The parts of a macromolecule that directly participate in its specific combination with another molecule.
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 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 sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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 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.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The rate dynamics in chemical or physical systems.
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.
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).
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Established cell cultures that have the potential to propagate indefinitely.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
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.
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 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.
Proteins prepared by recombinant DNA technology.
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.
Local surface sites on antibodies which react with antigen determinant sites on antigens (EPITOPES.) They are formed from parts of the variable regions of FAB FRAGMENTS.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
Nucleic acid sequences involved in regulating the expression of genes.
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.
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)
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.
Quantitative determination of receptor (binding) proteins in body fluids or tissue using radioactively labeled binding reagents (e.g., antibodies, intracellular receptors, plasma binders).
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.
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.
Proteins found in any species of bacterium.
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.
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.
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.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
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.
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.
Transport proteins that carry specific substances in the blood or across cell membranes.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Analogs of those substrates or compounds which bind naturally at the active sites of proteins, enzymes, antibodies, steroids, or physiological receptors. These analogs form a stable covalent bond at the binding site, thereby acting as inhibitors of the proteins or steroids.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
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.
Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693-5). Cell surface receptors, unlike enzymes, do not chemically alter their ligands.
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.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
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.
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.
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.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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.
A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.
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.
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.
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.
Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
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.
The making of a radiograph of an object or tissue by recording on a photographic plate the radiation emitted by radioactive material within the object. (Dorland, 27th ed)
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.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Measurement of the intensity and quality of fluorescence.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Unstable isotopes of iodine that decay or disintegrate emitting radiation. I atoms with atomic weights 117-139, except I 127, are radioactive iodine isotopes.
A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
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.
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.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Biologically active molecules which are covalently bound to the enzymes or binding proteins normally acting on them. Binding occurs due to activation of the label by ultraviolet light. These labels are used primarily to identify binding sites on proteins.
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.
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.
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 subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Proteins obtained from ESCHERICHIA COLI.
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).
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The sum of the weight of all the atoms in a molecule.
The relationship between the dose of an administered drug and the response of the organism to the drug.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
One of the two major classes of cholinergic receptors. Nicotinic receptors were originally distinguished by their preference for NICOTINE over MUSCARINE. They are generally divided into muscle-type and neuronal-type (previously ganglionic) based on pharmacology, and subunit composition of the receptors.
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.
Antibodies produced by a single clone of cells.
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).
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
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.
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)
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 computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.
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.
Organic or inorganic compounds that contain the -N3 group.
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).)
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.
CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.
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.
The characteristic three-dimensional shape of a molecule.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Cell surface receptors that bind signalling molecules released by neurons and convert these signals into intracellular changes influencing the behavior of cells. Neurotransmitter is used here in its most general sense, including not only messengers that act to regulate ion channels, but also those which act on second messenger systems and those which may act at a distance from their release sites. Included are receptors for neuromodulators, neuroregulators, neuromediators, and neurohumors, whether or not located at synapses.
Proteins that bind specific drugs with high affinity and trigger intracellular changes influencing the behavior of cells. Drug receptors are generally thought to be receptors for some endogenous substance not otherwise specified.
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.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A ubiquitously expressed zinc finger-containing protein that acts both as a repressor and activator of transcription. It interacts with key regulatory proteins such as TATA-BINDING PROTEIN; TFIIB; and ADENOVIRUS E1A PROTEINS.
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.
The commonest and widest ranging species of the clawed "frog" (Xenopus) in Africa. This species is used extensively in research. There is now a significant population in California derived from escaped laboratory animals.
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)
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
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.
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.
Thin layers of tissue which cover parts of the body, separate adjacent cavities, or connect adjacent structures.
Sites on an antigen that interact with specific antibodies.
A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.
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 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.
Biochemical identification of mutational changes in a nucleotide sequence.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
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.
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.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
A family of transcription factors that share a unique DNA-binding domain. The name derives from viral oncogene-derived protein oncogene protein v-ets of the AVIAN ERYTHROBLASTOSIS VIRUS.
An essential amino acid. It is often added to animal feed.
Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations or by parent x offspring matings carried out with certain restrictions. This also includes animals with a long history of closed colony breeding.
Sequential operating programs and data which instruct the functioning of a digital computer.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Computer-based representation of physical systems and phenomena such as chemical processes.
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).
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.
Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.
The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
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)
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
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.
Proteins that share the common characteristic of binding to carbohydrates. Some ANTIBODIES and carbohydrate-metabolizing proteins (ENZYMES) also bind to carbohydrates, however they are not considered lectins. PLANT LECTINS are carbohydrate-binding proteins that have been primarily identified by their hemagglutinating activity (HEMAGGLUTININS). However, a variety of lectins occur in animal species where they serve diverse array of functions through specific carbohydrate recognition.
A genus of the Torpedinidae family consisting of several species. Members of this family have powerful electric organs and are commonly called electric rays.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Elements of limited time intervals, contributing to particular results or situations.
Neurotoxic proteins from the venom of the banded or Formosan krait (Bungarus multicinctus, an elapid snake). alpha-Bungarotoxin blocks nicotinic acetylcholine receptors and has been used to isolate and study them; beta- and gamma-bungarotoxins act presynaptically causing acetylcholine release and depletion. Both alpha and beta forms have been characterized, the alpha being similar to the large, long or Type II neurotoxins from other elapid venoms.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Methods for determining interaction between PROTEINS.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.
Terbium. An element of the rare earth family of metals. It has the atomic symbol Tb, atomic number 65, and atomic weight 158.92.
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.
Peptides composed of between two and twelve amino acids.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
The process of cleaving a chemical compound by the addition of a molecule of water.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Proteins found in any species of fungus.
Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.
Tabular numerical representations of sequence motifs displaying their variability as likelihood values for each possible residue at each position in a sequence. Position-specific scoring matrices (PSSMs) are calculated from position frequency matrices.
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.
A family of DNA binding proteins that regulate expression of a variety of GENES during CELL DIFFERENTIATION and APOPTOSIS. Family members contain a highly conserved carboxy-terminal basic HELIX-TURN-HELIX MOTIF involved in dimerization and sequence-specific DNA binding.
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.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
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.
Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).
A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
Contractile tissue that produces movement in animals.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
An essential amino acid that is required for the production of HISTAMINE.

Extra-vesicular binding of noradrenaline and guanethidine in the adrenergic neurones of the rat heart: a proposed site of action of adrenergic neurone blocking agents. (1/81452)

1 The binding and efflux characteristics of [14C]-guanethidine and [3H]-noradrenaline were studied in heart slices from rats which were pretreated with reserpine and nialamide. 2 Binding of both compounds occurred at extra-vesicular sites within the adrenergic neurone. After a brief period of rapid washout, the efflux of [14C]-guanethidine and [3H]-noradrenaline proceeded at a steady rate. The efflux of both compounds appeared to occur from a single intraneuronal compartment. 3 (+)-Amphetamine accelerated the efflux of [14C]-noradrenaline; this effect was inhibited by desipramine. 4 Unlabelled guanethidine and amantadine also increased the efflux of labelled compounds. Cocaine in high concentrations increased slightly the efflux of [14C]-guanethidine but not that of [3H]-noradrenaline. 5 Heart slices labelled with [3H]-noradrenaline became refractory to successive exposures to releasing agents although an appreciable amount of labelled compound was still present in in these slices. 6 It is suggested that [14C]-guanethidine and [3H]-noradrenaline are bound at a common extravesicular site within the adrenergic neurone. Binding of guanethidine to the extra-vesicular site may be relevant to its pharmacological action, i.e., the blockade of adrenergic transmission.  (+info)

The bioavailability, dispostion kinetics and dosage of sulphadimethoxine in dogs. (2/81452)

The disposition kinetics of sulphadimethoxine were studied in six normal beagle dogs after intravenous injection of a single dose (55 mg/kg). The median (range) distribution and elimination half times of the drug were 2.36 (2.06-3.35) hours and 13.10 (9.71-16.50) hours, respectively. Total body clearance of the drug had a median value of 21.7 ml/kg/h and a mean value of 21.4 ml/kg/h. While the overall tissue to plasma level ratio (k12/k21) of the drug was 0.55 after distribution equilibrium had been attained, analogue computer simulated curves showed that at 24 hours the fractions (percentage) of the dose in the central and tissue compartments were 12 and 11%, respectively. The drug was shown, by equilibrium dialysis method, to be highly bound to plasma proteins (greater than 75%) within the usual therapeutic range (50 to 150 mug/ml) of plasma levels. The systemic availability of sulphadimethoxine from the oral suspension was 32.8% (22.5-80.0). Since the absorption half time, 1.87 (0.86-3.22) hours, was considerably shorter than the half-life, 13.10 (9.71-16.50) hours, of the drug, the rate of absorption would have little influence on the dosage regimen. Based on the experimental data obtained, a satisfactory dosage regimen might consist of a priming dose of 55 mg/kg by the intravenous route and maintenance doses of either 27.5 mg/kg of sulphadimethoxine injection given intravenously or 55 mg/kg of the oral suspension administered at 24 hour intervals. The adequacy and duration of therapy will depend upon the clinical response obtained.  (+info)

Specific receptors for glucocorticoid in the cytoplasm of the liver of AH 130 tumor-bearing rats. (3/81452)

Specific receptors for dexamethasone (11beta, 17alpha, 21-trihydroxy-9alpha-fluoro-16alpha-methyl-1,4-pregnadiene-3,20-dione) in the cytoplasm of the liver from AH 130 (solid type) tumor-bearing rats markedly increased in the advanced stage of tumor growth. The cytoplasmic receptors of the livers of normal and tumor-bearing rats differed in their affinities for dexamethasone, and their apparent equilibrium (dissociation) constants (K) for dexamethasone were 4.0 and 2.6 X 10(-9) M, respectively. The rates of dissociation of dexamethasone-receptor complexes and the heat denaturations of the receptors in the livers of normal and tumor-bearing rats were similar. The glucocorticoid receptors of tumor-bearing rat liver had slightly higher affinities than did those of normal liver for all the steroids tested. Only a trace amount of receptors for dexamethasone could be detected in the cytoplasm of AH 130 ascites cells.  (+info)

