degrees C and 25 degr …
Genes expressed in erythroid cells contain binding sites for a cell-specific nuclear factor, GF-1 (NF-E1, Eryf 1), believed to be an important transcriptional regulator. Previously we characterized murine GF-1 as a 413-amino acid polypeptide containing two cysteine-cysteine regions reminiscent of zinc-finger DNA-binding domains. By cross-hybridization to the finger domain of murine GF-1 we have isolated cDNA encoding the human homolog. Peptide sequencing of purified human GF-1 confirmed the authenticity of the human cDNA. The predicted primary sequence of human GF-1 is highly similar to that of murine GF-1, particularly in the DNA-binding region. Although the DNA-binding domains of human, murine, and chicken proteins are remarkably conserved, the mammalian polypeptides are strikingly divergent from the avian counterpart in other regions, most likely those responsible for transcriptional activation. By hybridization to panels of human-rodent DNAs we have assigned the human GF-1 locus to Xp21-11. ...
The initiation of transcription is accomplished via interactions of many different proteins with common and gene-specific regulatory motifs. Clearly, sequence-specific transcription factors play a crucial role in the specificity of transcription initiation. A group of sequence-specific DNA-binding proteins, related to the transcription factor Sp1, has been implicated in the regulation of many different genes, since binding sites for these transcription factors (GC/GT boxes) are a recurrent motif in regulatory sequences such as promoters, enhancers and CpG islands of these genes. The simultaneous occurrence of several homologous GC/GT box-binding factors precludes a straightforward deduction of their role in transcriptional regulation. In this review, we focus on the connection between functional specificity and biochemical properties including glycosylation, phosphorylation and acetylation of Sp1-related factors.. ...
The human ERYF1 gene (summary) NF-E1 DNA-binding protein GATA1, locus Xp11.23 [§§; †] containing 2 finger motifs referred to as ERYF1 of an erythroid-specific gene. The cDNA for the human ERYF1 gene is almost identical to that of chicken and mouse GATA1 gene consisting of 2 zinc finger type motifs its activator domain contains the binding…
Tumor protein p53, encoded in humans by the TP53 gene, was originally identified based on its interaction with the large T antigen of simian virus 40 (SV40). p53 is expressed at low levels in most cell types but is upregulated in many transformed (cancer) cell lines. In response to cellular stress, p53 regulates over 100 target genes that control cell cycle arrest, apoptosis, senescence, DNA repair, and metabolic changes. p53 protein has multiple domains that include DNA-binding, transactivation, and oligomerization activities. Mutations in the TP53 gene cause loss of tumor suppression activity and are found in more than 50% of human tumors. Multiple isoforms of p53 are known, with distinct DNA-binding and transcriptional activation properties. p53 is also known as cellular tumor antigen p53, p53 tumor suppressor, transformation-related protein 53, BCC7, LFS1, TRP53, and antigen NY-CO-13.. ...
Single stranded binding protein (SSB) is a prokaryotic DNA protein that binds to single stranded DNA during times when the DNA is rendered from its double stranded form during times of genetic recombination or DNA damage in order to stabilize and protect it from further unnecessary harm. The protein exists as a tetramer with each monomer being made of an N-terminal and Cterminal domain. The C-terminal domain is made of two smaller sub-domains, both of which have yet to resolve properly in a crystal structure, named the intrinsically disordered linker and the acidic tip, with limited understanding on how they function and relate to other proteins and SSB itself. Due to the disordered nature of its C-terminal domain limiting the ability to yield a concise crystal structure, much of the function and nearly all of the structure of the C-terminal domain has yet to be identified. While some function has been determined for these disordered regions, its relationship with other binding partners, DNA, ...
DNA-binding proteins from starved cells (DPS) are proteins that belong to the ferritin superfamily and are characterized by strong similarities but also distinctive differences with respect to canonical ferritins. DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. Dps proteins belong to the ferritin superfamily and the DNA protection is afforded by means of a double mechanism: The first was discovered in Escherichia coli Dps in 1992 and has given the name to the protein family; during stationary phase, Dps binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and ...
Zinc finger proteins contain DNA-binding domains and have a wide variety of functions, most of which encompass some form of transcriptional activation or repression. The majority of zinc finger proteins contain a Krueppel-type DNA binding domain and a KRAB domain, which is thought to interact with KAP1, thereby recruiting histone modifying proteins. Zinc finger protein 75 (ZNF75), also known as ZNF82, is a 289 amino acid member of the Krueppel C2H2-type zinc finger protein family. Localized to the nucleus, ZNF75 contains five C2H2- type zinc fingers and one KRAB domain through which it is thought to be involved in DNA-binding and transcriptional regulation ...
As a commentator up-thread noted, any slip-and-slide model of sequence-specific DNA binding activity by transcription factors fails the sniff test: how is the activator (or repressor) able to effectively scan the nucleotide side-groups to achive site-specificity when the latter are coated with histones (in most eukaryotes) and with other attendant DNA-binding molecules (in all organisms). The notion that the chromosomal DNA molecule exists in all of its double-helical beauty for all proteins to probe seems rather tired and readily debunked to my mind. Ive been a hesitant skeptic of the histone code as anything other than correlative observations, but given the ubiquitous habit of histone compaction of large chromosomal segments, some portions of which obviously remain accessible to transcription factors, it seems clear to me that were missing some vital pieces of the puzzle.. Delete ...
Recent analysis of a Gal4 mutant (Gap71) carrying three point mutations (S22D, K23Q and K25F) in its DNA-binding domain (DBD), has demonstrated that it cannot occupy GAL promoters efficiently in cells and that it is not mono-ubiquitylated, suggesting a functional link between this modification and stable DNA binding in cells. The mechanistic underpinning of this phenotype is that this protein is hypersensitive to a newly discovered activity of the proteasomal ATPases--their ability to actively dissociate transcription factor-DNA complexes after direct interaction with the activation domain. In this paper, we examine the roles of each of the three point mutations contained in Gap71 individually. These experiments have revealed that serine 22 is a site of phosphorylation in the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and ...
DNA binding capacity of Orf8 and Orf16 by electrophoretic mobility shift assays (EMSAs). Preparation of DNA substrate is graphically shown in panel A. US8 and U
Progression through the cell cycle is essential for the continued existence of all uni- and multicellular organisms. It is crucial for the survival of a cell that its DNA is correctly replicated. In mammals, the onset of DNA replication is regulated by the activity of the heterodimeric E2F-DP transcription factor. The mammalian E2F family contains six proteins (E2F1, E2F2, E2F3, E2F4, E2F5 and E2F6) (Trimarchi and Lees, 2002). All E2Fs have an N-terminally located DNA-binding domain immediately followed by a dimerization domain, allowing them to pair with a dimerization partner (DP1 or DP2). Dimerization of E2F with DP is a prerequisite for high affinity, sequence-specific binding to the E2F consensus DNA-binding site. E2F activity is negatively regulated by retinoblastoma (Rb), which binds to the transcriptional activation domain of the E2F-DP factor, rendering it inactive. Moreover, the recruitment by Rb of DNA-modifying enzymes, such as histone deacetylases and polycomb proteins, leads to ...
Enhancer factor C, EFC, EF-C, MHC class II regulatory factor RFX, MHC class II regulatory factor RFX1, regulatory factor X, 1 (influences HLA class II expression), Regulatory factor X 1, RFX, trans-acting regulatory factor 1, Transcription factor ...
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in ...
DNA-binding protein that preferentially recognizes a curved DNA sequence. It is probably a functional analog of DnaJ; displays overlapping activities with DnaJ, but functions under different conditions, probably acting as a molecular chaperone in an adaptive response to environmental stresses other than heat shock. Lacks autonomous chaperone activity; binds native substrates and targets them for recognition by DnaK. Its activity is inhibited by the binding of CbpM.
Predicted to have DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in pericyte cell differentiation and vascular smooth muscle cell development. Predicted to localize to the nucleus. Is expressed in head mesenchyme; pharyngeal arch 1; and pharyngeal arch 2. Orthologous to human FOXF2 (forkhead box F2 ...
The present invention provides a process of transfecting a cell with a polynucleotide mixed with one or more amphipathic compounds and an effective amount of a DNA-binding protein. Exemplary and preferred DNA-binding proteins are H1, H2A, and H2B. Exemplary and preferred amphipathic compounds are cationic amphipathic compounds.
Vol 9: Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
HSSB, MSTP075, MST075, replication protein A 70 kDa DNA-binding subunit, replication protein A1 (70kD), replication protein A1, 70kDa, REPA1RF-A protein 1, Replication factor A protein 1, RF-A, RP-A, RPA70RP-A p70, Single-stranded DNA-binding ...
On the other hand, if the same series of reaction is done not on purified DNA, but rather on DNA that has been allowed to interact with extracts containing DNA-binding proteins, these DNA-binding proteins can, if condition are appropriate, bind specifically to regions of DNA. Such a binding will interfere both with the Maxam-Gilbert sequencing reactions and with the cleavage of DNA by the deoxyribonuclease. As a result, those fragments that are produced by cleavage near a protein-binding site will fail to be formed or be formed at a much lower level leaving a gap in the ladder of reaction products. Such a gap is called a footprint and is evidence for the existence of a specific DNA-binding complex. A similar logic allows the DNA binding regions to be determined by using the Exonuclease III protection* approach. Although the basic idea of doing a footprint is straight forward executing one in practice is more complex because of the difficulty of non-specific binding reactions. DNA is a highly ...
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Although bats are recognized as major reservoir hosts of emerging infectious diseases, Joffrin and colleagues highlight that a significant knowledge gap on transmission mechanisms remains and needs further exploration. They question whether bat bites are the exception rather than the rule, and ask whether other animals can transmit bat-borne pathogens. They conclude by questioning what we can learn from bat-to-bat transmission.. ...
Summary: The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for ,500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes.. Availability: Contact: [email protected] ...
GT:ID BAD55361.1 GT:GENE BAD55361.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION complement(531217..531633) GB:FROM 531217 GB:TO 531633 GB:DIRECTION - GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD55361.1 LENGTH 138 SQ:AASEQ MADFAARLNKLFETVHPPGRKPHTNAEVAAALTASGHPISKPYLSQLRSGQRTNPSDETVAALAKFFKVKPDYFFNDIYAAKIDHDLELLSQLQGYGLRRLSSRAFDLSEESQNLLTSMAEKLRASEGLPEIPPDGTE GT:EXON 1,1-138:0, BL:SWS:NREP 1 BL:SWS:REP 1-,69,Y1416_COXBU,7e-04,37.9,58/100, RP:PDB:NREP 1 RP:PDB:REP 6-,104,2ao9A,3e-07,10.1,99/117, HM:PFM:NREP 1 HM:PFM:REP 33-,74,PF01381,4.7e-10,36.1,36/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 6-,104,2ao9A1,2e-07,10.1,99/117,a.4.1.17, HM:SCP:REP 39-,77,2a6cA1,0.00055,33.3,39/0,a.35.1.13,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 42 OP:NHOMOORG 31 OP:PATTERN -------------------------------------------------------------------- ...
High-resolution computational models of genome binding events. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands ...
This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves. As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed. It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins ...
The DNA triplets recognized by non-metazoan C2H2-ZF domains are also recognized by metazoan C2H2-ZFs based on experimental B1H data [16], often using identical basecontacting residues
Does anyone use DNA binding proteins expressed in rabbit reticulocyte lysates to do gel shift assays? This system would allow easy and quick expression of a suspected DNA binding protein that I could study (much easier than trying to express and purify the protein). I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow interfere in a gel shift assay (although I guess its no different than using cell/nuclear extracts). If anyone has experience with this or know of a reference could you please let me know? Thanks. -- Steve Some day I will get the hell out of Wisconsin Rodems Then I am here for the Lee family renioun ... shur-wajo-shur ...
A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... is a widespread qualitative technique to study protein-DNA interactions of known DNA binding proteins. DNA-Protein-Interaction ... Also proteins that repair DNA such as uracil-DNA glycosylase interact closely with it. In general, proteins bind to DNA in the ... DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or ...
DNA-binding domain DNA-binding protein DNA-binding protein from starved cells Transcription factor Drlica K, Rouviere-Yaniv J ( ... Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. Histone-like proteins were ... bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known ... In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein ...
... or UV-DDB is a protein complex that is responsible for repair of UV-damaged DNA. This complex is ... October 2012). "Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA ... Iovine B, Iannella ML, Bevilacqua MA (December 2011). "Damage-specific DNA binding protein 1 (DDB1): a protein with a wide ... DNA binds to DDB2 only when damaged by UV radiation. Binding with high affinity to a helical domain of DDB2 in the dimer form, ...
... (TDP-43, transactive response DNA binding protein 43 kDa) is a protein that in humans is encoded by ... TAR DNA-binding protein 43) at the PDBe-KB. (Genes on human chromosome 1, Commons category link is on Wikidata, DNA-binding ... "TARDBP TAR DNA binding protein [Homo sapiens (human)] - Gene - NCBI". Retrieved 2021-12-13. Qin H, Lim LZ ... Wikimedia Commons has media related to TAR DNA-binding protein 43, TDP-43. GeneReviews/NCBI/NIH/UW entry on TARDBP-Related ...
The precise function of the protein domain SAND remains to be determined. Nevertheless, it is thought to be a DNA binding ... Henceforth, this suggests that the SAND domain is the DNA-binding region of DEAF-1. The structure of this protein domain ... In molecular biology, the protein domain SAND is named after a range of proteins in the protein family: Sp100, AIRE-1, NucP41/ ... Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 ...
Protein families, DNA replication, Proteins, DNA-binding substances, DNA-binding proteins). ... Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single- ... DNA-binding protein Single-stranded binding protein Comparison of nucleic acid simulation software Shishmarev D, Wang Y, Mason ... "Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined ...
Inhibitor of DNA-binding/differentiation proteins, also known as ID proteins comprise a family of proteins that heterodimerize ... ID proteins can bind E-proteins, preventing them from binding bHLH proteins and halting transcription, a case often seen in ... transcription factors to inhibit DNA binding of bHLH proteins. ID proteins also contain the HLH-dimerization domain but lack ... The first helix-loop-helix proteins identified were named E-proteins because they bind to Ephrussi-box (E-box) sequences. In ...
"Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding ... DNA-binding proteins from starved cells (DPS) are bacterial proteins that belong to the ferritin superfamily and are ... Chiancone E, Ceci P (January 2010). "Role of Dps (DNA-binding proteins from starved cells) aggregation on DNA". Frontiers in ... DNA-binding protein from starved cells): a study with the wild-type protein and a catalytic centre mutant". Chemistry. 16 (2): ...
Zinc finger Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. Helix- ... Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a ... Three or four consecutive amino acid residues form a cation-binding feature. Sequence motif Short linear motif Protein tandem ... D-loop A displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated ...
... they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. DNA binding sites are often ... DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from ... that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding ... To quantify the binding affinity of proteins and other molecules to specific DNA binding sites the biophysical method ...
Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... These hotspots are binding sites for the PRDM9 Zinc Finger array. Upon binding to DNA, PRDM9 catalyzes trimethylation of ... minisatelite binding protein 3). This would later turn out to be the same PRDM9 protein independently identified later. In 2005 ...
There are 2 main steps involved: the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain ... The in vivo model mentioned above clearly explains 3-D and 1-D diffusion along the DNA strand and the binding of proteins to ... 2013), during the process of protein sliding, the protein searches the entire length of the DNA chain using 3-D and 1-D ... Blocker proteins participate in 1-D diffusion only i.e. bind to and diffuse along the DNA contour and not in the cytosol. ...
This list covers DNA-binding proteins. For other protein-related codes, see List of MeSH codes (D12.776). Codes before these ... ccaat-enhancer-binding protein-alpha MeSH D12.776. - ccaat-enhancer-binding protein-beta MeSH D12.776.260.108. ... sterol regulatory element binding proteins MeSH D12.776.260.103.500.750.500 - sterol regulatory element-binding protein 1 MeSH ... sterol regulatory element binding proteins MeSH D12.776. - sterol regulatory element binding protein 1 MeSH ...
Lyons PJ, Muise AM, Ro HS (2005). "MAPK modulates the DNA binding of adipocyte enhancer-binding protein 1". Biochemistry. 44 (3 ... AE binding protein 1 is a protein that in humans is encoded by the AEBP1 gene. AE binding protein 1 is a member of ... "Entrez Gene: AE binding protein 1". Human AEBP1 genome location and AEBP1 gene details page in the UCSC Genome Browser. Tumelty ... The protein may function as a transcriptional repressor and play a role in adipogenesis and smooth muscle cell differentiation ...
Catherine J. Murphy; Eric B. Brauns; Latha Gearheart (1996). "Quantum Dots as Inorganic DNA-Binding Proteins". MRS Proceedings ... Binding DNA to the surface of a quantum dot increases the stability of the quantum dots. The DNA chains provide more ... protein binding, and biomarkers. The ability to visualize the chemical and biological processes of DNA allows feedback to ... This results in fewer strands of DNA binding to each quantum dot. Lower ionic strength results in more stable quantum dots, but ...
A distinct group of DNA-binding proteins is the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although only B-DNA and Z-DNA have been ... DNA at Curlie DNA binding site prediction on protein DNA the Double Helix Game From the official Nobel Prize web site DNA under ... Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... type winged-helix DNA-binding domain, and a conserved N-terminal AT-rich DNA interaction domain-the last domain for which the ... "Nomenclature of the ARID family of DNA-binding proteins". Genomics. 86 (2): 242-51. doi:10.1016/j.ygeno.2005.03.013. PMID ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273-81. ...
"Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains ... proteins can bind to modify the protein's function. SUMO proteins may modify proteins to perform many functions, including ... a common structure in proteins that interact with DNA, including zinc-finger proteins. C8orf34 protein undergoes few ... Walter P, Roberts K, Raff M, Lewis J, Johnson A, Alberts B (2002). "DNA-Binding Motifs in Gene Regulatory Proteins". Molecular ...
... proteins have weak DNA-binding capacity. Therefore, to effectively bind DNA, NFAT proteins must cooperate with other ... This NFAT:AP-1 complex binds to the conventional Rel-family proteins DNA binding sites and is involved in gene transcription in ... Under normal circumstances the STIM proteins bind calcium ions but if most of them are released from ER the bound ions are ... This complex afterwards activates transcription of BATF which then also binds to NFAT and together with other proteins like ...
DNA-binding protein Transcription factor Razaghi, Ali; Huerlimann, Roger; Owens, Leigh; Heimann, Kirsten (1 December 2015). " ... Murguía, José R.; Serrano, Ramón (2012). "New functions of protein kinase Gcn2 in yeast and mammals". IUBMB Life. 64 (12): 971- ... Gcn4 is a highly conserved protein and its mammalian homolog is known as activating transcription factor-4 (ATF4). ... Overexpression of Gcn4 leads to the reduction in protein synthesis capacity which contributes to Gcn4-mediated increase of ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y (Nov 1998). "A novel DNA-binding motif shares structural homology to DNA ... a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome ... "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142-50. doi:10.1021/bi010476a. ...
... the proteins involved in mRNA transport (RNA-binding proteins, RBPs). DLM1 encodes a Z-DNA binding protein. Z-DNA formation is ... DLM1 then binds to cytosolic Viral DNA using two Z-DNA-binding domains (Zα and Zβ) at its N-terminus along with a DNA binding ... Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in ... "Entrez Gene: ZBP1 Z-DNA binding protein 1". Rathinam VA, Fitzgerald KA (Mar 2011). "Innate immune sensing of DNA viruses". ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome ... "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142-50. doi:10.1021/bi010476a. ... containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer". The Journal ...
1999). "Transcription factor Y-box binding protein 1 binds preferentially to cisplatin-modified DNA and interacts with ... Y box binding protein 1 also known as Y-box transcription factor or nuclease-sensitive element-binding protein 1 is a protein ... 1996). "The mouse poly(C)-binding protein exists in multiple isoforms and interacts with several RNA-binding proteins". Nucleic ... "A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif". Nucleic ...
GCC box DNA-binding protein interacts with an ocs element binding protein". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5961-6. ... Ohme-Takagi M, Shinshi H (February 1995). "Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive ... ethylene-responsive+element+binding+protein at the US National Library of Medicine Medical Subject Headings (MeSH) v t e ( ... Ethylene-responsive element binding protein (EREBP) is a homeobox gene from Arabidopsis thaliana and other plants which encodes ...
DNA Research. 7 (1): 65-73. doi:10.1093/dnares/7.1.65. PMID 10718198. "Entrez Gene: chromodomain helicase DNA binding protein 7 ... Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by ... In GeneReviews CHD7+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH) Human CHD7 genome ... This protein belongs to a larger group of ATP-dependent chromatin remodeling complexes, the CHD subfamily. Model organisms have ...
CRP protein binds cAMP, which causes a conformational change that allows CRP to bind tightly to a specific DNA site in the ... CRP binds to a DNA site that overlaps the promoter -35 element and activates transcription through two sets of protein-protein ... CRP binds to a DNA site located upstream of core promoter elements and activates transcription through protein-protein ... Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH (2004). "Catabolite activator protein: DNA binding and ...
DNA helicases, DNA clamps and DNA topoisomerases, and replication proteins; e.g. single-stranded DNA binding proteins (SSB). In ... All these control the binding of initiator proteins to the origin sequences. Because E. coli methylates GATC DNA sequences, DNA ... To prevent this, single-strand binding proteins bind to the DNA until a second strand is synthesized, preventing secondary ... In various bacterial species, this is named the DNA replication terminus site-binding protein, or Ter protein. Because bacteria ...
Schreiber J, Enderich J, Wegner M (May 1998). "Structural requirements for DNA binding of GCM proteins". Nucleic Acids Res. 26 ... in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain as a new class of Zn-containing DNA- ... binding domain with no similarity to any other DNA-binding domain. The GCM domain consists of a large and a small domain ... Akiyama Y, Hosoya T, Poole AM, Hotta Y (December 1996). "The gcm-motif: a novel DNA-binding motif conserved in Drosophila and ...
The BolA protein is a DNA-binding regulator; the Fra2 protein is an iron sulfur cluster protein that binds Grx3/4 and is ... In molecular biology, the BolA-like protein family consists of the morpho-protein BolA from Escherichia coli, the Fra2 protein ... It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5. Dressaire C, Moreira ... This article incorporates text from the public domain Pfam and InterPro: IPR002634 (Protein families). ...
2002). "Epstein-Barr virus encoded nuclear protein EBNA-3 binds a novel human uridine kinase/uracil phosphoribosyltransferase ... 2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. Bibcode:2001Natur.414.. ... 2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. ...
6 also known as DNA-binding protein RFX6 is a protein that in humans is encoded by the RFX6 gene. The nuclear protein encoded ...
... further enriching the phage library in binding proteins. Following further bacterial-based amplification, the DNA within in the ... Phage display is a laboratory technique for the study of protein-protein, protein-peptide, and protein-DNA interactions that ... By immobilizing a relevant DNA or protein target(s) to the surface of a microtiter plate well, a phage that displays a protein ... and in searching for protein-DNA interactions using specially-constructed DNA libraries with randomised segments. Recently, ...
... the cell grows in size and synthesizes mRNA and protein that are required for DNA synthesis. Once the required proteins and ... Three methods of preventing Cdk activity are found in G1 phase: pRB binding to E2F family transcription factors downregulate ... In these cases where the G1 phase is affected, it is generally because gene regulatory proteins of the E2F family have become ... Reasons the cell would not move into the S phase include insufficient cell growth, damaged DNA, or other preparations have not ...
... gene expression is mediated by decreased DNA binding of nuclear factor I proteins which control constitutive TTF-1 expression ... "DNA binding and transcriptional activation by the Ski oncoprotein mediated by interaction with NFI". Nucleic Acids Res. 25 (19 ... "DNA binding and transcriptional activation by the Ski oncoprotein mediated by interaction with NFI". Nucleic Acids Res. 25 (19 ... Nfix has been shown to interact with SKI protein and it is also known to interact with AP-1. NFI-X3 has been shown to interact ...
Stimulating protein 1, CCAAT/enhancer binding protein, GC box elements and HMG box-containing protein 1. Like previously ... "DNA folding results on 21Aug01-20-42-28 for". Retrieved 2021-08-01. "Protein BLAST: search ... PANO1 is a protein which in humans is encoded by the PANO1 gene. PANO1 is an apoptosis inducing protein that is able to ... These isoforms have proteins with 215 and 216 amino acids, respectively. No isoforms for the human PANO1 protein could be ...
Recognition sequence: Sequence of DNA recognized by the enzyme and to which it specifically binds. Cut: Cutting site and DNA ... Code used to identify the structure of a protein in the PDB database of protein structures. The 3D atomic structure of a ... Jeremy MB, John LT, Lubert S (2002). "3. Protein Structure and Function". Biochemistry. San Francisco: W. H. Freeman. ISBN 0- ... Kessler C, Manta V (August 1990). "Specificity of restriction endonucleases and DNA modification methyltransferases a review ( ...
Liu F, Wan Q, Pristupa ZB, Yu XM, Wang YT, Niznik HB (January 2000). "Direct protein-protein coupling enables cross-talk ... Jiang S, Yu J, Wang J, Tan Z, Xue H, Feng G, He L, Yang H (2001). "Complete genomic sequence of 195 Kb of human DNA containing ... Nymann-Andersen J, Wang H, Olsen RW (September 2002). "Biochemical identification of the binding domain in the GABA(A) receptor ... Liu F, Wan Q, Pristupa ZB, Yu XM, Wang YT, Niznik HB (January 2000). "Direct protein-protein coupling enables cross-talk ...
Nada S, Okada M, MacAuley A, Cooper JA, Nakagawa H (May 1991). "Cloning of a complementary DNA for a protein-tyrosine kinase ... domain which helps the SH3 domain interact with the flexible linker domain and thereby keeps the inactive unit tightly bound. ... c-Src can be activated by many transmembrane proteins that include: adhesion receptors, receptor tyrosine kinases, G-protein ... Proto-oncogene tyrosine-protein kinase Src, also known as proto-oncogene c-Src, or simply c-Src (cellular Src; pronounced "sarc ...
GLIMMER uses Interpolated Markov Models (IMMs) to identify the coding regions and distinguish them from the noncoding DNA. The ... Accord.NET in C# ghmm C library with Python bindings that supports both discrete and continuous emissions. Jajapy Python ... Durbin, Richard (23 April 1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge ... GENSCAN utilizes a general inhomogeneous, three periodic, fifth order Markov model of DNA coding regions. Additionally, this ...
... a novel jun N-terminal protein kinase (JNK)-binding protein that functions as a Scaffold factor in the JNK signaling pathway". ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (3): 197-205. doi: ... C-jun-amino-terminal kinase-interacting protein 3 is an enzyme that in humans is encoded by the MAPK8IP3 gene. The protein ... "Entrez Gene: MAPK8IP3 mitogen-activated protein kinase 8 interacting protein 3". Matsuura, Hiroshi; Nishitoh Hideki; Takeda ...
For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical ... In 2018, a Markov random field approach has been proposed to infer DNA motifs from DNA-binding domains of proteins. The E. coli ... The authors were able to show that the motif has DNA binding activity. A similar approach is commonly used by modern protein ... Akiyama Y, Hosoya T, Poole AM, Hotta Y (December 1996). "The gcm-motif: a novel DNA-binding motif conserved in Drosophila and ...
... or DNA fragmentation factor subunit beta is a protein that in humans is encoded by the DFFB gene. It breaks up the DNA during ... Therefore, a cavity (active site) where DNA can fit is produced, even though there is another binding region responsible for ... DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for ... The protein caspase DNase is an endonuclease involved in the cell apoptotic process that facilitates the DNA breakup. Cell ...
... which contains multiple binding sites for the initiator protein DnaA (a highly homologous protein amongst bacterial kingdom). ... It is hypothesized that DNA stretching by DnaA bound to the origin promotes strand separation which allows more DnaA to bind to ... of either parent DNA or newly formed DNA and thereafter the ligating activity ligates that broken DNA strand and so the two DNA ... Termination of DNA replication in E. coli is completed through the use of termination sequences and the Tus protein. These ...
... a mammalian-type single-stranded DNA-binding protein, in a halophilic archaeon". Applied Microbiology and Biotechnology. 98 (4 ... NRC-1. This work showed that its proteins are highly acidic, providing an understanding of how proteins may function in high ... Post-genomic research in his laboratory established the core and signature proteins in halophilic Archaea, and the function of ... Capes, Melinda D.; DasSarma, Priya; DasSarma, Shiladitya (2012-01-01). "The core and unique proteins of haloarchaea". BMC ...
doi:10.1089/dna.1997.16.1289. PMID 9407001. Yang X, Khosravi-Far R, Chang HY, Baltimore D (1997). "Daxx, a novel Fas-binding ... Daxx interacts with the TGF-β type II receptor by binding of C-terminal domain of the protein. When the cell is treated with ... Yang X, Khosravi-Far R, Chang HY, Baltimore D (1997). "Daxx, a novel Fas-binding protein that activates JNK and apoptosis". ... Death-associated protein 6 also known as Daxx is a protein that in humans is encoded by the DAXX gene. Daxx, a Death domain- ...