The interaction of rhodium(II) carboxylates with enzymes. (4/81452)

The effect of rhodium(II) acetate, propionate, and methoxyacetate on the activity of 17 enzymes was evaluated. The enzymes were preincubated with the rhodium(II) complexes in order to detect irreversible inhibition. All enzymes that have essential sulfhydryl groups in or near their active site were found to be irreversibly inhibited. Those enzymes without essential sulfhydryl groups were not affected. In each case, the rate of inactivation closely paralleled the observed toxicity and antitumor activity of rhodium(II) carboxylates; that is, rhodium(II) propionate greater than rhodium(II) acetate greater than rhodium(II) methoxyacetate. In addition, those enzymes that have been demonstrated to be most sensitive to established sulfhydryl inhibitors, such as glyceraldehyde-3-phosphate dehydrogenase, were also most sensitive to rhodium(II) carboxylate inactivation. Proton nuclear magnetic resonance measurements made during the titration of rhodium(II) acetate with cysteine showed that breakdown of the carboxylate cage occurred as a result of reaction with this sulfhydryl-containing amino acid.  (+info)

The direct spectrophotometric observation of benzo(a)pyrene phenol formation by liver microsomes. (5/81452)

Optical spectral repetitive scan analysis during the oxidative metabolism of benzo(a)pyrene by liver microsomal suspensions reveals the time-dependent formation of an intermediate(s) of which the visible spectra resemble those of several benzo(a)pyrene phenols. Liver microsomes from 3-methylcholanthrene-treated rats showed a greater rate of formation of the phenols than did microsomes from control animals; the rate of formation catalyzed by liver microsomes from phenobarbital-pretreated rats was intermediate. When 3-hydroxybenzo(a)pyrene was used as a standard for comparison of activity, the rates of formation of phenols were compared when measured by fluorometric, spectrophotometric, or high-pressure liquid chromatographic analytical techniques. An epoxide hydrase inhibitor, 1,1,1-trichloropropene-2,3-oxide, enhanced phenol formation regardless of the source of liver microsomes, and 7,8-benzoflavone inhibited control and 3-methylcholanthrene-induced microsomal metabolism of benzo(a)pyrene, 7,8-Benzoflavone did not effect benzo(a)pyrene metabolism by liver microsomes from phenobarbital-pretreated rats. The effect of inhibitors on the spectrophotometric assay correlates well with the results obtained from benzo(a)pyrene metabolite analysis using high-pressure liquid chromatography.  (+info)

Differences in benzo(a)pyrene metabolism between rodent liver microsomes and embryonic cells. (6/81452)

Differences in benzo(a)pyrene metabolite pattern have been shown by rodent liver microsomes (Sprague-Dawley) and rodent embryo cells from Syrian hamsters and NIH Swiss mice. Rodent liver induced by methylcholanthrene shows marked quantitative variation between species. Additional pattern changes were found in mouse and hamster embryo secondary cultures with a reduction of the K-region metabolites and a marked increase in 9-hydroxybenzo(a)-pyrene. These results are indicative of a region-specific attack on the carcinogen by the cell monooxygenases which is distinct from the liver attack of microsomal enzymes on benzo(a)pyrene. These results suggest that activation and detoxification of benzo(a)pyrene may be species and tissue variable, and susceptibility and resistence to malignant transformation may be predicted on induction of a fortuitous combination of intermediate metabolic steps.  (+info)

Action of partially thiolated polynucleotides on the DNA polymerase alpha from regenerating rat liver. (7/81452)

The effects of partially thiolated polynucleotides on the DNA polymerase alpha from regenerating rat liver were investigated. The enzyme was isolated from the nuclear fraction essentially according to the method of Baril et al.; it was characterized as the alpha polymerase on the basis of its response to synthetic templates and its inhibition with N-ethylmaleimide. Although polycytidylic acid had no effect on the DNA polymerase alpha either as a template or as an inhibitor, partially thiolated polycytidylic acid (MPC) was found to be a potent inhibitor, its activity being directly related to its extent of thiolation (percentage of 5-mercaptocytidylate units in the polymer). In comparison, the DNA polymerase beta which was purified from normal rat liver nuclear fraction, was much less sensitive to inhibition by MPC. Analysis of the inhibition of the alpha polymerase by the method of Lineweaver and Burk showed that the inhibitory action of MPC was competitively reversible with the DNA template, but the binding of the 7.2%-thiolated MPC to the enzyme was much stronger than that of the template (Ki/Km less than 0.03). Polyuridylic acid as such showed some inhibitory activity which increased on partial thiolation, but the 8.4%-thiolated polyuridylic acid was less active than the 7.2% MPC. When MPC was annealed with polyinosinic acid, it lost 80% of its inhibitory activity in the double-stranded configuration. However, 1 to 2%-thiolated DNA isolates were significantly more potent inhibitors than were comparable (1.2%-thiolated) MPC and showed competitive reversibility with the unmodified (but "activated") DNA template. These results indicate that the inhibitory activities of partially thiolated polynucleotides depend not only on the percentage of 5-mercapto groups but also on the configuration, base composition, and other specific structural properties.  (+info)

The effects of estrogens and antiestrogens on hormone-responsive human breast cancer in long-term tissue culture. (8/81452)

We have established or characterized six lines of human breast cancer maintained in long-term tissue culture for at least 1 year and have examined these lines for estrogen responsiveness. One of these cell lines, MCF-7, shows marked stimulation of macromolecular synthesis and cell division with physiological concentrations of estradiol. Antiestrogens are strongly inhibitory, and at concentrations greater than 3 X 10(-7) M they kill cells. Antiestrogen effects are prevented by simultaneous treatment with estradiol or reversed by addition of estradiol to cells incubated in antiestrogen. Responsive cell lines contain high-affinity specific estradiol receptors. Antiestrogens compete with estradiol for these receptors but have a lower apparent affinity for the receptor than estrogens. Stimulation of cells by estrogens is biphasic, with inhibition and cell death at concentrations of 17beta-estradiol or diethylstilbestrol exceeding 10(-7) M. Killing by high concentrations of estrogen is probably a nonspecific effect in that we observe this response with 17alpha-estradiol at equivalent concentrations and in the otherwise unresponsive cells that contain no estrogen receptor sites.  (+info)