The CLINT1 protein binds to the terminal domain of the clathrin heavy chain and stimulates clathrin cage vesicle assembly. ... DNA Res. 3 (1): 17-24. doi:10.1093/dnares/3.1.17. PMID 8724849. Hoja MR, Wahlestedt C, Höög C (2000). "A visual intracellular ... Kalthoff C, Groos S, Kohl R, Mahrhold S, Ungewickell EJ (November 2002). "Clint: a novel clathrin-binding ENTH-domain protein ... 2003). "Clint: a novel clathrin-binding ENTH-domain protein at the Golgi". Mol. Biol. Cell. 13 (11): 4060-73. doi:10.1091/mbc. ...
Regeneration occurs by a process involving DNA single-stranded binding protein and is likely a form of homologous ... "Extremely radiation-resistant mutants of a halophilic archaeon with increased single-stranded DNA-binding protein (RPA) gene ... To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point of H. ... To compensate, they have evolved a sophisticated DNA repair mechanism. The genome encodes DNA repair enzymes homologous to ...
Protein Science. 13 (10): 2819-24. doi:10.1110/ps.04682504. PMC 2286551. PMID 15340161. LILRA3+protein,+human at the US ... Like the closely related LILRA1, LILRA3 binds to both normal and 'unfolded' free heavy chains of HLA class I, with a preference ... Norman PJ, Carey BS, Stephens HA, Vaughan RW (June 2003). "DNA sequence variation and molecular genotyping of natural killer ... The function of LILRA3 is currently unknown; however, it is highly homologous to other LILR genes, and can bind human leukocyte ...
These biochemicals can be joined to make polymers such as DNA and proteins, essential macromolecules of life. Proteins are made ... Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take ... Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, ... Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or ...
"DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic ... Magee DA, Sikora KM, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE (October 2010). "DNA ... In both plants and mammals there are two major mechanisms that are involved in establishing the imprint; these are DNA ... Imprinting may cause problems in cloning, with clones having DNA that is not methylated in the correct positions. It is ...
Lecossier D, Bouchonnet F, Clavel F, Hance AJ (May 2003). "Hypermutation of HIV-1 DNA in the absence of the Vif protein". ... sterol-regulated element-binding proteins and androgen receptors are all controlled by the UPS and thus involved in the ... To recognize protein as designated substrate, 19S complex has subunits that are capable to recognize proteins with a special ... Accordingly, misfolded proteins and damaged protein need to be continuously removed to recycle amino acids for new synthesis; ...
"Entrez Gene: PIR pirin (iron-binding nuclear protein)". Dechend, R; Hirano F; Lehmann K; Heissmeyer V; Ansieau S; Wulczyn F G; ... oncoprotein suggest the encoded protein may act as a transcriptional cofactor and be involved in the regulation of DNA ... The encoded protein is an Fe(II)-containing nuclear protein expressed in all tissues of the body and concentrated within dot- ... 2004). "Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor". J. Biol. Chem. 279 (2): ...
This protein forms a very tight complex with alpha neurexins, a group of proteins that promote adhesion between dendrites and ... 2003). "The DNA sequence of human chromosome 7". Nature. 424 (6945): 157-164. Bibcode:2003Natur.424..157H. doi:10.1038/ ... Missler M, Hammer RE, Südhof TC (1999). "Neurexophilin binding to alpha-neurexins. A single LNS domain functions as an ... Neurexophilin-1 is a protein that in humans is encoded by the NXPH1 gene. This gene is a member of the neurexophilin family and ...
This protein contains a single BCL2 homology domain 3 (BH3), and has been shown to bind BCL2 proteins and function as an ... 2001). "Characterization of long cDNA clones from human adult spleen". DNA Res. 7 (6): 357-66. doi:10.1093/dnares/7.6.357. PMID ... The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form hetero- or homodimers and act as ... This protein is found to be sequestered to myosin V motors by its association with dynein light chain 2, which may be important ...
... independent of the occupational states of its other binding sites. This protein is deactivated by binding ATP, and activated by ... HSPA1A and HSPA1B produce nearly identical proteins because the few differences in their DNA sequences are almost exclusively ... Heat shock 70kDa protein 1B is a chaperone protein, cooperating with other heat shock proteins and chaperone systems to ... Mohanan V, Grimes CL (July 2014). "The molecular chaperone HSP70 binds to and stabilizes NOD2, an important protein involved in ...
Some viruses can encode proteins that bind to double-stranded RNA (dsRNA) to prevent the activity of RNA-dependent protein ... which leads to expression of proteins that will prevent the virus from producing and replicating its RNA and DNA. Overall, IFN- ... and phosphorylates a translational repressor protein called eukaryotic translation-initiation factor 4E-binding protein 1 ( ... Several poxviruses encode soluble IFN receptor homologs-like the B18R protein of the vaccinia virus-that bind to and prevent ...
Protein-Primed Replication of Bacteriophage Φ29 DNA". In Kusic-Tisma, Jelena (ed.). DNA Replication and Related Cellular ... domains of pRNA bind to the gp16 packaging enzyme and the structural connector molecule to aid in the translocation of DNA ... The structure of Φ29 is composed of seven main proteins: the terminal protein (p3), the head or capsid protein (p8), the head ... the portal or connector protein (p10), the tail tube or lower collar proteins (p11), and the tail fibers or appendage proteins ...
2002). "AU binding proteins recruit the exosome to degrade ARE-containing mRNAs". Cell. 107 (4): 451-64. doi:10.1016/S0092-8674 ... The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1". DNA Res ... Raijmakers R, Noordman YE, van Venrooij WJ, Pruijn GJ (2002). "Protein-protein interactions of hCsl4p with other human exosome ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ...
This binding in turn results in an inhibition of translation of the target protein or degradation of the target messenger RNA. ... 2009). "DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the ... WW domain binding protein 1-like), CACNA1C (Calcium channel, voltage-dependent, L type, alpha 1C subunit), DPYD ( ... Zinc finger E-box-binding homeobox 2) and PRKD3 (Serine/threonine-protein kinase D3). Neault et al. recently identified miR-137 ...
A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... is a widespread qualitative technique to study protein-DNA interactions of known DNA binding proteins. DNA-Protein-Interaction ... Also proteins that repair DNA such as uracil-DNA glycosylase interact closely with it. In general, proteins bind to DNA in the ... DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or ...
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protein coding gene. Chr7:73076386-73191578 (-). 129S1/SvImJ MGP_129S1SvImJ_G0032369. protein coding gene. Chr7:74983374- ... protein coding gene. Chr7:75937597-76051631 (-). CAST/EiJ MGP_CASTEiJ_G0031401. protein coding gene. Chr7:66420789-66540202 (-) ... protein coding gene. Chr7:75606169-75723911 (-). C57BL/6NJ MGP_C57BL6NJ_G0032852. protein coding gene. Chr7:78087150-78211143 ... protein coding gene. Chr7:76208160-76332162 (-). NOD/ShiLtJ MGP_NODShiLtJ_G0032186. protein coding gene. Chr7:80768436-80887788 ...
DNA-binding domain from tn916 integrase: *Protein DNA-binding domain from tn916 integrase from d.10.1.1: DNA-binding domain ... Protein DNA-binding domain from tn916 integrase from d.10.1.1: DNA-binding domain from tn916 integrase appears in SCOP 1.73. * ... Protein DNA-binding domain from tn916 integrase from d.10.1.1: DNA-binding domain from tn916 integrase appears in SCOPe 2.01. * ... Protein DNA-binding domain from tn916 integrase from d.10.1.1: DNA-binding domain from tn916 integrase appears in the current ...
... have demonstrated that the acidic carboxyl terminus of the protein is essential and that it mediates multiple protein-protein ... Gene 2.5 of bacteriophage T7 is an essential gene that encodes a single-stranded DNA-binding protein (gp2.5). Previous studies ... The carboxyl-terminal domain of bacteriophage T7 single-stranded DNA-binding protein modulates DNA binding and interaction with ... binds single-stranded DNA 40-fold more tightly than the wild-type protein and cannot physically interact with T7 DNA polymerase ...
Protein classi Protein class(es) of the gene product according to selected gene lists. List of protein classes. ... Protein classi Protein class(es) of the gene product according to selected gene lists. List of protein classes. ... Cell Cycle Dependent Proteini Cell cycle dependency of protein expression in the FUCCI U-2 OS cell line, determined by ICC-IF ... Cell Cycle Dependent Proteini Cell cycle dependency of protein expression in the FUCCI U-2 OS cell line, determined by ICC-IF ...
DNA binding proteins that alter nucleic acid flexibility. Micah McCauley, Philip R. Hardwidge, L. James Maher, Mark C. Williams ... DNA binding proteins that alter nucleic acid flexibility. / McCauley, Micah; Hardwidge, Philip R.; Maher, L. James et al. ... Proteins that bind to single stranded DNA (ssDNA) destabilize melting, provided that the rate of association is comparable to ... Proteins that bind to single stranded DNA (ssDNA) destabilize melting, provided that the rate of association is comparable to ...
Purified Human MSH2 Protein Binds to DNA Containing Mismatched Nucleotides1 Richard Fishel; Richard Fishel ... Richard Fishel, Amy Ewel, Mary Kay Lescoe; Purified Human MSH2 Protein Binds to DNA Containing Mismatched Nucleotides1. Cancer ... The human hMSH2 protein is a member of a highly conserved family of postreplication mismatch repair components found from ... Alterations of the gene coding for this protein cosegregate with, and are the likely cause of, chromosome 2-linked hereditary ...
RESULTS: Neuropathological examination revealed cytoplasmic deposition of the TDP-43 protein in three affected individuals. ... Examination of candidate genes by direct DNA sequencing. ... motor neuron disease and Tar DNA binding protein-43 positive ... Pedigree with frontotemporal lobar degeneration--motor neuron disease and Tar DNA binding protein-43 positive neuropathology: ... Pedigree with frontotemporal lobar degeneration--motor neuron disease and Tar DNA binding protein-43 positive neuropathology: ...
... including the telomeric DNA-binding proteins TRF1, TRF2 and Pot1 involved in telomere capping functions. The expression of ... Tax protein in HTLV-1 transformed T lymphocytes. In this study, we have examined the effects of Tax expression on the ... The functional state of human telomeres is controlled by telomerase and by a protein complex named shelterin, ... For instance, Pot1, a single-stranded telomeric DNA-binding protein, behaves as a terminal transducer of the cis-inhibitory ...
We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. ... We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. ... We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. ... We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. ...
The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ ... The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ ...
Campylobacter jejuni DNA-binding protein from starved cells in Guillain-Barré syndrome patients. In: Journal of Neuroimmunology ... Campylobacter jejuni DNA-binding protein from starved cells in Guillain-Barré syndrome patients. Journal of Neuroimmunology. ... Campylobacter jejuni DNA-binding protein from starved cells in Guillain-Barré syndrome patients. / Kawamura, Nobutoshi; Piao, ... title = "Campylobacter jejuni DNA-binding protein from starved cells in Guillain-Barr{\e} syndrome patients", ...
However, it is difficult to adequately describe the information of proteins in predicting DNA-binding proteins. In this study, ... we extract six features from protein sequence and use Multiple Kernel Learning-based on Centered Kernel Alignment to integrate ... DNA-Binding Proteins (DBP) plays a pivotal role in biological system. A mounting number of researchers are studying the ... From: A sequence-based multiple kernel model for identifying DNA-binding proteins ...
"Dynamics of nucleosome invasion by DNA binding proteins",. abstract = "Nucleosomes sterically occlude their wrapped DNA from ... Tims, H. S., Gurunathan, K., Levitus, M., & Widom, J. (2011). Dynamics of nucleosome invasion by DNA binding proteins. Journal ... Tims HS, Gurunathan K, Levitus M, Widom J. Dynamics of nucleosome invasion by DNA binding proteins. Journal of molecular ... Tims, HS, Gurunathan, K, Levitus, M & Widom, J 2011, Dynamics of nucleosome invasion by DNA binding proteins, Journal of ...
... cellspluripotent stem cellsregenerationadultalzheimer diseasecell culture techniquescytokinesdevelopmentaldnabinding proteins ...
Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. Nucleic Acids Res ... Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein.. ...
Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify ... Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind ... that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA ... their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, ...
Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. / Sing, Charles E.; ... Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. Nucleic acids ... title = "Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins", ... Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. ...
PhD Student: Alejandro Martín González. Date: 28/11/2019. PhD Supervisor: Fernando Moreno Herrero/ CNB-CSIC. Featured publication: The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems / NUCLEIC ACIDS RESEARCH / 10.1093/nar/gky370. Link: Thesis under embargo (availability from 28/05/2021) Request for manuscript ...
Here we show that RemA is a DNA-binding protein that binds to multiple sites upstream of the promoters of both operons and is ... Here we show that RemA is a DNA-binding protein that binds to multiple sites upstream of the promoters of both operons and is ... Here we show that RemA is a DNA-binding protein that binds to multiple sites upstream of the promoters of both operons and is ... Here we show that RemA is a DNA-binding protein that binds to multiple sites upstream of the promoters of both operons and is ...
Purchase Recombinant Oncorhynchus mykiss DNA-binding protein Ikaros(ikzf1) ,partial. It is produced in Yeast. High purity. Good ... Recombinant Oncorhynchus mykiss DNA-binding protein Ikaros(ikzf1) ,partial. Recombinant Oncorhynchus mykiss DNA-binding protein ... ikzf1; ikarosDNA-binding protein Ikaros; Ikaros family zinc finger protein 1. Species. Oncorhynchus mykiss (Rainbow trout) ( ... Protein Families. Ikaros C2H2-type zinc-finger protein family. Tissue Specificity. Expression mainly limited to thymus, spleen ...
Next Generation Sequencing with Bioinformatics Toolbox: Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data. In ...
DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate. Title: DNA methylation associated with ... TAR (HIV) RNA-binding protein 1. TAR RNA loop binding protein. TAR RNA-binding protein 1. TAR RNA-binding protein of 185 kDa. ... Protein interactions. Protein. Gene. Interaction. Pubs. Tat tat HIV-1 Tat downregulates TAR (HIV) RNA binding protein 1 in HEK ... tat regulates binding of the human immunodeficiency virus trans-activating region RNA loop-binding protein TRP-185. Wu F, et al ...
Yeast 01022734875 at Gentaur Methanosaeta thermophila DNA-binding protein Mthe_1571 (Mthe_1571) Yeast ... Order Methanosaeta thermophila DNA-binding protein Mthe_1571 Mthe_1571 - ... DNA-binding protein Mthe_1571 (Mthe_1571) is a recombinant protein expressed in Yeast . The protein can be with or without a ... This protein can be stored at -20 degrees Celsius. For extended periods of time it is recommended to keep the protein frozen at ...