The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an evolutionary model to study binding-site turnover that uses multiple sequence alignments to assess the evolutionary constraint on individual binding sites, and to map gain and loss events along a phylogenetic tree. We apply this model to study the evolutionary dynamics of binding sites of the Drosophila melanogaster transcription factor Zeste, using genome-wide in vivo (ChIP-chip) binding data to identify functional Zeste binding sites, and the genome sequences of D. melanogaster, D. simulans, D. erecta, and D. yakuba to study their evolution. We estimate that more than 5% of functional Zeste binding sites in D. melanogaster were gained along the D. melanogaster lineage or lost along one of the other lineages. We find that Zeste-bound regions have a reduced rate of binding-site loss and an increased rate of binding
TY - GEN. T1 - Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. AU - Huang, Shao-Shan. AU - Fulton, Debra L.. AU - Arenillas, David J.. AU - Perco, Paul. AU - Ho Sui, Shannan J.. AU - Mortimer, James R.. AU - Wasserman, Wyeth W.. PY - 2006/12/1. Y1 - 2006/12/1. N2 - Transcription regulation is mediated by combinatorial interactions between diverse trans-acting proteins and arrays of cis-regulatory sequences. Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes. The system is based on cross-species sequence comparisons for phylogenetic footprinting and motif models for binding site prediction. We introduce a new set of analysis algorithms for the ...
Reliable identification of targets of bacterial regulators is necessary to understand bacterial gene expression regulation. These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which typically leads to a large number of false positives. In contrast to the common approach, here we propose a novel concept, where overrepresentation of the scoring distribution that corresponds to the entire searched region is assessed, as opposed to predicting individual binding sites. We explore two implementations of this concept, based on Kolmogorov-Smirnov (KS) and Anderson-Darling (AD) tests, which both provide straightforward P value estimates for predicted targets. This approach is implemented for pleiotropic bacterial regulators, including σ70 (bacterial housekeeping σ factor) target predictions, which is a classical bioinformatics problem characterized by low specificity. We show that KS based approach is both faster and more accurate, departing from
Systems Biology/Bioinformatics research group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Search and prediction of transcription factor binding sites: challenges and solutions. Prediction of transcription factor binding sites (TFBSs) is an important step in promoter modeling and network inference. However, quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS search methods. We suggested a novel method (SiTaR), which allows significant reduction the number of false positives. The quality of predictions can be further improved by consideration of TFBS combinations (binding sites of cooperating TFs), which can be accomplished with the tool DistanceScan. In my talk I will give a short overview and comparison of the existing methods for TFBS search.. ...
Introduction: Competitive binding assays can be used to decipher not only the binding kinetics of studied ligands but also the binding site preference. Such assays are an essential step in the characterization of radioligands. However, the currently used competition assays require high concentrations of usually expensive ligands and still provide only binding site preference. By employing the time-resolved competition assay presented in this paper, binding characteristics including binding site preference can be obtained using less ligand. Methods: To demonstrate the appropriateness of the time-resolved competition assay, we developed an assay in which the ligand binding was interrupted with a competitor. Experiments were performed on human carcinoma cell lines expressing epidermal growth factor receptor (EGFR). The targeting of the receptor was performed with radio-iodinated epidermal growth factor (EGF). The employed competitors involved either natural ligand transforming growth factor alpha ...
In biochemistry, a binding site is a region on a protein or piece of DNA or RNA to which wigands (specific mowecuwes and/or ions) may form a chemicaw bond. An eqwiwibrium exists between unbound wigands and bound wigands.. Saturation is de fraction of totaw binding sites dat are occupied at any given time. When more dan one type of wigand can bind to a binding site, competition ensues.. Binding sites awso exhibit chemicaw specificity, a measure of de types of wigands dat wiww bond, and affinity, which is a measure of de strengf of de chemicaw bond.. Binding sites are often an important component of de functionaw characterization of biomowecuwes. For exampwe, de characterization of de active site of a substrate to an enzyme is essentiaw to modew de reaction mechanism responsibwe for de chemicaw change from substrate to product.. Binding sites on proteins can sometimes recognize oder proteins. When a binding site of one protein identifies wif anoder proteins surface, a non-covawent bond is formed ...
Fu Y, Weng Z. Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences. Genome Inform. 2005; 16(1):68-72 ...
Background: We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results: Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4-6 hours for transcription factor binding sites and 10-19
The size of the second binding site equals the total amount of 125I-apoA-I bound to the cell (100 ng/mg cell protein) minus the amount of protein bound specifically to ABCA1 (3 ng/mg of cell protein). However, from the biotinylation (Figure 2) and apoA-I displacement (Figure 3) experiments, it is apparent that only around 35% of the ABCA1 is present on the surface of the cells. Hence, the actual amount of apoA-I associated with the second binding site on the surface is equal to about 30 ng of apoA-I/mg cell protein [(100 ng · 0.35)−3 ng)]. It follows that the amount of apoA-I associated with the second site is some 10-fold greater than that bound to ABCA1 indicating that the second site is a high capacity binding site (Figure 6), as has been postulated previously.4. Cross-linking of bound apoA-I followed by immunoprecipitation with anti-apoA-I has demonstrated that, apart from ABCA1, apoA-I does not bind to any other cellular protein (Figure 4B). In fact, ≈90% of the bound apoA-I is ...
Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. Various experimental and computational approaches have been used to detect these sites; methods involving computational comparisons of related genomes have been particularly successful.
Beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics and are an increasing menace to public health. Several beta-lactamase structures have been determined, making this enzyme an attractive target for structure-based drug design. To facilitate inhibitor design for t …
Transcription factors are DNA-binding proteins that control gene transcription by binding specific short DNA sequences. Experiments that identify transcrip- tion factor binding sites are often laborious and expensive, and the binding sites of many transcription factors remain unknown. We present a computa- tional scheme to predict the binding sites directly from transcription factor se- quence using all-atom molecular simulations. This method is a computational counterpart to recent high-throughput experimental technologies that identify transcription factor binding sites (ChIP-chip and protein-dsDNA binding mi- croarrays). The only requirement of our method is an accurate 3D structural model of a transcription factor DNA complex. We apply free energy calcula- tions by thermodynamic integration to compute the change in binding energy of the complex due to a single base pair mutation. By calculating the binding free energy differences for all possible single mutations, we construct a position ...
To locate the ligand binding site on TLR3, we analyzed ,50 mutations within the TLR3-ECD. Remarkably, only 2 of the 50 residues tested resulted in abrogation of both the activation of TLR3 by pI:pC and the direct binding of pI:pC to purified TLR3-ECD protein. These two residues, H539 and N541, are conserved from zebrafish to humans (Fig. 10, which is published as supporting information on the PNAS web site) and position the ligand binding site on the glycan-free surface of the ECD at LRR20.. Replacing His-539 with an alanine has little effect on TLR3 responsiveness, whereas substitution of a negatively charged carboxyl group for an imidazole ring at this site results in a total loss of function. This finding suggests that a negative charge from a backbone phosphate group on dsRNA occupies a position in close proximity to residue 539 in the ligand-receptor complex. In the WT protein a protonated imidazole ring of His-539 would neutralize the negative charge of the phosphate, but in the H539E ...
The crystal structures of jacalin complexed with Gal alpha-(1,4) Gal and Gal alpha-(1,3) Gal beta-(1,4) Gal have been determined with the primary objective of exploring the effect of linkage on the location of reducing and non-reducing sugars in the extended binding site of the lectin, an issue which has not been studied thoroughly. Contrary to the earlier surmise based on simple steric considerations, the two structures demonstrate that alpha-linked sugars can bind to jacalin with nonreducing sugar at the primary binding site. This is made possible substantially on account of the hitherto underestimated plasticity of a non-polar region of the extended binding site. Modeling studies involving conformational search and energy minimization, along with available crystallographic and thermodynamic data, indicate a strong preference for complexation with Gal beta-(1,3) Gal with the reducing Gal at the primary site, followed by that with Gal alpha-(1,3) Gal, with the reducing or non-reducing Gal ...
Here we report experiments analysing the DNA‐binding activity of endo VII with respect to participating regions of the protein and their mode of interaction. The results show: (i) both ends of the endo VII polypeptide chain are involved in DNA binding; (ii) N‐ and C‐termini from different subunits are in close proximity in the active protein; (iii) one N‐ and one C‐terminus, each originating from a different subunit, form one DNA‐binding site; and (iv) the endo VII dimer has two DNA‐binding sites, either one of which is sufficient for specific binding to cruciform DNA.. It was found recently that the C‐terminus of endo VII is essential for DNA binding, and removal of more than three amino acids from the C‐terminus abolished the binding to cruciform DNA completely (Golz et al., 1997). This was confirmed in this study by using peptides lacking 10 or 37 C‐terminal amino acids which were also completely inactive in DNA binding. Here we describe that the N‐terminus is also ...
The interactions of the lead inhibitors, ASN03779174, Selleckchem MG132 ASN09646888 and ASN04208384, for RTP, SAH and SAM sites of MTase respectively, are shown in Table 3. Novel ligand interactions with active site of MTase are shown in Fig. 3. The dengue virus MTase has two binding sites; RNA binding site and SAM binding site, which can be targeted to find the lead molecules from the known ligands using e-pharmacophore. Glide ligand docking was performed using the known ligands of RTP, SAH and SAM with their respective binding sites of methyltransferase. These protein-ligand. complexes were further used to find the energy based pharmacophore. The pharmacophore features for the three ligands include ADDDN, ADNR and AADDNNR respectively. Three different pharmacophore hypothesis for the above three ligands (RTP, SAH and SAM) were taken to screen the Asinex database to find the novel molecules for the two different binding PF-01367338 mouse sites. Pharmacophore screening resulted in 38 molecules ...