Effects of extracellular DNA and DNA-binding protein on the development of a Streptococcus intermedius biofilm ... Effects of extracellular DNA and DNA-binding protein on the development of a Streptococcus intermedius biofilm ... Effects of extracellular DNA and DNAbinding protein on the development of a Streptococcus intermedius biofilm. J Appl ... and histone-like DNA binding protein (HLP) on Streptococcus intermedius biofilm development and rigidity.. Methods and Results ...
Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. In: ... Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. ... Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. / ... Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. ...
DNA anti‐DNA immune complexes reacting with a DNA binding protein, anti‐histone antibodies or anti‐Sm antibodies. It is ... DNA anti‐DNA immune complexes reacting with a DNA binding protein, anti‐histone antibodies or anti‐Sm antibodies. It is ... DNA anti‐DNA immune complexes reacting with a DNA binding protein, anti‐histone antibodies or anti‐Sm antibodies. It is ... DNA anti‐DNA immune complexes reacting with a DNA binding protein, anti‐histone antibodies or anti‐Sm antibodies. It is ...
Solution structure of the C2H2 type zinc-binding domain of human zinc finger protein 292 ... Classification: DNA BINDING PROTEIN. *Organism(s): Homo sapiens. *Mutation(s): No *Deposited: 2005-05-02 Released: 2005-11-02 ... Solution structure of the C2H2 type zinc-binding domain of human zinc finger protein 292. Yoneyama, M., Tomizawa, T., Tochio, N ... Solution structure of the C2H2 type zinc-binding domain of human zinc finger protein 292. *PDB DOI: 10.2210/pdb1X3C/pdb ...
Inhibition of transcription by DNA binding proteins of sarcoma-180 ascites cells. Indian Journal of Biochemistry & Biophysics. ... Inhibition of transcription by DNA binding proteins of sarcoma-180 ascites cells. ...
  • This alters the accessibility of the DNA template to the polymerase. (
  • gp2.5-F232L exhibits a 3-fold increase in binding affinity for single-stranded DNA and a slightly lower affinity for T7 DNA polymerase when compared with wild type gp2.5. (
  • gp2.5-F232L stimulates the activity of T7 DNA polymerase and, in contrast to wild-type gp2.5, promotes strand displacement DNA synthesis by T7 DNA polymerase. (
  • A carboxyl-terminal truncation of gene 2.5 protein, gp2.5-Delta 26C, binds single-stranded DNA 40-fold more tightly than the wild-type protein and cannot physically interact with T7 DNA polymerase. (
  • gp2.5-Delta 26C is inhibitory for DNA synthesis catalyzed by T7 DNA polymerase on single-stranded DNA, and it does not stimulate strand displacement DNA synthesis at high concentration. (
  • The biochemical and genetic data support a model in which the carboxyl-terminal tail modulates DNA binding and mediates essential interactions with T7 DNA polymerase. (
  • Mutations in RNA polymerase also reduce the toxic effect of RecFOR, providing a further link between DNA replication, transcription and repair. (
  • This element forms a stable stem-loop structure and can be bound by either the protein encoded by this gene or by RNA polymerase II. (
  • This protein may act to disengage RNA polymerase II from TAR during transcriptional elongation. (
  • The cellular factor TRP-185 regulates RNA polymerase II binding to HIV-1 TAR RNA. (
  • RNA polymerase was shown to bind to the new promoter motif using a DNA-binding protein assay and proteomics enabled the discovery of four candidates to potentially function directly in control of transcription of the WLP and other key genes of C 1 fixation metabolism. (
  • Lastly, a protein-protein interaction assay with the RNA polymerase (RNAP) shows that CAETHG_0459 directly binds to the RNAP. (
  • Reference: Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69. (
  • To examine protein-protein interactions at the DNA replication fork, we have established solution conditions for the formation of a discrete and homogeneous complex of RB69 DNA polymerase (gp43), primer-template DNA, and RB69 single-stranded DNA-binding protein (gp32) using equilibrium fluorescence and light scattering. (
  • We have characterized the interaction between DNA polymerase and single-stranded DNA-binding protein and measured a 60-fold increase in the overall affinity of RB69 single-stranded DNA-binding protein (SSB) for template strand DNA in the presence of DNA polymerase that is the result of specific protein-protein interactions. (
  • Our data further suggest that the cooperative binding of the RB69 DNA polymerase and SSB to the primer-template junction is a simple but functionally important means of regulatory assembly of replication proteins at the site of action. (
  • We have also shown that a functional domain of RB69 single-stranded DNA-binding protein suggested previously to be the site of RB69 DNA polymerase-SSB interactions is dispensable. (
  • The data from these studies have been used to model the RB69 DNA polymerase-SSB interaction at the primer-template junction. (
  • The presence of the RB69 DNA polymerase at the primer terminus results in a 57-fold increase in gp32 (SSB) affinity for ssDNA as a result of DNA polymerase:SSB cooperativity. (
  • TBP recruits other transcriptions factors and eventually the RNA polymerase II to transcribe the DNA in mRNA. (
  • Static and kinetic site-specific protein-DNA photocrosslinking has major implications for transcription in general, for the topology determinants specifically for RNA polymerase II transcription, and the mechanistic determinants of contacts involved in nucleoprotein complexes. (
  • Transcription begins when the double-stranded DNA is unwound to allow the binding of RNA polymerase. (
  • Once transcription is initiated, RNA polymerase is released from the DNA. (
  • Polymerase chain reaction: locates and makes copies of parts of the DNA contained in the castor bean plant. (
  • Extradenticle (Exd) and Homothorax (Hth) function as positive transcriptional cofactors of Hox proteins, helping them to bind specifically their direct targets. (
  • Here we show that RemA is a DNA-binding protein that binds to multiple sites upstream of the promoters of both operons and is both necessary and sufficient for transcriptional activation in vivo and in vitro. (
  • Next, in vivo experiments showed that a TetR-family transcriptional regulator (CAETHG_0459) and the housekeeping sigma factor (σ A ) activate expression of a reporter protein (GFP) in-frame with the new promoter motif from a fusion vector in E. coli . (
  • The transcriptional repressive results of H3K27me3 are identified to become mediated because of the chromatin modulator 303997-35-5 In Vitro Polycomb99, suggesting that these proteins have a central job in limiting the lytic cycle gene programme and chromatin structure of KSHV throughout latency. (
  • DNA imitate protein are available in pathogen, bacterias and eukaryotic cells, and they're involved with many essential control systems, including DNA fix, limitation, transcriptional control and DNA product packaging (2). (
  • The Wilms' tumor suppressor gene, WT1, encodes a transcription factor in the zinc finger family, which binds to GC-rich sequences and functions as transcriptional activator or repressor. (
  • Thus, coexpression of the PKA catalytic subunit with wild type WT1 reduced the level of WT1 DNA-binding activity detected in nuclear extracts, and decreased transcriptional repression activity in vivo. (
  • ABSTRACT DNA methylation is an epigenetically inherited chemical modification that is associated with transcriptional silencing and is essential for mammalian development. (
  • Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. (
  • The family includes homodimers and heterodimers of five component proteins, which mediate different transcriptional responses and bind preferentially to different DNA sequences. (
  • Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea. (
  • Non-cytotoxic concentrations of PN significantly inhibited UVB-induced activator protein-1 DNA binding and transcriptional activity. (
  • Since its discovery, BRCA1 has been associated with many cellular processes, including transcriptional regulation, chromatin remodeling, cell cycle control, and repair of double strand DNA breaks. (
  • PLU-1, a large multi-domain nuclear protein with strong transcriptional repression activity, is a member of the ARID family of DNA binding proteins. (
  • The effects of endoplasmic stress inducers on resistin mRNA and secreted protein levels were examined in differentiated 3T3-L1 adipocytes, focusing on the expression and genomic binding of transcriptional regulators of resistin. (
  • The effects of ER stress were transcriptional because of downregulation of CAAT/enhancer binding protein-α and peroxisome proliferator-activated receptor-γ transcriptional activators and upregulation of the transcriptional repressor CAAT/enhancer binding protein homologous protein-10 (CHOP10). (
  • As there are no reports on the transcriptional regulation of this gene, the DNA sequence from -2612 to +682 bp (relative to the transcription start site) of the JDP2 gene was cloned and promoter activity analyzed. (
  • The gatekeepers of transcriptional initiation are "transcription factors" (TFs): proteins that engage DNA in a sequence-specific manner to either promote or inhibit transcription of targeted genes. (
  • In contrast, other proteins have evolved to bind to specific DNA sequences. (
  • Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. (
  • Our results explain the previously known strong position dependence on the equilibrium accessibility of nucleosomal DNA, which is characteristic of both selected and natural sequences. (
  • Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. (
  • article{Schneider-walker1997, author = "T. D. Schneider", title = "Sequence Walkers: a graphical method to display how binding proteins interact with {DNA} or {RNA} sequences", journal = "Nucleic Acids Res. (
  • Predicting the latest properties of these protein away from priino acids sequences was to be one of the leading demands into the useful annotations out of genomes. (
  • Inside report, we propose a deep training centered way of pick DNA-binding protein away from top sequences alone. (
  • They makes use of one or two level regarding convolutional simple community so you can position the brand new function domains out-of protein sequences, in addition to enough time small-label recollections sensory network to identify its overall dependencies, a keen digital mix entropy to check the standard of brand new neural systems. (
  • Citation: Qu Y-H, Yu H, Gong X-J, Xu J-H, Lee H-S (2017) Into anticipate from DNA-binding healthy protein merely regarding top sequences: An intense reading method. (
  • Associated with these proteins are hard to recognize because their amino acidity sequences and proteins structures are really divergent (2). (
  • Based on the performance, the developed methods will be useful in predicting the function of given protein sequences (DNA, RNA-binding and transcription factor) of model species as well as non-model crops. (
  • The deduced amino acid sequences of the proteins are homologous to those from monocotyledonous plants, yeast and mammals. (
  • Binding of specific proteins to short sequences of bases in DNA regulates gene expression. (
  • The effects on nuclear protein binding to NF- kB DNA consensus sequences were examined using an electrophoretic mobility shift assay. (
  • In-vitro treatment with crocidolite caused significant dose related increases in p65 binding to NF-kB consensus DNA sequences in both RLE and RPM cells. (
  • For example, structural biologists use The Protein Data Bank to store protein structures ( 4 ), geneticists use GenBank to share genomic sequences ( 5 ) and genomics researchers use the Gene Expression Omnibus to organize gene expression profiles ( 6 ) among many experimental databases routinely used in biology. (
  • This will ultimately allow us to predict consequences of small changes to non-gene DNA sequences, such as single nucleotide polymorphisms, that underlie interpersonal differences in disease susceptibility and drug response. (
  • Protein factors as well as sequences in mRNA are involved in the recognition of the initiation codon and formation of the initiation complex. (
  • With ChIP, the experimenter can determine if a specific protein binds to the exact sequences of a gene in residing cells by combining it with PCR (ChIP-PCR), microarray (ChIP-chip), or sequencing (ChIP-Seq) strategies. (
  • Telomeric DNA sequences show a higher susceptibility to certain DNA damaging agents than random DNA sequences. (
  • There were two different mismatches in the probe target sites of the HA gene sequences of all isolates ( n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT-PCR isolates. (
  • Examination of candidate genes by direct DNA sequencing. (
  • Thus, in some instances, the main positive cofactor complex for anterior Hox proteins can act as a negative factor for the posterior Hox protein Abd-B. This antagonistic interaction uncovers an alternative way in which MEIS and PBC cofactors can modulate Abd-B like posterior Hox genes during development. (
  • Using a comparative approach, we characterize the contribution of this and additional conserved sequence motifs to the regulation of specific target genes for three Drosophila Hox proteins. (
  • Cross-validation testing reveals that ligand-binding positions for 2152 domains are highly consistent and can be used to identify residues facilitating interactions in ∼63-69% of human genes. (
  • By organizing chromatin structure, the SATB2 protein coordinates the activity of multiple genes involved in the development of certain body systems. (
  • Some of these mutations are deletions of large pieces of DNA that remove several genes, including SATB2 . (
  • This sequence occurs in a regulatory region of DNA near the beginning of many genes. (
  • The TDP-43 protein attaches (binds) to DNA and regulates an activity called transcription, which is the first step in the production of proteins from genes. (
  • Genomic elements such as proteins or genes are the basic unit of the genome and involved in the functioning of every biological process. (
  • Farmington, Conn.-Jackson Laboratory Associate Professor Jeffrey Chuang, Ph.D., has been awarded a two-year grant totaling $519,750 from the National Human Genome Research Institute for his studies of how RNA (molecules vital to protein formation in cells) interacts with proteins to change how genes are expressed. (
  • Binding to DNA molecules, these proteins can change how genes are expressed. (
  • What is less commonly appreciated is that there is another major class of DNA segments called "enhancers' that control the activities of genes, and arguably play an equally important role as genes. (
  • These genes are involved in DNA repair. (
  • Thyroid receptors are linked to a DNA sequence known as the thyroid-response element ( TRE ) which initiates the transcription of thyroid-responsive genes. (
  • Sydney Brenner: Fred realized very early on that if we could sequence DNA, we would have direct contact with the genes. (
  • The study started examining the role of BMAL1, which is a protein that is involved in the transcription of various genes that affect the circadian clock mechanisms in all mammals, including humans. (
  • To identify the genes that give B. henselae this ability, the researchers began inducing random mutations in the DNA of the bacteria and seeing whether the mutated bacteria could still make the endothelial cells multiply. (
  • The Ataxin -family protein ATXN1L has beforehand been reported to work together with CIC in each developmental and illness contexts to facilitate the repression of CIC goal genes and promote the post-translational stability of CIC. (
  • These proteins organize the DNA into a compact structure called chromatin. (
  • Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA. (
  • Furthermore, specialised elements this kind of as CCCTC-binding issue (CTCF) are identified to function as chromatin-organizing factors10204. (
  • These regions help determine the structure of chromatin, which is the complex of DNA and proteins that packages DNA into chromosomes. (
  • In humans, the UV-damaged DNA-binding protein (UV-DDB) is part of a ubiquitin E3 ligase complex (DDB1-CUL4ADDB2) that initiates NER by recognizing damaged chromatin with concomitant ubiquitination of core histones at the lesion. (
  • Our findings provide unique structural and conformational insights into the molecular architecture of the DDB1-CUL4ADDB2 E3 ligase, with significant implications for the regulation and overall organization of the proteins responsible for initiation of NER in the context of chromatin and for the consequent maintenance of genomic integrity. (
  • Background: MeCP2- A chromatin-binding protein associated with Rett syndrome-has two main isoforms, MeCP2-E1 and MeCP2-E2, differing in a few N-terminal amino acid residues. (
  • In the new study, the researchers discovered that Dsup binds to a structure called chromatin, a package that holds a cell's long strands of DNA in a dense package, Kadonaga told Live Science. (
  • We found it binds to chromatin. (
  • the cloud surrounds the DNA's chromatin envelope, blocking hydroxyl radicals and preventing them from disrupting cellular DNA, the researchers reported. (
  • Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. (
  • Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. (
  • Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. (
  • This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation. (
  • Eukaryotic DNA is packaged into chromatin, a highly compacted structure made up of repeating nucleosome units. (
  • H1 belongs to a class of chromatin architectural proteins (CAPs) that are responsible for maintaining, modulating and stabilizing chromatin architecture. (
  • The ability of H1 to compact chromatin may be antagonized by other CAPs, such as the highly abundant high mobility group proteins (HMGs). (
  • Thus, H1 and HMG proteins are both chromatin architectural proteins that may serve as active regulators of transcription. (
  • Here we apply genome-wide profiling and gene specific approaches to study these proteins in D. melanogaster S2 cells and to better understand their roles in gene regulation and chromatin structural changes. (
  • We also found that PLU-1 localises diffusely over the nucleus, which indicates a potential chromatin binding ability of this protein. (
  • Our data point to a role for PLU-1 in meiotic transcription, which may be restricted to certain meiotic stages and may be mediated by the ability of this protein to associate with the chromatin. (
  • Petryk N, Reverón-Gómez N, González-Aguilera C, Dalby M, Andersson R, Groth A. Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. (
  • Background Knowledge Chromatin immunoprecipitation (ChIP) offers an advantageous system for locating out protein-DNA interaction. (
  • The CHD7 protein is involved in the epigenetic regulation of transcription and plays a role in the control of gene expression through chromatin remodeling and thus in early embryonic development. (
  • SimpleChIP ® Mouse Pdk4 Promoter Primers were tested on DNA isolated from cross-linked cells using the SimpleChIP ® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005. (
  • These primers can be used to amplify DNA that has been isolated using chromatin immunoprecipitation (ChIP). (
  • As oligomerization of these MBD proteins could constitute a factor contributing to the chromatin clustering effect, we addressed potential associations among the MBD family performing a series of different interaction assays in vitro as well as in vivo. (
  • However, the intricacies of how pioneer factors target their DNA motifs within the complex chromatin environment are largely unknown. (
  • Chromatin immunoprecipitation (ChIP), followed by quantitative PCR, will be performed after CRISPRi to diagnose how pioneer factor binding changes after ectopically introducing H3K9me3 over its binding sites. (
  • In the smallest repeating unit of the packaged genetic material, or chromatin, ~150 DNA base pairs wrap around a core of histone proteins, forming the nucleosome. (
  • In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. (
  • Postreplication mismatch repair has been found to faithfully replace misincorporated nucleotides, thereby increasing the overall fidelity of DNA replication. (
  • PriA protein provides a means to load the DnaB replicative helicase at DNA replication fork and D loop structures, and is therefore a key factor in the rescue of stalled or broken forks and subsequent replication restart. (
  • We suggest that binding of RdgC to DNA limits RecA loading, avoiding problems at replication forks that would otherwise require PriA to promote replication restart. (
  • Replication Protein A (RPA), the major single stranded DNA binding protein in eukaryotes, is composed of three subunits and is a fundamental player in DNA metabolism, participating in replication, transcription, repair, and the DNA damage response. (
  • Here, we demonstrate experimentally that the T . cruzi RPA complex interacts with DNA via RPA-1 and is directly related to canonical functions, such as DNA replication and DNA damage response. (
  • Replication Protein A (RPA) is a single stranded DNA binding protein involved in many functions of DNA metabolism, such as DNA replication and repair. (
  • The studies of SSB-binding mode transition and cooperativity are therefore critical to many cellular processes like DNA repair and replication. (
  • The organization and proper assembly of proteins to the primer-template junction during DNA replication is essential for accurate and processive DNA synthesis. (
  • DNA replication in RB69 (a T4-like bacteriophage) is similar to those of eukaryotes and archaea and has been a prototype for studies on DNA replication and assembly of the functional replisome. (
  • The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication (PMID:11988766). (
  • Functionally, UDGs take away the uracils in DNA that derive from the spontaneous deamination of cytosine or the incorporation of dUTP during replication (3,4). (
  • Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair, in both eukaryotic and archaeal cells. (
  • Current models propose that during DNA replication, thymine is incorporated across from O 6 mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double-strand breaks (DSBs). (
  • DNA Replication, Protein synthesis, Transcription and translation. (
  • Enigmatic roles of Mcm10 in DNA replication. (
  • 1990. Cell replication and unscheduled DNA synthesis (UDS) activity of low molecular weight chlorinated paraffins in the rat liver in vivo. (
  • 2007. Ortholog of BRCA2-interacting protein BCCIP controls morphogenetic responses during DNA replication stress in Ustilago maydis. . (
  • Within chromosomes, DNA is held in complexes with structural proteins. (
  • Nucleosomes sterically occlude their wrapped DNA from interacting with many large protein complexes. (
  • Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. (
  • Here, we characterize the DNA binding activity of Hox transcription factor complexes on eight experimentally verified cis-regulatory elements. (
  • Hox factors regulate the activity of each element by forming protein complexes with two cofactor proteins, Extradenticle (Exd) and Homothorax (Hth). (
  • Using comparative DNA binding assays, we found that a number of flexible arrangements of Hox, Exd, and Hth binding sites mediate cooperative transcription factor complexes. (
  • Moreover, analysis of a Distal-less regulatory element (DMXR) that is repressed by abdominal Hox factors revealed that suboptimal binding sites can be combined to form high affinity transcription complexes. (
  • Additional experiments indicated that cell surface IgG binding was not due to antibodies binding to cell surface DNA, DNA anti‐DNA immune complexes reacting with a DNA binding protein, anti‐histone antibodies or anti‐Sm antibodies. (
  • We analyzed JAK activation, STAT protein phosphorylation, and the formation of specific DNA-binding complexes containing STAT proteins, in a series of leukemia cell lines transformed by Bcr/Abl or other oncogenes. (
  • DNA-STAT complexes were detected in all Bcr/Abl-transformed cell lines and they were supershifted by antibodies against STAT1 and STAT5. (
  • DNA-STAT complexes in 32Dp210Bcr/Abl cells were similar, but not identical, to those formed after IL-3 stimulation. (
  • 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). (
  • In sharp contrast, however, information on electronic processes in biomolecules such as isolated proteins and DNA (and their complexes) is still in its infancy. (
  • The structures of DNA-protein complexes have illuminated the diversity of DNA-protein binding mechanisms shown by different protein families. (
  • Three-dimensional structures have been used to understand the variables that affect and mediate the formation of DNA-Protein complexes. (
  • Analysis of the free energies of several forms of interactions including electrostatics, hydrogen bonds, Van der Waals and packing has demonstrated that Van der Waals contributions mediate the formation of DNA-Protein complexes whilst electrostatic forces are unfavorable. (
  • 73% of protein-DNA complexes were found to involve such interactions, and these were found to function over long ranges. (
  • Crystal structures of DNA complexes show that the dimers of the Rel-homology regions are structurally very similar. (
  • Carriers in this study were DOTAP/DOPE/PS liposomes, methacrylamide based (PDMAEMA) micelles, and anionic lipid coated DNA complexes (LCDCs). (
  • 1 Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. (
  • Remodelers are multi-subunit complexes characterized by a conserved core ATPase responsible for breaking histone-DNA contacts. (
  • Gene 2.5 of bacteriophage T7 is an essential gene that encodes a single-stranded DNA-binding protein (gp2.5). (
  • Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. (
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (
  • Dual - beam optical tweezers experiments subject single molecules of DNA to high forces (∼ 300 pN) with 0.1 pN accuracy, probing the energy and specificity of nucleic acid - ligand structures. (
  • Although computational analysis suggests similarities in DNA binding and Ob-fold structures of RPA from T . cruzi compared with mammalian and fungi RPA, the predicted tridimensional structures of T . cruzi RPA-1 and RPA-2 indicated that these molecules present a more flexible tertiary structure, suggesting that T . cruzi RPA could be involved in additional responses. (
  • Here, we introduce an approach to identify perdomain- position interaction 'frequencies' by aggregating protein co-complex structures by domain and ascertaining how often residues mapping to each domain position interact with ligands. (
  • We perform this domain-based analysis on ∼91000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions or small molecules across 4128 domains, which we refer to collectively as the InteracDome. (
  • In particular, the SATB2 protein promotes the maturation of cells that build bones (osteoblasts) and directs development of structures in the head and face. (
  • The protective protein binds to cell structures that contain DNA. (
  • And now, scientists have discovered how Dsup binds to chromosome structures and protects DNA from the harmful effects of radiation, the researchers reported in a new study. (
  • By using an integrative approach that combines three crystal structures, four cryo-EM structures in complex with single-stranded DNA (ssDNA) of different length. (
  • We further validate the method on DNAbinding protein structures determined in DNA-free (apo) state. (
  • Weshow that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. (
  • Comparison of the wild-type and the mutant structures shows that removal of the charged group from the protein core, and its substitution by a neutral isosteric moiety, does not disrupt the functional architecture of the active center. (
  • Here , we report the solution structures of the extended murine PTPN13 PDZ3 domain in its apo form and in complex with its physiological ligand , the carboxy-terminus of protein kinase C-related kinase-2 (PRK2), determined by multidimensional NMR spectroscopy. (
  • Recent crystal structures of uracil-DNA glycosylases show a novel uracil-binding pocket that explains the enzyme's selectivity for uracil-containing DNA and provide a structural basis for exploring the catalytic mechanism of amino-glycosylic bond cleavage. (
  • Ellenberger, T 1995, ' Pocketing the difference: structures of uracil excision repair proteins ', Chemistry and Biology , vol. 2, no. 6, pp. 351-354. (
  • Most cells contain ribosomes , which are structures that combine amino acids to create proteins. (
  • In the manual for protein docking, there is another application for preparing structures for docking: docking prepack protocol. (
  • This prepack protocol can generate input structures from bound protein-protein complex. (
  • So how can I generate input structures from unbound protein components (for example, if protein A and B form a complex, and I have the structures for A alone and B alone)? (
  • Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. (
  • These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. (
  • The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to read the DNA sequence. (
  • Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the lattice models. (
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (
  • Here we show that for a selected high-affinity nucleosome positioning sequence, the spontaneous DNA unwrapping rate decreases dramatically with distance inside the nucleosome. (
  • To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. (
  • We generated two synthetic zinc-finger DNA-binding domains (ZF-DBDs) targeting this sequence. (
  • Up to now, numerous framework otherwise sequence established predictors getting determining DNA-joining necessary protein had been advised [2-4]. (
  • The protein is a sequence-specific DNA-binding protein that recognizes both single- and double-stranded DNA. (
  • Repair of DNA double-strand breaks in vertebrate cells occurs mainly by anend-joining process that often generates junctions with sequence homologies of a few nucleotides. (
  • Here, we show that Mre11 exonuclease activity is sensitive to the presence of heterologous DNA, and to thestructure and sequence of its ends. (
  • Addition of mismatched DNA ends stimulatesdegradation of DNA by Mre11, whereas cohesive ends strongly inhibit it.Furthermore, if a sequence identity is revealed during the course of degradation,it causes Mre11 nuclease activity to pause, thus stabilizing the junction at asite of microhomology. (
  • To date, various types of computational methods have been developed to predict the function of a given protein sequence. (
  • Due to these reasons, the immediate requirement for development of sophisticated computational methods to predict the function of a given protein sequence is raised. (
  • Each DNA-binding domain of the subclass of nuclear hormone receptors binds to the consensus sequence AGGTCA. (
  • Furthermore, analysis of DNA-binding sites has revealed discontinuous sequence segments form hydrophilic surfaces which are prime sites of hydrogen binding interactions. (
  • Differing DNA sequence preference together with structural similarity suggests that the dimers may differ in their dynamics. (
  • Where necessary, we are engineering enzymes using ancestral sequence reconstruction to obtain proteins with novel properties. (
  • The recognition of abnormal DNA structure by proteins is fundamentally different from sequence-specific DNA binding. (
  • 2001. Molecular dynamics studies of sequence-directed curvature in bending locus of Trypanosome kinetoplast DNA . (
  • The TDP-43 protein is involved in processing molecules called messenger RNA (mRNA), which serve as the genetic blueprints for making proteins. (
  • By cutting and rearranging mRNA molecules in different ways, the TDP-43 protein controls the production of different versions of certain proteins. (
  • The majority of these changes affect the region of the protein involved in mRNA processing, likely disrupting the production of other proteins. (
  • In previous studies, high levels of expression of Plu-1 mRNA and PLU-1 protein were detected in breast cancers, while expression in normal adult tissues was detected only in the testis, ovary and transiently in the mammary gland of the pregnant female. (
  • Using in situ hybridisation and immunostaining of testis sections we show that Plu-1 mRNA and PLU-1 protein are both highly expressed in the mitotic spermatogonia. (
  • Resistin protein was also substantially downregulated, showing a close correspondence with mRNA levels in 3T3-L1 adipocytes as well as in the fat pads of obese mice. (
  • ER stress is a potent regulator of resistin, suggesting that ER stress may underlie the local downregulation of resistin mRNA and protein in fat in murine obesity. (
  • Marchal C, de Dieuleveult M, Saint-Ruf C, Guinot N, Ferry L, Olalla Saad ST, Lazarini M, Defossez PA, Miotto B. Depletion of ZBTB38 potentiates the effects of DNA demethylating agents in cancer cells via CDKN1C mRNA up-regulation. (
  • The information for protein synthesis is generally stored in DNA, which is transcribed to messenger RNA (mRNA), and then translated into a protein. (
  • Translation or protein synthesis is a multi-step process that requires a lot of molecules including transfer RNAs (tRNA), amino acids, ATP, GTP and other cofactors to transfer information from mRNA to protein in ribosomes. (
  • During initiation, the small subunit of the ribosome bound to initiator t-RNA searches for the mRNA starting at the 5' terminal to identify and bind the initiation codon (AUG). The large subunit of the ribosome then joins the small ribosomal subunit to generate the initiation complex at the initiation codon. (
  • To control protein quantities in the organism, we must control transcription, a step from DNA to mRNA and translation, a step from mRNA to protein. (
  • New Scientist - In a first for any infectious disease, a vaccine against flu has been made out of messenger RNA (mRNA) - the genetic material that controls the production of proteins. (
  • An injection of mRNA is picked up by immune cells, which translate it into protein. (