The binding modes of a DNA or RNA binding protein refer to the different possible stable binding conformations between the protein and the nucleic acids. There are two main factors that can produce multiple modes of binding:. 1. Many proteins can contain multiple DNA and RNA binding domains with different sequence-binding preferences. When different combinations of these domains bind to different binding sites, we refer to each DNA or RNA interacting combination as a binding mode of the protein.. 2a. Many proteins can oligomerize into homo- and heterodimers and tetramers - whereby the protein-complex now has more DNA and/or RNA binding domains to bind to larger binding sites. In addition, many of these oligomerizing proteins can also bind as monomers to smaller sites. Often, differently sized protein-complexes have different binding properties and are referred to as having different binding modes. Latent specificity is when the binding specificity of a protein changes significantly when bound ...
Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance.
There are many different groups that are developing software for finding transciption factor binding sites, alongside our own development of the BIFA tool which forms part of the Apples framework. ...
One of the greatest challenges facing modern molecular biology is understanding the complex mechanisms regulating gene expression
We next asked why the mutations we had identified in primary patient T-ALLs were clustered in a defined genomic location. A search for predicted transcription factor binding sites near the MuTE site identified the preferred binding sequences for RUNX1, GATA3, and ETS1, as well as E-box motifs characteristic of binding by TAL1/E-protein heterodimers (fig. S5). The absence of predicted MYB binding sites in the wild-type sequence suggests that the MuTE is critical for MYB binding and supports our hypothesis that MYB binding to its de novo motif is crucial to binding by members of the TAL1 complex at this hotspot. To explore this concept further, we extracted the raw ChIP-seq reads and determined the allelic frequency of mutant to wild-type reads of bound DNA fragments at the mutation site. Note that, in MOLT-3 cells, both MYB and TAL1 bound predominantly to the mutant allele, with 67 of the 68 reads, and 37 of 38 reads, revealing the mutant sequence in the bound DNA. Likewise, in Jurkat cells, 404 ...
The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.. The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to ...
The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.. The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to ...
The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.. The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to ...
The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.. The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to ...
Influenza A virus M2 (A/M2) forms a homotetrameric channel in viral membranes that is highly selective for protons. A/M2 has been extensively studied by electrophysiologists, biophysicists, structural biologists and biochemists in order to understand the mechanism and selectivity of proton conductance from the structural basis. Medicinal chemists have also studied A/M2 as therapeutic target for anti-flu drugs. However, research on A/M2 drug binding lead to entirely different binding sites of two very similar anti-flu drugs. In light of the urgency in developing novel antivirals against drug resistant A/M2 mutants, it is imperative to solve this discrepancy in order to guide the next generation of antiviral discovery. This highly contentious debate was settled in favor of pore blocking through collaborate efforts with Dr. Mei Hong in Iowa State University. We showed by solid state NMR that the single high affinity pharmacologically relevant drug binding site locates at the N-terminal lumen with amine
We study a set of transcription factors (TFs) including the hypoxia-inducible factor 1 (HIF-1) involved in regulation of hypoxia response in human cells. We demonstrate that binding sites for a pair of interacting TFs can be found at distances that are dr
DBSI :: DESCRIPTION DBSI (DNA Binding Site Identifier), is a binding site predictor for DNA, and it has also successfully identified binding sites for RNA and heparin. ::DEVELOPER Mitchell Lab :: SCREENSHOTS
Conservation of information between prokaryotic and eukaryotic regulatory proteins and their cognate binding sites on DNA and RNA (operators and response elements) has been observed and is proposed as a basis for site-specific recognition. We present anal
IL-17C is an associate of the IL-17 family of cytokines. to bind to all three recognized binding sites. Moreover NF-κB binding to these sites was inducible by TNFα. Supershift evaluation revealed binding from the NF-κB subunits p50 and p65 to all or any 3 NF-κB binding sites. To look for the contribution of NF-κB in IL-17C appearance we executed luciferase gene reporter tests and demonstrated a 3204-bp promoter fragment of IL-17C filled with three putative NF-κB binding sites was highly turned on by TNFα. Oddly enough mutations from the three NF-κB binding sites uncovered that one particular NF-κB binding site was essential for the TNFα-mediated IL-17C induction because mutation of the specific site totally abolished TNFα-induced KU-60019 IL-17C promoter activation. We conclude which the activation of NF-κB (p65/p50) is essential for the TNFα-induced arousal of IL-17C appearance in individual keratinocytes. (1). It is one of the IL-17 category of cytokines which includes six ...
User warning: The following module is missing from the file system: imagcache_actions. In order to fix this, put the module back in its original location. For more information, see the documentation page. in _drupal_trigger_error_with_delayed_logging() (line 1128 of /var/www/html/agri/en/includes/bootstrap.inc ...
The β-galactosidase enzyme from Bacillus circulans ATCC 31382 BgaD is widely used in the food industry to produce prebiotic galactooligosaccharides (GOS). Recently, the crystal structure of a C-terminally truncated version of the enzyme (BgaD-D) has been elucidated. The roles of active site amino acid residues in β-galactosidase enzyme reaction and product specificity have remained unknown. On the ...
A new method for identifying sites of protein-DNA interaction genome-wide, |I cmid=Science Spotlight Article:Abstract|in vivo|/i| reveals binding kinetics. 
This article is of two parts: (a) the development of a protein reduced representation and its implementation in a Web server; and (b) the use of the reduced protein representation in the modeling of the binding site of a given ligand and the screening for the model in other protein 3D structures. Current methods of reduced protein 3D structure representation such as the Cα trace method not only lack essential molecular detail, but also ignore the chemical properties of the component amino acid side chains. This chapter describes a reduced protein 3D structure representation called
TY - JOUR. T1 - Functional roles of Mg 2+ binding sites in ion-dependent gating of a Mg 2+ channel, MgtE, revealed by solution NMR AU - Maruyama, Tatsuro. AU - Imai, Shunsuke. AU - Kusakizako, Tsukasa. AU - Hattori, Motoyuki. AU - Ishitani, Ryuichiro. AU - Nureki, Osamu. AU - Ito, Koichi. AU - Maturana, Andrès D.. AU - Shimada, Ichio. AU - Osawa, Masanori. PY - 2018/4/3. Y1 - 2018/4/3. N2 - Magnesium ions (Mg 2+ ) are divalent cations essential for various cellular functions. Mg 2+ homeostasis is maintained through Mg 2+ channels such as MgtE, a prokaryotic Mg 2+ channel whose gating is regulated by intracellular Mg 2+ levels. Our previous crystal structure of MgtE in the Mg 2+ -bound, closed state revealed the existence of seven crystallographically-independent Mg 2+ -binding sites, Mg1-Mg7. The role of Mg 2+ -binding to each site in channel closure remains unknown. Here, we investigated Mg 2+ -dependent changes in the structure and dynamics of MgtE using nuclear magnetic resonance ...
A peptide which stabilizes RT dimers and displays potent antiviral activity in vitro has also been described. Since PAW appears to interact with a site not overlapping the NNRTI binding CHIR99021 GSK-3 pocket, it points to another potential target site for enhancers of Gag Pol dimer stabilization. However, PAW has so far only been reported to interact with the dimeric forms of RT. it Inhibitors,Modulators,Libraries remains to be investi gated whether this peptide or compounds targeting the same binding site on RT could also promote Gag Pol dimer formation. Conclusion In summary, the results presented here are consistent with the following model, which we propose as a work ing hypothesis as a basis for further investigation cer tain NNRTIs can increase intracellular Gag Pol dimer concentration upon binding to the RT domain of Gag Pol and thereby stimulate intracellular PR activity.. Enhanced activation of PR reduces virion formation through Inhibitors,Modulators,Libraries depletion of the ...
It has not eluded note that calcium ion is also a significant parameter; after all, it has been documented for more than half a century [4] that secretion rate is proportional to [Ca]M, where [Ca] is Ca2+ concentration and M is the number of cooperating ions (0 ≤ M ≤ 5), reflecting that multiple Ca2+ ions binding to M-sites are required for fusion acceleration [2]. Such relation, well documented for exocytosis and recently confirmed also for homotypic fusion [25], is not surprising; Ca2+ ions are the key ions required for the finalization of membrane fusion. In the case of Ca2+ ion binding, the first Ca2+ ion has three to five different locations (depending on the ligand protein) where it can bind [2,8-13]. In case M , 1, the reaction is positively cooperative, namely the first Ca2+ ion binding to a site increases the protein-Ca2+ ion complex affinity at other binding sites. This represents a state of higher entropy compared with binding the last Ca2+ ion, which has only one location where ...
ystem, a functional putative binding site was identified by simply measuring luciferase activ http://www.selleckchem.com/products/VX-770.html ity. In LS174T cells, only the upstream binding site responded to miR 145 over e pressed e o genously, and in normal colon cells endogen ously over e pressing miR 145. Specific targeting of the DFF45 putative binding site by miR 145 To test the specificity of miR 145 at the 854 876 site, we co transfected LS174T cells with luc 854 and the miR 145 mimic at various abundances, and found that the inhibition of the luciferase activity by miR 145 was dose dependent. In normal colon cells trans fected with the miR 145 inhibitor, the luciferase activity was increased significantly compared to the inhibitor control at 24 hours and 36 hours. To further demonstrate the importance of the putative binding site, a substitution mutation was gen erated to test its activity.. In the DFF45 854 Mutation vector, seven nucleotides were replaced with ctcgGcct. We cloned the ...
Ralf Eggeling, Teemu Roos, Petri Myllymäki, and Ivo Grosse authored a paper Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data that was accepted for publication in BMC Bioinformatics.. Eggeling recently defended his PhD thesis at the Halle-Wittenberg University in Germany, supervised by Grosse. Ralf then joined HIIT as a postdoctoral researcher.. ...
1Yang et al. identified the binding site of PhoB Yang C,2012but did not identify the promoter regulated; therefore, there is a possibility that this binding site corresponds to another promoter, according to the function of PhoB. The binding site of this regulator, TTGTATGACAAATGTCACA, is located at bp -31 relative to the translation start site of yegH Yang C,20121Yang et al. identified the binding site of PhoB Yang C,2012but did not identify the promoter regulated; therefore, there is a possibility that this binding site corresponds to another promoter, according to the function of PhoB. The binding site of this regulator, TTGTATGACAAATGTCACA, is located at bp -31 relative to the translation start site of yegH Yang C,2012 ...
Julio Collado-Vides speaking at BIRS workshop, Rules of Protein-DNA Recognition: Computational and Experimental Advances, on Tuesday, June 5, 2018 on the topic: A global analysis of the distance to transcription initiation of binding sites in bacterial promoters.