  • But CureVac, a company in Tübingen, Germany, has found that a protein called protamine, binds to mRNA and protects it. (
  • Stitz's team made an mRNA vaccine to one such protein from an ordinary seasonal flu. (
  • Through transcription the information contained in a section of DNA is replicated to form a new piece of messenger RNA (mRNA). (
  • mRNA is used to manufacture proteins through a process called translation. (
  • The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ light chain locus. (
  • Hop1 or its ZnF were able to bind different recombination intermediates. (
  • Interestingly, the binding affinity of Hop1 and its ZnF was much higher for the Holliday junction as compared to other recombination intermediates. (
  • Taken together, these results implicate that Hop1 protein might coordinate the physical monitoring of meiotic recombination intermediates during the process of branch migration and that Hop1 ZnF acts as a structural determinant of Hop1 protein functions. (
  • Meropenem resistance seen in the S. pneumoniae 15A-ST63 clone in Japan was thought to be due to acquisition of penicillin-binding protein (PBP) 1a (type 13) via recombination with a formerly predominant global serotype 19A-ST320 vaccine strain ( 3 ). (
  • 2003. The BRCA2-interacting protein DSS1 is vital for DNA repair, recombination, and genome stability in Ustilago maydis. . (
  • 2002. BRCA2 homolog required for proficiency in DNA repair, recombination, and genome stability in Ustilago maydis. . (
  • FA is the result of a genetic defect in a cluster of proteins responsible for DNA repair via homologous recombination . (
  • DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. (
  • This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules. (
  • A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligandbinding sites within structurally uncharacterized proteins. (
  • We report the X-ray crystal structure of the human UV-DDB in a complex with damaged DNA and show that the N-terminal domain of DDB2 makes critical contacts with two molecules of DNA, driving N-terminal-domain folding and promoting UV-DDB dimerization. (
  • ii) indirect contact between the protein and DNA, mediated predominantly by water molecules and conformational changes in the structure of DNA. (
  • These changes are thought to arise from changes in the structure of intramolecular water molecules and bridging amino acids and bases, conformational shifts in the DNA structure and/or its flexibility. (
  • the solvent interface area ranges between 1120 and 5800 Å2 and the binding site is populated with positively charged groups predominantly contributed by Lysine and Arginine side chains and the phosphate groups of DNA molecules. (
  • N ovel protein targets that can be used by candidate drug molecules to kill antibiotic-resistant strains of Staphylococcus aureus , including vancomycin-resistant S. aureus , have been identified by researchers at the Indian Institute of Science Education and Research (IISER) Pune. (
  • The team is also screening other small molecules that can potentially be used as a candidate drug to target the specific proteins already identified. (
  • Boston Molecules is a leading provider of comprehensive, high quality recombinant protein services. (
  • With extensive training from world-renown enzymology laboratory and crystallography laboratory, scientists in Boston Molecules provide customers with highly purified, properly folded (including ion optimized and disulfide bond correctly positioned) recombinant protein production services. (
  • This process occurs with the tyrosine residues attached to thyroglobulin, so that, at any one time, this protein is festooned with molecules of T1, T2, T3 and T4 (Fig. 45b). (
  • Three of the molecules were chosen from different structural clusters for evaluation of binding to PPIP5K, using isothermal calorimetry. (
  • This code is the process by which cells in our body translate information stored in our DNA into proteins, vital molecules important to the structure and functioning of cells. (
  • In this method, catalytically dead Cas9 is fused to a H3K9me3-writing protein domain, which is targeted to a pioneer factor binding site via guide RNA molecules specific to the region of interest. (
  • As a result, there are now two double-stranded DNA molecules in the nucleus that contain the same information. (
  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (
  • SCOP: Structural Classification of Proteins and ASTRAL. (
  • CTCF also can perform in DNA-loop formation, and it can be probable that these structural loops serve as being the molecular basis for oth. (
  • Components AND Strategies Bioinformatic seek out possible DNA imitate applicants in the proteins structure database To operate being a DNA imitate, a proteins will need to have two important properties: a DNA-like agreement of adverse fees on its surface area and a proper structural conformation (2,13). (
  • A zinc finger is a common protein structural motif characterized by stabilization of its folds by zinc ions. (
  • The method is generalized to apply to the entire structural class of NR proteins, with specific examples for well-studied NRs. (
  • Such processes in DNA are also of interest to both the biological and materials communities as memory devices and structural building blocks. (
  • The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. (
  • Finally, we apply the method to ~1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. (
  • Research reported in this document was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number 1R21HG007554-01, "Combinatorial RNA Structural Features that Control RNA-Protein Binding. (
  • The conformational changes of DNA allow structural rearrangements to take place that are essential in mediating complex formation. (
  • Rec BCD is an E. coli protein with DNA helicase activity capable of making single-stranded nicks. (
  • The defect is caused by mutations (frameshift, nonsense, missense, or splice-site) in the CHD7 (Chromodomain [ chr omatin o rganisation mo difier] Helicase DNA-Binding Protein 7) gene, which has been mapped to chromosome 8q12.2. (
  • expressed in middle/late meiosis,IV" YDR525W 1 5 7 YDR525W "Ydr525wp,IV" YDR526C 1 5 8 YDR526C "Ydr526cp,IV" YER187W 1 5 9 YER187W "similar to killer toxin,V" YER188W 1 5 10 YER188W "Yer188wp,V" YER190W 1 5 11 YER190W "Yrf1-2p,V" YFL002C 1 5 12 YFL002C "ATP-dependent RNA helicase,VI" YFL002W-B 1 5 13 YFL002W-B "TyA gag protein. (
  • In most cases, CHARGE syndrome is due to heterozygous mutations in CHD7 (8q12.2) encoding the chromodomain helicase DNA-binding protein. (
  • Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, usually the expression of a gene. (
  • Previous studies have demonstrated that the acidic carboxyl terminus of the protein is essential and that it mediates multiple protein-protein interactions. (
  • Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo. (
  • Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein-DNA, protein-RNA and other protein-ligand interactions, a systematic assessment of their various interaction modes is still lacking. (
  • They are involved in protein-protein interactions. (
  • Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions. (
  • This lack of generality could pose a great challenge for predicting DNA-protein interactions. (
  • While DNA-protein interactions for hundreds of proteins have been cataloged and studied, protein interactions with RNA are less well known. (
  • Excitingly, several groups around the world, notably our collaborators in the Brenton Graveley lab at the University of Connecticut, have started to generate new types of experimental data on RNA-protein interactions. (
  • DNA-Protein interactions play an essential role in the regulation of transcription. (
  • This further supports the role of indirect readout and the significance of intramolecular interactions for DNA-Protein binding. (
  • Acidic residues carry a negative charge, which would result in energetically unfavorable interactions with DNA. (
  • Another important mediator of DNA-Protein binding is cation-π interactions. (
  • In general, local variations particularly in the minor groove of the DNA alongside electrostatic interactions mediate the general mechanism for DNA binding specificity. (
  • She work concentrates on dynamic protein-DNA interactions in real time and at the single-molecule level using techniques developed by her group to perform a unique DNA tight-rope assay. (
  • Besides demonstrating that these homo- and hetero-interactions occur in the absence of DNA, we could confirm them in mammalian cells using co-immunoprecipitation analysis. (
  • The large number of histone-DNA interactions within a nucleosome would make its DNA largely inaccessible, turning the nucleosome into a roadblock to DNA-based transactions. (
  • E05 478 566 350 170 or Enzyme-Linked Immunosorbent Assays,E05 478 566 350 170 or Enzyme-Linked Immunosorbent Assays,Human proteins, cDNA and human recombinants are used in human reactive ELISA kits and to produce anti-human mono and polyclonal antibodies. (
  • Antibodies ctuted from the 28-30 kD strip inhibited the binding of 3H.DNA to human PBMC. (
  • It is hypothesized that this autoimmune response could be one component of an idiotypic network involving anti‐DNA antibodies. (
  • Its high selectivity towards antibodies facilitates the effective clearance of host cell proteins, DNA, and viruses. (
  • Modification in the structure of the native Protein A, such as single domain multimer and multiple binding sites, results in its high specificity towards the Fc region of antibodies, high binding capacity, and good physicochemical stability. (
  • Therefore, it doesn't break or get damaged even during harsh elution conditions, such as while removing bound antibodies. (
  • The process works on the principle of the binding of specific antibodies to immobilized Protein A ligands. (
  • Antibodies bound to the blocking peptide no longer bind to the epitope on the target protein. (
  • The ChAdOx1-S [recombinant] vaccine uses a DNA adenovirus vector to elicit antibodies to the SARS-CoV-2 spike protein. (
  • Mutations modifying ssDNA-binding (SSB) protein also negate this toxic effect, suggesting that the toxicity reflects inappropriate loading of RecA on SSB-coated ssDNA, leading to excessive or untimely RecA activity. (
  • Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. (
  • Other mutations add, remove, or rearrange smaller pieces of DNA within the SATB2 gene. (
  • Still other mutations change single DNA building blocks (nucleotides) in the SATB2 gene. (
  • Most mutations change single protein building blocks (amino acids) in the TDP-43 protein. (
  • Most TARDBP gene mutations that cause FTD change single amino acids in the TDP-43 protein. (
  • These mutations are thought to affect only part of the protein, leaving other parts of the protein functional. (
  • Because these TARDBP gene mutations result in a protein with some residual function, the features of the condition tend to appear later in life, in one's late sixties or early seventies. (
  • They contribute to preserving the optimal functioning of cells and protecting them from potential DNA damage which could result in mutations and disease. (
  • Photoinduced charge transfer processes have been implicated in a variety of oxidative processes which ultimately lead to mutations, compromising the biological function of DNA. (
  • While the majority of these are frameshift and nonsense mutations that result in a severely truncated and non-functional protein, a minority are point mutations that substitute a single amino acid in the 1,863-amino-acid-long BRCA1 protein. (
  • These mice develop tumors almost as rapidly as mice with null mutations in BRCA1," Baer said, suggesting that the binding of BRCA1 to other phosphorylated proteins is critical for tumor suppression. (
  • More than 2,500 tumour genomes of 36 types of cancer were analysed and the team found DNA mutations pointing to one of the two known mechanisms to lengthen telomeres in 13 of the cases . (
  • The protein targets identified are crucial for the growth and survival of the bacteria and hence S. aureus are less likely to cause mutations in them to confer drug-resistance. (
  • Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. (
  • Homeotic selector (Hox) proteins often bind DNA cooperatively with cofactors such as Extradenticle (Exd) and Homothorax (Hth) to achieve functional specificity in vivo. (
  • We propose that using different binding mechanisms with the same cofactor may be one strategy to achieve functional specificity in vivo. (
  • Specificity in binding site selection (and responses) is achieved using different dimerization modes subunit pairings define the spacing and orientation of the factors and thereby the binding sites. (
  • Understanding how DNA binds to specific residues to mediate binding specificity alongside determining the recognition mechanism has presented a molecular and computational challenge to scientists. (
  • Numerous studies have demonstrated that this conformational switching of DNA has also been found to mediate specificity. (
  • abstract = "Previous experiments have established the presence of a 30‐kD DNA binding protein on the surface of human leukocytes. (
  • abstract = "Stage-specific activator protein (SSAP) is a 43-kDa polypeptide that binds to an enhancer element of the sea urchin late histone H1 gene. (
  • 1984. Covalent binding of benzidine to rat hemoglobin [Abstract]. (
  • We have shown that in this system, MMR proteins are enriched on MNU-treated DNA and we observed robust, MMR-dependent, repair synthesis. (
  • Cross-linking of IgE bound to mast cells by FcεRI triggers the release of preformed vasoactive mediators, synthesis of prostaglandins and leukotrienes, and the transcription of cytokines. (
  • Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression. (
  • However, in eukaryotes, the processes of transcription and translation are spatially separated and occur sequentially with transcription happening in the nucleus and translation, or protein synthesis, occurring in the cytoplasm. (
  • Although there are some particular differences existed, the overall process of protein synthesis is similar in both prokaryotes and eukaryotes with three stages of initiation, elongation and termination. (
  • Other important actions of thyroid hormones include a generalized increase in protein turnover (i.e. breakdown and synthesis), an increase in cardiac output caused by the enhancement of the effects of adrenaline (epinephrine) at β-adrenoceptors (Chapters 7 and 49), and a strong lipolytic effect that arises from the potentiation of responses to cortisol, glucagon, growth hormone and adrenaline. (
  • Likewise, its HCMV counterpart, UL45 (RRL), M45 is a putative homolog of the large subunit R1 of cellular ribonucleotide reductase (RNR), an enzyme that converts ribonucleoside diphosphates into the corresponding deoxyribonucleoside diphosphates, required for de novo synthesis of both viral and cellular DNA (Lembo et al. (
  • Through these experiments, the scientists determined that B. henselae can stimulate angiogenesis in human endothelial cells only if it possesses a functional copy of the gene that "codes for," or guides the synthesis of, the BafA protein. (
  • LIFE SCIENCES WILLIAM F. LOOMISIS Department of Biology University of California, SAN Diego La Jolla, Calif. " The gene coding for the chemoattractant receptor of Diet Dictyostellium amoebae has been isolated, characterized, and inactivated by antisense RNA The predicted protein product is similar to adrenergic and acetylcholine receptors as well as bovine rhodopsin suggesting that G protein-linked receptors evolved from a common progenitor before the appearance of metazoans. (
  • Sing, CE , De La Cruz, MO & Marko, JF 2014, ' Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins ', Nucleic acids research , vol. 42, no. 6, pp. 3783-3791. (
  • A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. (
  • In addition, this session will also deal with the photo-repair of nucleic acids and proteins. (
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing ANK domain in the selected taxonomic class. (
  • Although the functions of hMSH2 can be anticipated based on its similarity to well-characterized bacterial and yeast proteins, proof of its functions has not been established. (
  • Recent work has demonstrated concentrationdependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (
  • inhibitors (UGI and p56) previously recognized to research were both within phages, which is the initial record of the bacterial Aripiprazole (Abilify) IC50 GP5 DNA imitate that may regulate SAUDGs useful jobs in DNA fix and host protection. (
  • SAUGI can be which means third uracil-DNA glycosylase inhibitor that is identified, as well as the initial in a types apart from bacterial phage. (
  • Bacterial regulatory proteins [Interproscan]. (
  • Other than Protein A, the bacteria also have other immunoglobulin-binding bacterial proteins, such as Protein A/G, Protein L, and Protein G. (
  • Overexpressed proteins can be perceived as detrimental by bacterial immune system and packed into inclusion bodies. (