The main cavities available for ligand binding in FtsZ monomer are the nucleotide-binding cup in the N-terminal domain and the long cleft between N- and C-terminal domains, known as PC190723 binding site (Figure A). The nucleotide binding site in FtsZ is conserved among FtsZs from different organisms (Oliva et al., 2007). Some compounds targeting the nucleotide site have similar chemical structure to the nucleotide, such as the C8-GTP derivatives that selectively inhibit FtsZ but promote tubulin assembly (Lappchen et al., 2008), while others have different chemical structures such as PC170942 (Stokes et al., 2005). In this Thesis, the effects on the functional activity of FtsZ of both types of ligands have been examined. The discovery of the PC190723 binding site in FtsZ is recent(Haydon et al., 2008) andthe crystal structure of FtsZ with bound PC190723 was made available last year (Elsen et al., 2012; Tan et al., 2012 and Matsui et al., 2012). Few compounds that bind to this site have been ...
A Binding Site Plan (BSP) is a division of land for office, commercial or industrial zoned properties or a manufactured home park. A pre-application meeting with staff is required to discuss your proposal before a formal application is submitted. Additionally, lots may be established through a record of survey subsequent to the recording of the initial binding site plan. To find out more information, go to Section 20.60.040 in the Municipal Code. You will need the application listed as Establish Lots w/in a BSP Application to apply ...
Dear Colleagues, I am doing some research about angiotensin II receptor in brain. To terminate the reaction between the radioligand and the membrane, there are two major methods: centrifugation, filtration. People usually use the filtration because it is easier and faster. My question is whether the filtration will lose some very high affinity binding sites because the background is very high? Is centrifugation able to detect the extremely high affinity binding sites? Thank you in advance for your kind replies. I am looking forward to receiving your precious suggestions. Your sincerely, Han ...
of HIV-1 protease is inhibited by Crixivan when the molecule interacts with the specific sites that a Gag protein peptide would normally interact with. The active site contains Asp25, which is involved in peptide cleavage, Thr26, which is involved in stabilizing the active site conformation, and Gly27, which is involved in the binding of a protein in a position that gives Asp25 access to its cleavage site.[3] Arg8 also plays a role in holding a substrate in place in the enzyme active site. When the Crixivan molecule enters the protease active site it imitates the transition state of Gag protein peptides during the cleavage reaction. The virus peptide bonds [-NH-CO-] can be cleaved via aspartic catalysis[1]. Crixivan contains a hydroxyethylene [-CH2-CH(OH)-] site instead that cannot be cleaved by Asp25.[4] The molecule becomes stuck inside the active site because of the hydrogen bonds between Arg8 and Crixivans pyridine ring and the interactions between Gly27 and Crixivans aromatic rings.[5] ...
A list of sequences for which to calculate binding affinities relative to the sequence found in the starting structure. This is a text file specifying the sequences for which we want to calculate relative binding affinities. One sequence should be specified per line. These can either be the full sequence of the complex (RNA and protein), or just the RNA sequence. If the protein sequence is not specified, then no mutations to the protein will be made ...
2QOS: Crystal structure of complement protein C8gamma in complex with a peptide containing the C8gamma binding site on C8alpha: Implications for C8gamma ligand binding.
Dive into the research topics of Sequence-Specific Interaction of R17 Coat Protein with Its Ribonucleic Acid Binding Site. Together they form a unique fingerprint. ...
IL-15 and IL-2 are two structurally and functionally related cytokines whose high affinity receptors share the IL-2R beta-chain and gamma-chain in association with IL-15R alpha-chain (IL-15R alpha) or IL-2R alpha-chain, respectively (Mortier et al 2004). The 2.8 angstrom crystal structure of IL-2 with the IL2RA was resolved by (Rickert et al. 2005). It revealed that the binding of IL-2R to IL-2 stabilizes a secondary binding site for presentation to IL-2R-beta. Gamma-c is then recruited to the composite surface formed by the IL-2/IL-2R-beta complex ...
A Proliferation Inducing Ligand (APRIL) is a TNF ligand that, via its receptors TACI and BCMA, is involved in both B cell physiology as well as in proliferation and survival of malignant B cells. To target APRIL-dependent stimulation of B cell cancers, we recently produced and characterized two monoclonal antagonistic anti-human APRIL antibodies called humanAPRIL.01A (hA.01A) and humanAPRIL.03A (hA.03A). In a first biochemical assay to validate their blocking activity, hA.01A was shown to fully prevent APRIL from binding to its receptors, whereas a substantial difference was detected for hA.03A, which inhibited APRIL binding to BCMA less efficiently than hA.01A. Epitope mapping subsequently revealed that hA.01A and hA.03A bind distinct sites on APRIL, which provided a structural rationale of their different blocking activities. Importantly, this differential inhibition profile can be used to functionally dissect BCMA and TACI-dependent signals and indicated that B cell survival and IgA ...
Succinate binding site[edit]. SdhA provides the binding site for the oxidation of succinate. The side chains Thr254, His354, ... Ubiquinone binding site[edit]. Two distinctive ubiquinone binding sites can be recognized on mammalian SDH - matrix-proximal QP ... The succinate-binding site and ubiquinone-binding site are connected by a chain of redox centers including FAD and the iron- ... form the hydrophobic environment of the quinone-binding pocket Qp.[6] In contrast, ubiquinone binding site QD, which lies ...
Binding site[edit]. A schematic structure of a HIV-1 protease. The monomers are shown in green and cyan, the Asp-25 and Asp-25 ... An extended beta-sheet region on the monomers, known as the flap, constitutes in part the substrate binding site with the two ... A simplified image of a protease inhibitor binding to the active site of the HIV-1 protease. The central core motif is shown in ... residues in the binding site.[16][27] Hydrogen bonds between the water molecule, which is linked to Ile50 and Ile50', and ...
Multiple binding sites, cooperativity. Technology[edit]. MST is based on the quantifiable detection of a fluorescence change in ... Quantitative binding parameters are obtained by using a serial dilution of the binding substrate. By plotting Fnorm against the ... "Label-free microscale thermophoresis discriminates sites and affinity of protein-ligand binding". Angew. Chem. Int. Ed. Engl. ... and the bound complex Fnorm(AT) superpose linearly. By denoting x the fraction of molecules bound to targets, the changing ...
In the case of a transcription factor binding site, there may be a single sequence that binds the protein most strongly under ... Includes the transcription start site (TSS) and elements directly upstream. *A binding site for RNA polymerase *RNA polymerase ... which in turn are often brought to the promoter DNA by an activator protein's binding to its own DNA binding site nearby.. In ... Identifying a Protein Binding Sites on DNA molecule YouTube tutorial video. *Pleiades Promoter Project - a research project ...
GABAA receptor binding sites. It is believed that honokiol acts on GABAA receptors similarly to benzodiazepines and Z-drugs. ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
The FMN binding domain is homologous to flavodoxins, and the two domain fragment containing the FAD and NADPH binding sites is ... The oxygenase domain is a unique extended beta sheet cage with binding sites for heme and pterin. NOSs can be dimeric, ... Liu Q, Gross SS (1996). "Binding sites of nitric oxide synthases". Meth. Enzymol. 268: 311-24. doi:10.1016/S0076-6879(96)68033- ... which is linked in the middle of the protein to a calmodulin-binding domain. Binding of calmodulin appears to act as a " ...
Pinkus LM (1977). "Glutamine binding sites". Methods in Enzymology. 46: 414-27. doi:10.1016/S0076-6879(77)46049-X. ISBN 978-0- ... Due to its similarity to glutamine it can enter catalytic centres of these enzymes and inhibits them by covalent binding, or ...
... the two GABA active binding sites at the α1 and β2 interfaces, and the benzodiazepine (BZD) allosteric binding site at the α1 ... the binding site of neurosteroids in the GABAA receptor is not known[8] and barbiturates bind at a beta subunit that is ... Unlike GABAA receptor agonists, GABAA PAMs do not bind at the same active site as the γ-Aminobutyric acid (GABA) ... Benzodiazepines function by binding to the benzodiazepine site on most, but not all, GABAA receptors. GABAA modulation by ...
ATP binds first to the top of the active site near a cation binding site, while glutamate binds near the second cation binding ... and serine bind to the glutamate substrate site. GDP, AMP, ADP bind to the ATP site.[6] L-serine, L-alanine, and glycine bind ... which is the site of three distinct substrate binding sites: nucleotide, ammonium ion, and amino acid.[4][6][10][11] ATP binds ... The middle of the bifunnel contains two sites in which divalent cations bind (Mn+2 or Mg+2). One cation binding site is ...
"Transcription Factor Binding Sites". ElDorado. Genomatix. "SAPS". Biology Workbench. SDSU.[permanent dead link] "Large-scale ... CCDC82 has several predicted phosphorylation sites. There are 32 predicted serine phosphorylation sites, 5 threonine, and 3 ... Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (November 2006). "Global, in vivo, and site-specific ...
... putative phosphoinositide binding site and putative peptide binding sites. The FAM43A gene has been identified in cDNA ... MicroRNA binding sites were identified and then compared to species conservation of FAM43A to determine likely 3' untranslated ... "FAM43A microRNA binding sites". Targetscan. Retrieved 21 May 2018. "FAM43A". PSORT II Prediction. Retrieved 8 April 2018. " ... Three phosphorylation sites were identified with conservation between human and mouse genotypes at T112-p, S114-p, and T-379-p ...
... or antigen-binding sites, to exist. This region is known as the hypervariable region. Each of these variants can bind to a ... Online web servers such as Web Antibody Modeling (WAM)[84] and Prediction of Immunoglobulin Structure (PIGS)[85] enables ... Mian I, Bradwell A, Olson A (1991). "Structure, function and properties of antibody binding sites". J Mol Biol. 217 (1): 133- ... The arms of the Y, for example, contain the sites that can bind to antigens (in general, identical) and, therefore, recognize ...
Madhusudan; Vijayan, M. (July 1992). "Additional binding sites in lysozyme. X-ray analysis of lysozyme complexes with ... side chain conformation in proteins and additional binding sites in lysozyme. Vijayan has published more than 260 peer reviewed ... M. Vijayan profile on Biomed Experts Mamannamana Vijayan publications list M. Vijayan home page at Indian Institute of Science ... The specific systems studied by him include RecA, RuvA, uracil DNA glycosylase, single stranded DNA binding protein, ribosome ...
Other, less well characterised substrate-binding sites also exist. One such site (the DEF site) is formed by the activation ... This site can accommodate peptides with an FxFP consensus sequence, typically downstream of the phosphorylation site.[33] Note ... There are indeed a number of proteins involved in ERK signaling, that can bind to multiple elements of the pathway: MP1 binds ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
Klein M, Musacchio JM (October 1989). "High affinity dextromethorphan binding sites in guinea pig brain. Effect of sigma ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Cinnarizine is classified as a selective antagonist of T-type voltage-operated calcium ion channels, because its binding blocks ... binding to H1 histamine receptors, and dopaminergic (D2) receptors.[22] The IC50 (half-maximal inhibitory concentration) of ...
These voids are adjacent to the base pairs and may provide a binding site. As the strands are not symmetrically located with ... A distinct group of DNA-binding proteins is the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... The latter is a binding site for the Hoechst stain dye 33258. ... DNA binding site prediction on protein. *DNA the Double Helix ... Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted ...
This is a tripodal metal-ion binding site,[15] and Suslick has proposed that the ORs are in fact metalloproteins (most likely ... Crabtree, R.H. (1978). "Copper(I) - Possible Olfactory Binding-Site". J. Inorg. Nucl. Chem. 1978 (40): 1453. doi:10.1016/0022- ... However, these authors also found that MOR244-3 lacks the specific metal ion binding site suggested by Suslick, instead showing ... that serve as a Lewis Acid site for the binding of many odorant molecules. In 1978, Crabtree suggested that Cu(I) is "the most ...
For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical ... Stormo GD (January 2000). "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16-23. doi:10.1093/ ... 34 (Web Server issue): W369-73. doi:10.1093/nar/gkl198. PMC 1538909. PMID 16845028. Weirauch MT, Cote A, Norel R, Annala M, ... For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, ...
Stormo, G. D. (1 January 2000). "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16-23. doi:10.1093/ ... The first use of PWMs was in the discovery of RNA sites that function as translation initiation sites. The advantages of PWMs ... algorithm to distinguish translational initiation sites in E. coli". Nucleic Acids Research. 10 (9): 2997-3011. doi:10.1093/nar ... work involves analysis of these interactions and developing pattern recognition algorithms to discover regulatory sites in DNA ...
The binding characteristic of 3H-dihydroalprenolol can also be used to study tumor growth because tumor binding sites typically ... In 1976, research conducted on rat and monkey brain membranes paved the road for research on dihydroalprenolol binding sites ... Although dihydroalprenolol's binding in the midbrain was the same, there was an increased binding of 30% in the pons and 15% in ... Different studies have indicated that adrenocortical carcinoma have beta-adrenergic receptor-binding sites that are not usually ...
There are two ATP binding sites; a substrate site where the phosphate transfer occurs, and an allosteric site where allosteric ... In addition to the catalytic binding sites, there are 4 additional binding sites for allosteric regulation. 1- ... AMP and ADP are both positive effectors of 1-phosphofructokinase and bind allosterically to activate the reaction. This ... 1-Phosphofructokinase is a tetramer of 4 identical subunits that each have a catalytic site. ...
CBDA synthase has four binding sites; two for FAD and two for the substrate. Cannabidiolic acid synthase catalyses the ... It covalently binds FAD, and does require coenzymes & molecular oxygen for the oxidocyclization reaction. The optimum pH for ...
The Outward Bound Trust, Marketing and Communications. "Outward Bound website". Outwardbound.org.uk. Archived from the original ... "The Public Whip website". Publicwhip.org.uk. Retrieved 13 April 2010. Sapsted, David (2 January 2001). "Hoey criticises ban on ... Hoey was Parliamentary Under-Secretary of State at the Home Office from 1998 to 1999, and Minister for Sport in the Department ... Hoey has been a trustee of the Outward Bound charity since October 2002. A vice-president of the Great Britain Wheelchair ...
Birmingham: Binding Site. ISBN 0-7044-2437-1. Slater NG, Cameron JS, Lessof MH (September 1976). "The Crithidia luciliae ... Serum is incubated with the beads and in the presence of anti-dsDNA antibodies, or any other ANA, the antibodies will bind and ... As a result of the highly specific nature of antibodies, they can be engineered to target and bind key motifs. These motifs can ... If anti-dsDNA antibodies are present, incubation of serum and the microarray allow for binding and the dots can then be ...
The ribosome contains three RNA binding sites, designated A, P and E. The A-site binds an aminoacyl-tRNA;[36] the P-site binds ... Affinity label for the tRNA binding sites on the E. coli ribosome allowed the identification of A and P site proteins most ... mRNA binds to the P site of the ribosome first. The ribosome is able to identify the start codon by use of the Shine-Dalgarno ... During 1977, Czernilofsky published research that used affinity labeling to identify tRNA-binding sites on rat liver ribosomes ...
... is a benzodiazepine site agonist and binds unselectively to type 1 and type 2 benzodiazepine site types as well as ... In vitro and in vivo interactions with benzodiazepine binding sites". The Journal of Pharmacology and Experimental Therapeutics ... "The usefulness of patch testing on the previously most severely affected site in a cutaneous adverse drug reaction to ...
JSR-231 Java Bindings for OpenGL website. *tool kiet, The OpenGL Programming Guide examples using JOGL ... In order to facilitate maximum community participation for the Java Binding for the OpenGL API, we use the JOGL project on java ... Website. jogamp. .org. Java OpenGL (JOGL) is a wrapper library that allows OpenGL to be used in the Java programming language.[ ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
... the 3D structure of a particular motif representing an active site or binding site can be targeted. The Structurally Aligned ... Garma LD, Medina M, Juffer AH (November 2016). "Structure-based classification of FAD binding sites: A comparative study of ... Mattos C, Ringe D (May 1996). "Locating and characterizing binding sites on proteins". Nature Biotechnology. 14 (5): 595-9. doi ... Porter CT, Bartlett GJ, Thornton JM (January 2004). "The Catalytic Site Atlas: a resource of catalytic sites and residues ...
So many men had left to carry their booty home, that his artillery was in jeopardy. One article stated that the boat carried a ... Unknown Binding). Oklahoma Historical Society. p. 61. ASIN B0007IYQNC. Baird, W. David, Editor (1991) [1988]. A Creek Warrior ... Later that day, Colonel John Ritchie and 200 men from the 2nd Regiment of the Indian Home Guard arrived from the Union camp and ... The inscription reads: Battle of the J. R. Williams Site of Civil War naval battle. Confederate Indian forces led by Cherokee ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Senior Judge Linn concurred separately, saying that he was "bound by the sweeping language of the test set out in Mayo."[9] He ...
"Westminster Abbey Official site. Retrieved 22 August 2013.. *^ Wyatt, Michael, The Italian Encounter with Tudor England: A ... Under canon law, Margaret was not bound by her first marriage contract as she was entered into the marriage before reaching the ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Her lavishly illuminated Book of Hours is open before her, with its protective cloth wrapper (called a "chemise" binding), ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Bile acids bind to some other proteins in addition to their hormone receptors (FXR and TGR5) and their transporters. Among ... Bile acid sequestrants bind bile acids in the gut, preventing reabsorption. In so doing, more endogenous cholesterol is shunted ... They bind less specifically to some other receptors and have been reported to regulate the activity of certain enzymes [11] and ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Once released into the blood and lymph, these antibody molecules bind to the target antigen (foreign substance) and initiate ... These T cells bind to the MHC II-antigen molecule and cause activation of the B cell. This is a type of safeguard to the system ... by selection for the ability to bind antigen with higher affinity, the activation and growth of B cell clones able to secrete ...
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Limongi MZ, Pelliccia F, Gaddini L, Rocchi A (2000). "Clustering of two fragile sites and seven homeobox genes in human ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... ER RBA = Relative binding affinity to estrogen receptors of rat uterine cytosol. Uterine weight = Percentage change in uterine ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Given his background, although he was a vassal of king Philip, Henry was bound by few national ties, an aspect of his ... These sites served however only as the individual residence for a particular sovereign. A number of cities held official status ... When Regensburg served as the site of the Diet, France and, in the late 1700s, Russia, had diplomatic representatives there.[87 ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... It has the authority to enact binding solutions for disputes between editors, primarily related to serious behavioural issues ... That site is now on the Wikipedia blacklist. Let me know if you have any further questions about this assessment. DMacks (talk ... If you obtained it from a website, please add a link to the page from which it was taken, together with a brief restatement of ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... The agreements negotiated by a union are binding on the rank and file members and the employer and in some cases on other non- ... Eurofound website "FREEDOM OF ASSOCIATION/TRADE UNION FREEDOM", "Archived copy". Archived from the original on 17 April 2011. ... "SITRAPEQUIA website (in Spanish). San José: Sindicato de Trabajadores(as) Petroléros Químicos y Afines. 2014. Archived from the ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Kornhuber J., Herr B., Thome J., Riederer P. (1995). "The antiparkinsonian drug budipine binds to NMDA and sigma receptors in ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... This upper bound given by Shannon's work set up a long journey in designing ECCs that can go close to the ultimate performance ...
a b c d e f g h i Arya Samaj Singapore Website ... Outward Bound Singapore. *Red Cross Youth. *Singapore Scout ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
protein binding. 细胞成分. · nucleus. · nuclear envelope. · lamin filament. · nuclear lamina. · nucleoplasm. · cytoplasm. · cytosol ... removes the site for the second endoproteolytic cleavage. Consequently, no mature lamin A is formed, and a farnesylated mutant ... sterol regulatory element binding protein import into nucleus. · regulation of apoptotic process. · cellular protein metabolic ... Lamin A/C binding protein LAP2alpha is required for nuclear anchorage of retinoblastoma protein. Mol. Biol. Cell. December 2002 ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Protein binding. 60%. Metabolism. Hepatic via CYP3A4. Elimination half-life. 1.8 ± 0.4 hours. ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Matrix bound[edit]. Main article: Matrix Chernoff bound. Rudolf Ahlswede and Andreas Winter introduced a Chernoff bound for ... Sometimes, the bound. D. (. (. 1. +. x. ). p. ‖. p. ). ≥. 1. 4. x. 2. p. ,. −. 1. 2. ≤. x. ≤. 1. 2. ,. {\displaystyle D((1+x)p ... and the generic Chernoff bound gives:[3]:64. Pr. [. X. ≥. (. 1. +. δ. ). n. p. ]. ≤. e. δ. n. p. (. 1. +. δ. ). (. 1. +. δ. ). ...
"Tyrosine 151 is part of the substrate activation binding site of bovine trypsin: identification by covalent labelling with p- ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... "Km+, a mannose-binding lectin from Artocarpus inegrifolia: amino acid sequence predicted tertiary structure, carbohydrate ...
"Cysteine residues in a synthetic peptide corresponding to human follicle-stimulating hormone beta-subunit receptor-binding ... "DNA Cloning Using In Vitro Site-Specific Recombination". Genome Res. 10 (11): 1788-95. PMC 310948. . PMID 11076863. doi ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... The majority of institutions educating such specialists will be forced to diversify their offerings, which are bound to ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... For a bacterium to bind, take up, and recombine exogenous DNA into its chromosome, it must enter a special physiological state ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... which could weaken the links that bind Galicia and Spain and ultimately favor the people's aspiration toward an independent ... as being an author or bringing reputed troubadours into one's home became a way of promoting social prestige; as a result many ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Language is an important element of Bengali identity and binds together a culturally diverse region. ... A Bengali sign in Brick Lane in London, which is home to a large Bengali diaspora ...