  • Study published in Nature Communications provides insight about a protein named BafA which stimulates the production of new blood vessels that support bacterial lesions. (
  • A research team from Fujita Health University, Japan, has found that bacteria of the genus Bartonella release a protein - which they have named BafA - that stimulates the production of new blood vessels that support bacterial lesions. (
  • We find that Sex combs reduced (Scr) uses a simple interaction mechanism, where a single tryptophan-containing motif is necessary for Exd-dependent DNA-binding and in vivo functions. (
  • The DNA-binding domain of the protein was localized to the conserved RNA recognition motif (RRM). (
  • The molecular modeling study showed that Hop1 ZnF folded into unique helix-loop-helix motif and bound to center of the Holliday junction. (
  • Most DNA-binding proteins have the zinc finger motif. (
  • Cloning and characterization of a p53 and DNA damage down-regulated gene PIQ that codes for a novel calmodulin-binding IQ motif protein and is up-regulated in gastrointestinal cancers. (
  • XV" YOL105C 1 15 18 YOL105C "Putative integral membrane protein containing novel cysteine motif. (
  • Opacity-associated protein A LysM-like domain, Opacity-associated protein A N-terminal motif [Interproscan]. (
  • The likelihood that a motif will be bound by its pioneer factor has been found to be influenced by local pioneer factor concentration, similarity to its consensus motif, cofactor availability, and competition and cooperation with other factors. (
  • MCMV infection is known to trigger cellular necroptosis as a part of antiviral response, but M45 acts as a cell death suppressor by binding to receptor-interacting protein 3 (RIP3) via its RIP homotypic interaction motif (RHIM) (Daley-Bauer et al. (
  • Lastly, we revealed that the PAM2 motif of ATX2, which mediates its interplay with poly(A)-binding protein (PABP), is probably mandatory for the lower of FMRP in sure neuronal stress situations. (
  • It is likely that these genetic changes reduce the amount of functional SATB2 protein. (
  • These genetic elements, normally dormant within human genomes, can be (re)-activated by environmental factors such as infections with other viruses, leading to the expression of viral proteins and, in some instances, even to viral particle production. (
  • All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). (
  • These changes and markers of genetic instability are driven by a failure of DNA repair systems and cell cycle regulation. (
  • argylesock says… Zinc finger nucleases (ZFN) are proteins which can be used in genetic modification (GM, genetic engineering, GE). (
  • Fanconi anaemia ( FA ) is a rare genetic disease resulting in impaired response to DNA damage. (
  • [2] Because of the genetic defect in DNA repair, cells from people with FA are sensitive to drugs that treat cancer by DNA crosslinking , such as mitomycin C . The typical age of death was 30 years in 2000. (
  • Gene therapy involves the delivery of exogenous DNA into the target cells in order to produce therapeutic protein or to correct a genetic defect. (
  • DNA is the genetic material of the cell. (
  • All living organisms have cells that contain genetic material ( DNA ). (
  • ED: Today, the structure of DNA and how genetic information is translated into proteins are established scientific canon, but in the 1950s, the hypotheses generated at the LMB were dismissed as inconceivable nonsense. (
  • Gene expression is the process by which the genetic information encoded in DNA is translated into the arsenal of proteins required to orchestrate diverse biological processes in living systems. (
  • Its protein is one of the four founder proteins that structurally define the superfamily of MADS DOMAIN PROTEINS. (
  • Three structurally divergent families of MBPs have been identified so far: the MBD family, the SRA family and a family of proteins with Zinc fingers. (
  • Structurally, Protein A contains five Ig-binding domains, each of which can bind a wide variety of mammalian proteins- especially human IgG . (
  • Their results show that Rvb1 and Rvb2 form a single heterohexameric ring upon which the two substrate-binding modules, which form structurally discrete entities, dock side-by-side. (
  • i) direct contact between the base pairs of DNA and specific amino acids in the protein structure. (
  • Furthermore, mutational analysis of specific bases on DNA that not in direct contact with amino acids often affect binding affinity. (
  • PDZ3 of PTPN13 binds five carboxy-terminal amino acids of PRK2 via a groove located between the EB-strand and the DB-helix. (
  • The PRK2 peptide resides in the canonical PDZ3 binding cleft in an elongated manner and the amino acid side chains in position P0 and P-2, cysteine and aspartate, of the ligand face the groove between EB-strand and DB-helix, whereas the PRK2 side chains of tryptophan and alanine located in position P-1 and P-3 point away from the binding cleft. (
  • In a new study published today (October 27) in Science , researchers pegged this crucial function to a specific region of the protein known as the BRCT domains: two nearly identical stretches, around 90 amino acids long, that lie toward the carboxyl-end of the protein and are responsible for binding phosphorylated proteins. (
  • the BRCT domains in the carboxyl end of the protein, and a region about 110 amino acids long on the opposite end of the protein known as the RING domain. (
  • The small molecule was found to bind to a particular amino acid (cysteine) that is very important for many catalytic functions in the cell. (
  • Proteins are large biomolecules consisting of one or more long chains of amino acid residues. (
  • During elongation, tRNAs binding to their designated amino acids move to the ribosome where amino acids are polymerized to form a peptide. (
  • I think there were only forty-five amino acids [the building blocks of proteins] that were in insulin. (
  • Protein deacetylases are enzymes that remove acetyl groups from lysine (a common amino acid/protein). (
  • Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. (
  • Britanova O, Akopov S, Lukyanov S, Gruss P, Tarabykin V. Novel transcription factor Satb2 interacts with matrix attachment region DNA elements in a tissue-specific manner and demonstrates cell-type-dependent expression in the developing mouse CNS. (
  • TATA-binding protein works as part of a larger transcription factor, TFIID, that starts the process of transcription. (
  • Here we report that, after IA learning, the levels of the transcription factor CCAAT enhancer binding protein δ (C/EBPδ) are significantly increased in both the hippocampus and amygdala. (
  • Transcription factor binding motifs help to elucidate regulatory mechanism. (
  • The human hMSH2 protein is a member of a highly conserved family of postreplication mismatch repair components found from bacteria to humans. (
  • This session will discuss recent progress in the photoinduced processes related to proteins that are responsible for vision that include i) rhodopsin in the photoreceptor cells of the vertebrate ii) retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. (
  • Bacteria were used as sensitive indicators for DNA damage and mammalian liver extracts for metabolic conversion of carcinogens to their active metabolic forms. (
  • The researchers used a small molecule (quinone epoxide) and attached an indole residue to it to increase the ability of the molecule to cross the cell barrier of the bacteria and then bind to the proteins. (
  • The small molecule was found to bind to multiple proteins, including a few that are crucial for growth and survival of the bacteria. (
  • Now that we have found a new small molecule that can cross the cell barrier, bind to proteins and kill the bacteria, we can always decorate the molecule with functional groups and make it more bioavailable in animals. (
  • Most bacteria are, however, surrounded by a rigid cell wall made out of peptidoglycan , a polymer composed of linked carbohydrates and small proteins. (
  • Originally, it was found as a type 1 membrane protein in the cell wall of the bacteria Staphylococcus aureus , where it's regulated by cellular osmolarity, cellular topology, and a two-component system called ArlS-ArlR. (
  • Facilitating the binding of bacteria to the host surface for pathogenesis. (
  • As a maestro harmonizes music, let's harmonize proteins in the bacteria! (
  • The ATP-binding cassette proteins (ABC) are very similar across species, including in bacteria, plants and animals. (
  • This is the very first report of a vascular endothelial growth factor (VEGF for short)-like protein produced by bacteria. (
  • Is predicted to encode a protein with the following domains: Cation-channel complex subunit UNC-79 and UNC79. (
  • The lungs were sliced into 5 micrometer thick sections which were examined for p65, a protein subunit of NF-kB, using an immunofluorescence technique. (
  • Their work revealed that the 14 subunits of SWR1 associate as 4 functional modules: the catalytic subunit Swr1, two multi-subunit modules that interact with the substrate nucleosome and the H2A.Z/H2B dimer, and the putative hexameric AAA+ proteins Rvb1/Rvb2. (
  • DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. (
  • Many proteins, however, exhibit some affinity for both dsDNA and ssDNA. (
  • We also established the structure from the SAUGI/SAUDG complicated, and used surface area plasmon resonance (BIAcore) showing that SAUGI includes a high binding affinity to UDG. (
  • The CK2-, cdc2- and cdc2/CK2-phosphorylated forms of HMGA1a each exhibit a different binding affinity towards the PRD2 element of the NFκB promoter. (
  • Moreover, ITC data reveal that the CK2-phosphorylated HMGA1a exhibits a different DNA promoter binding affinity for the PRD2 element. (
  • Protein A resin is a high-affinity chromatography medium. (
  • The modified features have also resulted in the formation of a highly stable and robust Protein A affinity resin, which is extensively used in biotechnology and immunology research studies for downstream processing and purification processes. (
  • Protein A resin has a myriad of applications, ranging from its use in affinity chromatographic assays, and immunoprecipitation, to biomanufacturing and bioprocessing assays. (
  • The Protein A affinity chromatography technique is extensively used in labs to capture and purify immunoglobulins, such as IgG and monoclonal antibody products. (
  • Thus, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. (
  • c-Jun (Cellular Jun) is a protein encoded by gene Jun, that participates in the cell cycle and apoptosis. (
  • TDP-43 is a nuclear DNA/RNA-binding protein with cellular functions in RNA transcription and splicing. (
  • A protein found only in tardigrades provides cellular DNA with a unique form of protection. (
  • The proteins are crucial as they bind to the DNA to activate it for normal cellular functioning. (
  • The use of cationic liposomes and polymers as carriers of DNA is based on observations that positively charged carriers bind to anionic DNA protecting its premature degradation and facilitating its cellular uptake in transfection. (
  • With manipulation of cellular distancing and upon activation of bone morphogenetic protein 4 (BMP4), stem cells differentiate into two regions: non-neural brachyury (BRA) and neural sex determining region Y-box 2 (SOX2) positive cells. (
  • iCeMS cellular biochemist Kazumitsu Ueda has studied human ABC proteins for 35 years, ever since he and his colleagues identified the first eukaryote ABC protein gene. (
  • How NAD+ supplementation altering the circadian rhythm, restores repressed BMAL1 binding, cellular oscillations, respiration rhythms, and activity rhythms back to youthful levels. (
  • A special class of eukaryotic TFs, called pioneer factors, are the first to bind during cellular differentiation and reprogramming, facilitating the binding of non-pioneer transcription factors and initiating gene cascades associated with the new cell type. (
  • RNA is similar in structure to DNA but is involved in different cellular functions. (
  • Biofilm formation in Bacillus subtilis requires expression of the eps and tapA-sipW-tasA operons to synthesize the extracellular matrix components, extracellular polysaccharide and TasA amyloid proteins, respectively. (
  • Expression of both operons is inhibited by the DNA-binding protein master regulator of biofilm formation SinR and activated by the protein RemA. (
  • We further show that SinR negatively regulates eps operon expression by occluding RemA binding and thus for the P eps promoter SinR functions as an anti-activator. (
  • Expression of protein TARBP1 in human hepatocellular carcinoma and its prognostic significance. (
  • Direct protein delivery of ZF-DBDs that compete with transcription regulatory proteins will have broad implications for modulating gene expression in analytical or therapeutic settings. (
  • Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression. (
  • One of the gene expression cascades found to play an evolutionarily conserved role in long-term memory formation is that controlled by the transcription factors cAMP response element binding protein (CREB) and C/EBPs. (
  • Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. (
  • Protein Expression and Purification. (
  • To address this, we analysed the pattern of expression and localisation of this protein in mouse testicular cells during postnatal development and adulthood. (
  • We offer a variety of recombinant protein expression and purification services from gene to protein to crystallography. (
  • The modification of carriers and the engineering of DNA are proposed to enable efficient and prolonged protein expression after transfection. (
  • Last week, I completed a purification of the full-length huntingtin protein Q23 from baculovirus expression system (BVES). (
  • As well as the uniqueness of proteins, the expression levels of proteins contribute to the marvelous functions of living things. (
  • The T box-binding element (TBE) between -191 and -141 bp was identified as the cis-element responsible for CSF1-dependent JDP2 expression. (
  • In summary, CSF1 upregulates JDP2 expression by inducing Tbx3 binding to the JDP2 promoter. (
  • Sputum samples were collected from 156 workers employed in 15 cotton textile mills, and expression of epithe- lial membrane antigen (EMA) and cytokeratin (CK) marker proteins was investigated. (
  • In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones. (
  • They occur in a large number of functionally diverse proteins mainly from eukaryotes. (
  • ADP ribosylation factors (ARFs), which are members of the Ras superfamily of GTP-binding proteins, are critical components of vesicular trafficking pathways in eukaryotes. (
  • In other eukaryotes, this protein is recruited to specific promoters by DNA binding transcription factors and is thought to promote transcription by acetylating the N-terminal tail of histone H3. (
  • We describe experiments upon DNA + HMGB2 (box A), a nuclear protein that is believed to facilitate transcription. (
  • It's also identified by the synonym ''Activator protein 1 or V-jun avian sarcoma virus 17 oncogene homolog'' , it's a liquid who targets the c-Jun (Phospho-Ser243) in Hela Nuclear Extract that's cultured 3 days with 10% FBS in DMEM and were stimulated by UV (100J/M2) and harvested for nuclear extract. (
  • High Mobility Group Protein A1a (HMGA1a) is a highly abundant nuclear protein, which plays a crucial role during embryogenesis, cell differentiation, and neoplasia. (
  • XIII" YMR047C 3 13 3 YMR047C "Nuclear pore complex protein that is member of GLFG repeat-containing family of nucleoporins and is,XIII" YMR049C 3 13 4 YMR049C "Ymr049cp,XIII" YMR051C 3 13 5 YMR051C "TyA Gag protein. (
  • DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate. (
  • The DNA methylation signal is read out by methyl-CpG binding proteins (MBPs) that specifically bind to methylated DNA. (
  • In this review, we describe how the distinct families of methyl-CpG binding proteins have evolved, how they each recognize and maintain the DNA methylation mark, and finally how they turn this mark into biological effect. (
  • Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. (
  • The methyl-cytosine binding domain (MBD) protein family recognizes and translates this methylation mark. (
  • Blood cell DNA methylation biomarkers in preclinical malignant pleural mesothelioma: The EPIC prospective cohort. (
  • A nuclease-deficient Mre11 mutant that still binds DNA canalso stimulate degradation by wild-type Mre11, suggesting that Mre11-DNAcomplexes may interact to bridge DNA ends and facilitate DNA joining. (
  • In summary, this study shows that Hop1 protein or its ZnF interact specifically with the Holliday junction and distort its structure. (
  • Results: Here, we show that the N-terminal domains (NTD) of MeCP2-E1 and E2 modulate the ability of the methyl-binding domain (MBD) to interact with DNA as well as influencing the turn-over rates, binding dynamics, response to neuronal depolarization, and circadian oscillations of the two isoforms. (
  • We have developed a new mathematical and computational approach to decipher how RNAs interact with proteins from these types of data, which will be critical for understanding the root causes of many diseases. (