... or into molecules that bind to receptors or other sites of drug action. Such labelled compounds are known as radiotracers. PET ... Radioligands that bind to dopamine receptors (D1,[14] D2 receptor,[15][16] reuptake transporter), serotonin receptors (5HT1A, ... Use of this tracer to explore the possibility of cancer metastasis (i.e., spreading to other sites) is the most common type of ... The presence of the small on-site cyclotron promises to expand in the future as the cyclotrons shrink in response to the high ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... ability to bind to and infect targeted cells.[51] The viral RNA polymerase, encoded by the L gene, partially uncoats the ... In July 2019, an infected man travelled to Goma, home to more than two million people.[219] One week later, on 17 July 2019, ... Transmission risk reduction of filoviruses in home-care settings" (PDF). World Health Organization (WHO). Archived (PDF) from ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Scan the nascent protein in order to recognize and bind sequons.. *Move these two large substrates into their proper locations ... Nilsson IM, von Heijne G (March 1993). "Determination of the distance between the oligosaccharyltransferase active site and the ... The active site of OST is located about 4 nm from the lumenal face of the ER membrane.[4] ...
... chemicals custom tailored to bind at these sites are most effective at altering respiratory rhythm. Adenosine modulates the ... AIH causes homeostatic changes in multiple sites of the respiratory system; the pre-BötC is likely the site for the LTF, since ... A lack of serotonin binding to the serotonin receptor 2 leads to the inability to autoresuscitation due to the lack of drive ... by G protein-coupled receptors that can activate or inhibit the NALCN channels depending on the neurotransmitter that binds the ...
Bindings. University of Iowa Libraries. Spring 2004. Archived from the original (PDF) on 2008-06-25. Retrieved 2008-02-26.. ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... the Ministers of Culture of the federal states in West Germany officially declared the Duden spellings to be binding as of ... Currently, local dialects are used mainly in informal situations or at home and also in dialect literature, and more recently a ... Though about 10%, or 830,000 Swiss residents speak High German a.k.a. Standard German at home. ...
a b Museum of Antiquites web site Archived 2007-11-21 at the Wayback Machine. . Retrieved February 13, 2008. ... Antarctica was ice-bound throughout the Pleistocene and the preceding Pliocene. The Andes were covered in the south by the ... Roche H et al., 2002, Les sites archaéologiques pio-pléistocènes de la formation de Nachuku 663-673, qtd in Scarre, 2005 ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ...
... identification of a unique diazepam-insensitive binding site". Eur. J. Pharmacol. 291 (3): 319-325. doi:10.1016/0922-4106(95) ... By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At ...
By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia ... Measurements bound to a range and repeating (like degrees in a circle, clock time, etc.), graded membership categories, and ... On line] https://web.archive.org/web/20070926232755/http://www2.umassd.edu/swpi/ISERN/isern-95-04.pdf ...
A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA ... it is not considered a ribosome binding site.[2][8] Internal ribosome entry site (IRES)[edit]. Eukaryotic ribosomes are known ... 9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ... "Ribosome binding site recognition using neural networks". Genetics and Molecular Biology. 27 (4): 644-650. doi:10.1590/S1415- ...
CpG Conservation Predicts PRC2-Binding Sites.. The distribution of HCGDs was compared with genome-wide binding profiles of the ... Hyperconserved CpG domains underlie Polycomb-binding sites. Amos Tanay, Anne H. ODonnell, Marc Damelin, and Timothy H. Bestor ... high Suz12 binding, and substantial numbers of McrBC and HpaII sites. High-molecular-weight DNA was subjected to two rounds of ... indicating that sequence properties on scales much larger than standard transcription factor-binding sites may play an ...
... does anyone know how many binding sites in a single yeast genome (approximately) would bind this probe assuming that it binds ... 16S/18S Binding Sites?. David Singleton dsingle at uga.cc.uga.edu Mon Oct 20 00:05:47 EST 1997 *Previous message: *Free* online ... One of the oligo probes which I am using is described as Universal, and it does indeed bind to yeast genomic DNA (as well as ...
Edmundson A.B., Ely K.R., Herron J.N., Gibson A.L. (1985) Probing the Binding Sites in Crystals of Immunoglobulins. In: Reid E ... The Bence-Jones dimer binds 2 molecules of bis(DNP)lysine in solution and one in trigonal crystals. The IgG1 does not bind this ... Light Chain Peptide Bond Ammonium Sulphate Binding Cavity Chemotactic Peptide These keywords were added by machine and not by ... Investigation and Exploitation of Antibody Combining Sites pp 33-50 , Cite as ...
Ben-Naim A. (2001) Large Linear Systems of Binding Sites. In: Cooperativity and Regulation in Biochemical Processes. Springer, ... In this section we introduce the matrix method to rewrite the GPF of a linear system of m sites in a more convenient form. This ... We use cookies to improve your experience with our site. More information Accept. ... Large Eigenvalue Pair Correlation Cyclic System Intrinsic Binding Constant Large Linear System ...
... There are many different groups that are developing software for ... A Java application that reuires a local installation of a database that provides binding site information (eg the Public ... finding transciption factor binding sites, alongside our own development of the BIFA tool which forms part of the Apples ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... Sulphate/thiosulphate-binding site (IPR034408) Sulphate-binding protein (gene sbp or sbpA) and thiosulphate-binding protein ( ... Fumarate reductase/succinate dehydrogenase, FAD-binding site (IPR003952) In bacteria two distinct, membrane-bound, enzyme ... Coenzyme A transferase binding site (IPR004163) Coenzyme A (CoA) transferases belong to an evolutionary conserved family of ...
Binding site plan land use permit for unincorporated King County from the King County Department of Permitting and ... A binding site plan provides an alternative method for division of land for commercial and industrial zoned property, mobile ... Affidavit of Correction Alteration Binding site plan Boundary/lot line adjustment Clearing & grading Conditional use Critical ... Refer to the binding site plans packet for application materials *Request an application packet by mail by calling the ...
Citations may include links to full-text content from PubMed Central and publisher web sites. ... their binding sites, and species selectivity. Many cell-surface proteins have been reported to bind Aβ. Binding sites for Aβ ... Binding Sites for Amyloid-β Oligomers and Synaptic Toxicity.. Smith LM1, Strittmatter SM1. ... Cellular prion protein (PrPC) is a high-affinity Aβ oligomer binding site, and a range of data delineates a signaling pathway ...
We show that spatial atomic position specific scoring matrices of binding sites for each peptide residue can capture the ... important for binding and when used to scan the surface of target proteins can accurately identify candidate binding sites for ... The accurate prediction of protein-peptide binding without prior structural knowledge will ultimately enable better functional ... Here, we present a general approach for predicting protein-peptide interaction sites. ...
GLUTATHIONE REDUCTASEFlavin-adenine DinucleotideNicotinamide-adenine-dinucleotide
Bind your UI controls to generated objects generically; Author: Christopher R Davis, Ben Traynor; Updated: 1 Jun 2011; Section ... An edit page overrides these methods to add any custom code needed to the bind. Below is a class diagram of my main site ... How you choose to bind or map a user interface is specific, based on your technology such as web forms, MVC, WinForms, etc. You ... In this sample, all fields bind to the same object; however this is not necessary. We could just as easily bind some of the UI ...
In line with the latter, recent studies reported existence of p53 binding sites in sequences of primate LTRs3, Alus4,5 and ... one of the reported p53 binding sites was composed of the low complexity repeat. In summary, the original work of el-Deiry et ... it has been observed that many p53 binding sites are species-specific2, indicating that a remarkable flexibility resided in the ... a highly influential paper describing the consensus binding site for the key transcription factor p53 was published in Nature ...
... binding sites are not known. Due to the high flexibility of GABAA receptors and the existence of multiple drug-binding sites, ... Allosteric modulation of GABAA receptors via multiple drug-binding sites Adv Pharmacol. 2015;72:53-96. doi: 10.1016/bs.apha. ... Although multiple binding sites make GABAA receptor pharmacology even more complicated, the exploitation of ligand interaction ... Keywords: Allosteric modulation; GABA(A) receptor structure; Ligand-binding sites; Pharmacology; Receptor subtype-selective ...
Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains ... Frequent gain and loss of functional transcription factor binding sites PLoS Comput Biol. 2007 May;3(5):e99. doi: 10.1371/ ... We also estimate that there is a high rate of binding site gain, as more than half of experimentally identified S. cerevisiae ... We estimate that nearly half of all loss events cannot be explained by binding site turnover. Recreating the mutations that led ...
Amino Acids Involved in Mn2+ Binding. The percentage of aspartic acid residues in Mn2+ binding sites is equal to 34.16%. The ... result in reorganization of binding sites for certain ligands or even in the availability of potential binding sites. ... Mn2+ binding sites which consist of two histidines and a single glutamic or aspartic acid. The percentage of sites with three ... One may think that there should be many Asp-Xaa-Asp-Xaa-Asp-Gly motifs in Mn2+ binding sites; see Table 2. However, this type ...
Cryptic binding sites are the binding sites that are transiently formed in an apo form or that are induced by ligand binding. ... a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding ... Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites". Cell Biochemistry and ... Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered ...
Folate binding site of flavin-dependent thymidylate synthase. Eric M. Koehn, Laura L. Perissinotti, Salah Moghram, Arjun ... thought you would like to see the PNAS web site. ... Folate binding site of flavin-dependent thymidylate synthase ... Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX ... and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate ...
The antiviral drug remdesivir binds to a newly identified section of a SARS-CoV-2 enzyme that is part of the virus replication ... Cite this: Remdesivir Fits Binding Site in SARS-CoV-2 Enzyme - Medscape - Apr 20, 2020. ... All material on this website is protected by copyright, Copyright © 1994-2020 by WebMD LLC. This website also contains material ... With remdesivir bound to this domain, the polymerase is effectively prevented from functioning normally. This mechanism may ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... AP endonuclease 1, binding site (IPR020847). Short name: AP_endonuclease_F1_BS ... This entry represents a motif containing a glutamate residue which has been shown in the Escherichia coli enzyme to bind a ... Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3 termini. DNA repair ...
Welcome to Kutztown Universitys Upward Bound, a federally-funded educational program that partners with William Allen High ... TRIO Upward Bound provides free academic enrichment and college preparatory services to eligible William Allen High School ...