  • PDZ domains are among the most abundant protein modules and they play a crucial role in signal transduction of protein networks. (
  • The resultant accumulation of cholesterol in the inner leaflet triggers the recruitment of proteins to the membrane and modulates the signal transduction. (
  • Aims: The aim of this study was to clarify the effects of homologous and heterologous extracellular DNAs (eDNAs) and histone-like DNA binding protein (HLP) on Streptococcus intermedius biofilm development and rigidity. (
  • After homologous chromosomes align, a single strand of each DNA breaks and invades the other DNA. (
  • After homologous chromosomes align, a single strand of DNA is nicked and replicated. (
  • The whisker invades the homologous double-helix and displaces that DNA, which is excised. (
  • 2016. Homologous Pairing between Long DNA Double Helices . (
  • Alterations of the gene coding for this protein cosegregate with, and are the likely cause of, chromosome 2-linked hereditary nonpolyposis colon cancer. (
  • As a consequence, loss of telomeric DNA results in replicative senescence through chromosome damage and decrease in cell viability [ 5 ]. (
  • DNA start text, D, N, A, end text is found in a central region of the cell called the nucleoid , and it typically consists of a single large loop called a circular chromosome. (
  • It has been previously found that hTERT activity is down-regulated by the human T cell leukaemia virus type 1 (HTLV-1) Tax protein in HTLV-1 transformed T lymphocytes. (
  • Our results point to slow nucleosome conformational fluctuations as a potential source of cell-cell variability in gene activation dynamics, and they reveal the dominant kinetic path by which multiple DNA binding proteins cooperatively invade a nucleosome. (
  • An immunomatrix of 28-30 kD reactive immunogtobulins was able to extract a 29‐kD DNA binding protein from a PBMC cell membrane preparation. (
  • Tyrosyl phosphorylation and DNA binding activity of signal transducers and activators of transcription (STAT) proteins in hematopoietic cell lines transformed by Bcr/Abl. (
  • This protein is found within the cell nucleus in most tissues and is involved in many of the steps of protein production. (
  • The TDP-43 protein can influence various functions of a cell by regulating protein production. (
  • It is unclear whether TDP-43 protein aggregates causes the nerve cell death that leads to ALS or if they are a byproduct of a dying cell. (
  • DNA provides the blueprint for building and running a living organism, but some proteins in the cell act like change orders in a construction plan. (
  • They increased the small molecule's ability to cross the cell barrier and bind to multiple proteins. (
  • Genomic instability is characterized by an elevated propensity of alterations in the genome throughout the cell cycle, where coordinated cell cycle progression and error-free repair of DNA damage are crucial for maintaining genomic integrity. (
  • Proteins are synthesized when needed in the cell normally. (
  • Tafasitamab is a humanized Fc-modified cytolytic CD19-directed monoclonal antibody that binds to the CD19 antigen expressed on the surface of pre-B and mature B lymphocytes and on several B-cell malignancies. (
  • For instance, although archaea also have a cell wall, it's not made out of peptidoglycan-although it does contain carbohydrates and proteins. (
  • Whilst the purification of the full-length huntingtin protein from the insect cell system we have working in the lab, gives high yields so plenty of protein to do experiments with, the protein is not made in a way which 100 % represents how it is made in humans. (
  • The nucleus of a eukaryotic cell contains its DNA. (
  • The small amounts of free T3 and T4 in plasma readily cross the cell membranes to bind to thyroid hormone receptors (the most important of which is TRa1 ). (
  • The BMP4 ligand (L) was chosen since it can be bound to the BMPR2 receptor (R) on the cell membrane of the cells being cultured to form the receptor-ligand complex (C). The BMP4 ligand diffuses throughout the colony of cells by forming a long range concentration profile. (
  • In regards to the performance of an accurate simulation in one dimension, BMP4 is administered to the system by pipetting a very small amount of a medium in which BMP4 has much lower solubility in comparison to the original solution and dispensing it on the walls of the microtube, thus allowing for a very thin layer of protein on top of the cell culture solution. (
  • Could DNA quadruple helices be causing abnormal cell growth in cancer? (
  • Such ligand-binding sites will be expected and then be successfully occupied by polar substances that usually do not easily combination cell buy Protopanaxatriol membranes, hence possibly deeming inositol phosphate binding storage compartments to become undruggable [23]. (
  • The ABCA1 protein flips the cholesterol from the inner to the outer layer of the cell membrane. (
  • Almost four decades of research have led scientists at Japan's Institute for Integrated Cell-Material Sciences (iCeMS) to propose that a family of transporter proteins has played an important role in species evolution. (
  • One protein in particular, called ABCA1, was likely crucial for vertebrate evolution by helping regulate when signals involved in cell proliferation, differentiation and migration enter a cell. (
  • There are different types of ABC proteins with different transportation roles, importing nutrients into cells, exporting toxic compounds outside them, and regulating lipid concentrations within cell membranes. (
  • plasma membrane of the cell, the heavy chain is called an integral membrane protein. (
  • Genome-wide studies have shown that pioneer factors bind only a small fraction of their putative motifs, and these binding events differ across cell types. (
  • The cell regulates DNA accessibility by fine-tuning this property. (
  • Previous studies on Bartonella henselae (B. henselae for short), the bacterium responsible for cat-scratch disease, have shown that it can directly "inject" proteins that inhibit programmed cell death (apoptosis) into the endothelial cells. (
  • Useful in vitro research using ATXN1L human cell traces revealed that lack of ATXN1L results in the buildup of polyubiquitinated CIC protein, selling its degradation by means of the proteasome. (
  • Though transcriptomic signatures of ATXN1L KO cell traces indicated upregulation of the mitogen-activated protein kinase pathway, ERK exercise was discovered to contribute to CIC operate however not stability. (
  • Degradation of CIC protein following lack of ATXN1L was as an alternative noticed to be mediated by the E3 ubiquitin ligase TRIM25 which was additional validated utilizing glioma-derived cell traces and the TCGA breast carcinoma and liver hepatocellular carcinoma cohorts. (
  • fragile X psychological retardation protein (FMRP), decreased in each cell our bodies and dendrites when neurons had been confronted with aberrant upregulation of ATX2. (
  • Before a cell divides and DNA is passed from one cell to another, a complex process occurs. (
  • Binds and activates the enhancer (delta-A element) of the CD3-delta gene. (
  • In this study, we show that the WT1 protein expressed exogenously in fibroblasts was phosphorylated in vivo, and that treatment with forskolin, which activates the cAMP-dependent protein kinase (PKA) in vivo, induced phosphorylation of additional sites in WT1. (
  • The exact objective of this study was to design a system wherein cells differentiate into BRA positive cells within a certain distance from the BMP4 edge that activates the protein and cells greater than the decay length differentiate into SOX2 positive cells. (
  • Proteins that bind to the double strand will tend to stabilize dsDNA, and melting will occur at higher forces. (
  • AID-dependent generation of resected double-strand DNA breaks and recruitment of Rad52/Rad51 in somatic hypermutation. (
  • The association is referring to zinc finger nucleases (ZFNs), a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at user-specified locations. (
  • DNA double-strand breaks promote endoreduplication in radish cotyledon. (
  • The SATB2 protein attaches to special regions of DNA called matrix attachment regions (MARs). (
  • Bcr/Abl-encoded proteins exhibit elevated kinase activity compared to c-Abl, but the mechanisms of transformation are largely unknown. (
  • PAPbeta, a protein that binds to and is phosphorylated by the non-receptor tyrosine kinase PYK2, contains several modular signaling domains including a pleckstrin homology domain, an SH3 domain, ankyrin repeats and an ARF-GAP domain. (
  • The DNA-binding domain of human c-Abl tyrosine kinase promotes the interaction of a HMG chromosomal protein with DNA. (
  • Avapritinib is a tyrosine kinase inhibitor that binds to and inhibits specific mutant forms of platelet-driven growth factor receptor (PDGFR)?alpha and c-Kit, including the PDGFR-alpha D842V mutant and various KIT exon 17 mutants. (
  • For the existing research we posited the fact that even more hydrophobic nucleotide-binding site of the inositol phosphate kinase would provide a possibly even more tractable focus on [23]. (
  • Aberrations in Capicua (CIC) have lately been implicated as a adverse prognostic consider a mess of most cancers sorts by means of the derepression of targets downstream of the mitogen-activated protein kinase (MAPK) signaling cascade, similar to oncogenic E26 transformation-specific (ETS) transcription components. (
  • This recombinant protein was biotinylated in vivo by AviTag-BirA technology, which method is BriA catalyzes amide linkage between the biotin and the specific lysine of the AviTag. (
  • Developing biologically active recombinant protein is a challenge to many researchers in both academia and industry. (
  • Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. (
  • The goal of her current research is to use two highly innovative and complementary single-molecule imaging techniques (atomic force microscopy and fluorescence imaging) together with quantum dot labeled proteins to investigate the effects of DNA damage on the conformational and dynamic properties of telomeric DNA structure and telomere binding proteins. (
  • This assay has enabled visualization of DNA in its extended form several micrometers above the surface and to observe movements of individual proteins with up to 17 nm positional accuracy and 50 ms temporal resolution using oblique-angle fluorescence microscopy. (
  • We will discuss fluorescence as a general language used to read out biological phenomena as diverse as protein localization, membrane tension, surface phenomena, and enzyme activity. (
  • Campylobacter jejuni enteritis is frequently associated with an axonal form of Guillain-Barré syndrome (GBS) and C. jejuni DNA-binding protein from starved cells (C-Dps) induces paranodal myelin detachment and axonal degeneration through binding with sulfatide in vivo. (
  • How proteins gain access to nucleosomal DNA target sites in vivo is not known. (
  • Using WT1 mutants in which Ser-365 and Ser-393 were mutated to Ala individually and in combination, we showed that phosphorylation of these sites was critical for inhibition of DNA binding in vivo. (
  • Analysis of the mutants showed that phosphorylation of Ser-365 and Ser-395 had additive inhibitory effects on WT1 DNA-binding in vivo and that phosphorylation at both sites was required for neutralization of repression activity. (
  • Therefore, we conclude that PKA modulates the activity of WT1 in vivo through phosphorylation of Ser-365 and Ser-393, which inhibits DNA binding. (
  • A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. (
  • Employing a modified form of the fluorescent two-hybrid protein-protein interaction assay, we could clearly visualize these associations in single cells in vivo. (
  • To do this, I am employing an in vivo technique called CRISPR interference (CRISPRi) to artificially "write" H3K9me3 marks to nucleosomes near strongly-bound pioneer factor binding sites throughout the genome. (
  • Membrane proteins roughly constitute 30% of open reading frames in a genome and form 70% of current drug targets. (
  • They are classified as integral, peripheral membrane proteins and polypeptide toxins. (
  • called peripheral membrane proteins. (
  • Alternatively, transcription factors can bind enzymes that modify the histones at the promoter. (
  • One of the first steps in gene transcription is recognition of the promoter site by the TATA box Binding Protein (TBP). (
  • After it binds to the promoter, it recruits additional transcription factors. (
  • You may think that the strongest promoter and RBS lead the maximal yield of the proteins. (
  • The functional significance of the dimeric UV-DDB [(DDB1-DDB2)2], in a complex with damaged DNA, is validated by electron microscopy, atomic force microscopy, solution biophysical, and functional analyses. (
  • This gene encodes a nephrocystin protein that interacts with calmodulin and the retinitis pigmentosa GTPase regulator protein. (
  • A prokaryote is a simple, single-celled organism that lacks a nucleus and membrane-bound organelles. (
  • Eukaryotic cells have a membrane-bound nucleus where their DNA is stored. (
  • This geometry is captured in the form of an elastic network (EN), namely a network of edges between its residues. (
  • We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. (
  • Despite this, basic residues, which carry net positive charges are found to mediate favorable contribution to binding despite a desolvation penalty which arises. (
  • In this study, we present the first near-complete 15 N, 13 Cα/β , and HN backbone resonance assignments of two dimers of the dimerization domain (DD) of the NFκB1 (p50) protein (residues 241-351): the homodimer of two p50 domains and a heterodimer of the p50 DD with the p65 DD. (
  • Based on protein dock, I assume I can do the same (get rid of the extra residues in whichever PDB is larger, or re-do the earlier steps for the smaller PDB to get them back into the larger PDB) to make use of the native pdb for RMSD calculations, right? (
  • INTRODUCTION Research before decade has uncovered several types of regulatory proteins that imitate DNA. (
  • DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. (
  • There are 1471345 ANK domains in 265757 proteins in SMART's nrdb database. (
  • There are 1809 Mre11_DNA_bind domains in 1809 proteins in SMART's nrdb database. (
  • Is predicted to encode a protein with the following domains: UNC-50 family and UNC-50. (
  • The modular structure of PTPN13 consists of an N-terminal KIND domain, a FERM domain, and five PDZ domains, followed by a C-terminal protein tyrosine phosphatase domain. (
  • Protein tyrosine phosphatase PTPN13, also known as PTP-BL in mice, represents a large multi-domain non-transmembrane scaffolding protein that contains five consecutive PDZ domains. (
  • While both the BRCT and RING domains have been implicated in tumor suppression, Columbia University cancer researchers Thomas Ludwig and Richard Baer , who led the current study, wanted to definitively find out if it was the binding of phosphorylated proteins by the BRCT domains, the ubiquitinating capability of the RING domain, or both, which were helping to keep cancer at bay. (
  • The encoded protein has a central coiled-coil region and two calmodulin-binding IQ domains. (
  • When the trp repressor associates with its operator, the helix-turn-helix structure of this protein binds to the phosphate backbone of deformed DNA. (
  • We propose that the binding of UV-damaged DNA results in conformational changes in the N-terminal domain of DDB2, inducing helical folding in the context of the bound DNA and inducing dimerization as a function of nucleotide binding. (
  • Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to permanently remedy blood disorders, although its application in engrafting hematopoietic stem cells (HSCs) remains unexplored. (
  • Using the nucleotide-binding sites of proteins TNR kinases specifically at heart as drug-targets, several chemical libraries have already been curated that consist of substances either knownor forecasted and purified to homogeneity [8]. (
  • however, it exhibits striking homology to a large family of proteins involved in RNA processing. (
  • In 1997, the United States banned the use of "most mammalian proteins" in the manufacture of feed for cattle and other ruminants ( Federal Register 1997 ). (
  • Unlike C2H2 proteins, DNA binding by NRs requires dimerization of subunits. (
  • While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. (
  • We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. (
  • Cross-species comparison helps us understand how gene regulation and its encoding in DNA evolves. (
  • But DNA vaccines seem unlikely ever to be approved, because of worries that they might be incorporated into human DNA, disrupting gene regulation. (
  • To ameliorate this issue, interest is continuing to grow in rendering screening process more efficient, with the curation and program of smaller, concentrated libraries that focus on proteins households with functionally or chemically related binding sites [17]. (