A PCR primer binding site is a site where a polymerase chain reaction (PCR) primer binds, to prime duplication of a complement ... A primer binding site is a region of a nucleotide sequence where an RNA or DNA single-stranded primer binds to start ... The HIV primer binding site is a structured RNA element in the genomes of retroviruses to which tRNA binds to initiate reverse ... The primer binding site is on one of the two complementary strands of a double-stranded nucleotide polymer, in the strand which ...
Binding Wounds, Pushing Boundaries: African Americans in Civil War Medicine looks at the men and women who served as surgeons ... Copyright, Privacy, Accessibility, Site Map, Viewers and Players U.S. National Library of Medicine, 8600 Rockville Pike, ...
A Method for Identifying Transcription Co-regulator Binding Sites in ChIP-seq Data. A typical ChIP-seq experiment profiles the ... one or both motif binding sites. Based on the estimates of the parameters from the EM procedure, we compute the posterior ... This website may not display properly with Internet Explorer. For the best experience, please use a more recent browser such as ... Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure youre on a federal ...
7: Localization of opiate binding sites *8: Opiates binding to opiate receptors in the nucleus accumbens: increased dopamine ... 1: Localization of cocaine binding sites. When a person smokes or snorts cocaine, it travels quickly to the brain. Although ... Home » Publications » Section III: Introduction to Drugs of Abuse: Cocaine, Opiates (Heroin) and Marijuana (THC) » 1: ... 10: Summary: opiate binding in nucleus accumbens and activation of the reward pathway ...
Imaging Dopamine D2 Agonist Binding Sites in Schizophrenia Official Title Imaging Dopamine D2 Agonist Binding Sites in ... Imaging Dopamine D2 Agonist Binding Sites in Schizophrenia. The safety and scientific validity of this study is the ... base line Binding Potential (BPND) [ Time Frame: 37 Days ]. PET outcome measure of the density of available neuroreceptors ... Antagonist ([11C]raclopride) and agonist ([11C]NPA) radiotracer will be used sequentially to measure binding potential (BPND) ...
7: Localization of opiate binding sites *8: Opiates binding to opiate receptors in the nucleus accumbens: increased dopamine ... 7: Localization of opiate binding sites When a person injects heroin or morphine, it too travels quickly to the brain. Point to ... Home » Publications » Section III: Introduction to Drugs of Abuse: Cocaine, Opiates (Heroin) and Marijuana (THC) » 7: ... The opiates bind to opiate receptors that are concentrated in areas within the reward system. Indicate that the action of ...
BIND Discussion List: The discussion list for the BIND protocol is ,[email protected],. Joining this discussion list makes ... The WebDAV BIND protocol has been published as RFC 5842 in April 2010.. (the information below will be kept here just for ...
In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets ... Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by ... Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a ... RNA-binding site; bioinformatics; prediction; macromolecular docking RNA-binding proteins (RBPs); RNA-binding site; ...
Comparative ChIP-seq data reveal adaptive evolution of insulator protein CTCF binding in multiple Drosophila species. ... DNA-binding proteins Is the Subject Area "DNA-binding proteins" applicable to this article? Yes. No. ... Binding analysis Is the Subject Area "Binding analysis" applicable to this article? Yes. No. ...
  • At a higher-than-usual temperature (~42 °C), the RBS secondary structure of heat shock proteins becomes undone thus allowing ribosomes to bind and initiate translation. (wikipedia.org)
  • Sulphate/thiosulphate-binding site (IPR034408) Sulphate-binding protein (gene sbp or sbpA) and thiosulphate-binding protein (gene cysP) are two structurally related periplasmic bacterial proteins which specifically bind sulpha. (ebi.ac.uk)
  • A number of cell-surface proteins have been described as Aβ binding proteins, and one or more are likely to mediate Aβ oligomer toxicity in AD. (nih.gov)
  • Further study of Aβ binding proteins will define the molecular basis of this crucial step in AD pathogenesis. (nih.gov)
  • Many cell-surface proteins have been reported to bind Aβ. (nih.gov)
  • Crystal structures of proteins and receptors homologous to GABAA receptors as well as homology modeling studies have provided insights into the possible location of ligand interaction sites. (nih.gov)
  • However, the information on preferable 3D structural motifs is available mostly for Ca 2+ and Zn 2+ binding proteins. (hindawi.com)
  • Recently, other proteins, able to bind Ca 2+ containing the abovementioned motif but lacking one or both helices, have been described [ 8 ]. (hindawi.com)
  • We hypothesize that the multiplicity associated with the YY1 and CTCF binding sites may be designed for attracting and maintaining the relatively high levels of YY1 and CTCF proteins or for covering the relatively large genomic sizes of the associated ICRs. (mendeley.com)
  • Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). (mdpi.com)
  • Is the Subject Area "DNA-binding proteins" applicable to this article? (plos.org)
  • The splicing factor proteins themselves, as well as the location where these proteins bind, dictate which pieces of the RNA are included or excluded in the final gene transcript - in much the same way that removing and inserting scenes, or splicing, can alter the plot of a movie. (ucsd.edu)
  • ABC (ATP-binding cassette) transporters are clinically important because drug pumps like P-glycoprotein (P-gp, ABCB1) confer multidrug resistance and mutant ABC proteins are responsible for many protein-folding diseases such as cystic fibrosis. (mendeley.com)
  • The binding of transcription factor proteins (TFs) to DNA promoter regions upstream of gene transcription start sites (TSSs) is one of the most important mechanisms by which gene expression, and thus many cellular processes, are controlled. (bioconductor.org)
  • Curious binding-sites - in membrane transport proteins. (ebooks.com)
  • 125 I]-SFTPA1 bound to two myometrial cell proteins (55 and 210 kDa). (bioone.org)
  • Scientists from the iMolecule group at Skoltech Center for Computational and Data-Intensive Science and Engineering (CDISE) developed BiteNet, a machine learning (ML) algorithm that helps find drug binding sites, i.e. potential drug targets, in proteins. (phys.org)
  • To produce a therapeutic effect, drugs should attach to proteins at specific sites called binding sites. (phys.org)
  • Skoltech CDISE assistant professor Petr Popov and Ph.D. student Igor Kozlovskii developed a new computational approach for spatio-temporal detection of binding sites in proteins by applying deep learning algorithms and computer vision to protein structures treated as 3-D images. (phys.org)
  • A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. (scirp.org)
  • Hendlich, M., Rippmann, F. and Barnickel, G. (1997) LIGSITE: Automatic and Efficient Detection of Potential Small Molecule-Binding Sites in Proteins. (scirp.org)
  • Phaseolicola (HrpZ Pph ) shows affinity to peptides with a consensus amino acid motif W(L)ARWLL(G/L). To localize the peptide-binding site, the hrpZ Pph gene was mutagenized with randomly placed 15-bp insertions, and the mutant proteins were screened for the peptide-binding ability. (apsnet.org)
  • Antiserum raised against one of the hrpZ Pph -binding peptides recognized small proteins in bean, tomato, parsley, and Arabidopsis thaliana but none in tobacco. (apsnet.org)
  • Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. (rsc.org)
  • Hence, understanding the interactions of PGH2 and characterizing its binding sites in these synthases is crucial for developing novel therapeutics based on these proteins as targets. (sciweavers.org)
  • but a hybrid dimer of the Weir and Mcg light chains binds one ligand molecule with the same affinity as the Mcg dimer. (springer.com)
  • Although multiple binding sites make GABAA receptor pharmacology even more complicated, the exploitation of ligand interaction with novel-binding sites also offers additional possibilities for a subtype-selective modulation of GABAA receptors. (nih.gov)
  • The metal ions (K+, Ba2+, Ca2+, Mg2+, Ni2+) span a range of ligand binding strengths, and the ligands include several dipeptides and tripeptides, and one tetrapeptide. (uva.nl)
  • Enerjik yöntem, farklı amino asit kalıntılarının ligand ile etkileşim enerjisini hesaplamalı olarak analiz eder ve bağlanma enerjisi en az olanların potansiyel bağlanma bölgeleri olduğunu tahmin eder. (jove.com)
  • The binding partner of the macromolecule is often referred to as a ligand. (wikipedia.org)
  • Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. (wikipedia.org)
  • At the regulatory site, the binding of a ligand may elicit amplified or inhibited protein function. (wikipedia.org)
  • The binding of a ligand to an allosteric site of a multimeric enzyme often induces positive cooperativity, that is the binding of one substrate induces a favorable conformation change and increases the enzyme's likelihood to bind to a second substrate. (wikipedia.org)
  • Furthermore, the amount of bound ligand at each site can be determined from changes in resonance intensities. (uniprot.org)
  • Laurie, A.T.R. and Jackson, R.M. (2005) Q-Site Finder: An Energy-Based Method for the Prediction of Protein-Ligand Binding Sites. (scirp.org)
  • In those studies, ligand specificity was confirmed with a congenital OXTR knockout mouse as well as competitive binding techniques. (frontiersin.org)
  • Previously identified regions of significant OXTR ligand binding in the mouse were analyzed for comparison: rostral and lateral periodontium, olfactory epithelium, ciliary bodies of the eye, whisker pads, adrenal gland, and anogenital area. (frontiersin.org)
  • While there were some areas that showed conserved OXTR ligand binding in the prairie vole (e.g., ciliary body of the eye and the anogenital area), areas showing OXTR ligand binding in the neonatal prairie vole were not identical to OXTR ligand binding in the periphery of the C57BL/6J neonatal mouse. (frontiersin.org)
  • Further, some of the regions measured in the prairie vole suggest sex differences in OXTR ligand binding. (frontiersin.org)
  • Collectively, as is well-established in the central nervous system, these data indicate that patterns of OXTR ligand binding in the infant periphery are species-specific. (frontiersin.org)
  • Previous work from our lab examined OXTR in the periphery of neonatal C57Bl/6J mice, finding OXTR ligand binding was regionally specific in wild-type mice and absent in the Oxtr knockout mouse ( Greenwood and Hammock, 2017 ). (frontiersin.org)
  • The goal of the current study was to assess regions previously identified in the mouse for possible OXTR ligand binding in the neonatal prairie vole ( Microtus ochrogaster ). (frontiersin.org)
  • Data within this paper will expand upon these species comparisons by investigating OXTR ligand binding in the periphery of the neonatal prairie vole. (frontiersin.org)
  • Individual regions of interest were chosen based on our prior report of the distribution of OXTR ligand binding in neonatal mice. (frontiersin.org)
  • While it is known that mifepristone exerts its clinical effect by binding to the ligand binding domain of the progesterone receptor, there was no three-dimensional structure of it bound to the receptor. (esrf.eu)
  • Therefore, the aim of this research was to obtain a crystal structure of the mifepristone-progesterone receptor in order to better understand the specificity of the receptors ligand binding domain. (esrf.eu)
  • These studies have extended our knowledge on the structural requirements of the progesterone receptor ligand binding domain. (esrf.eu)
  • Mifepristone (ball and stick representation) viewed within the progesterone receptor ligand binding domain (worms representation). (esrf.eu)
  • Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. (rsc.org)
  • Cellular prion protein (PrP C ) is a high-affinity Aβ oligomer binding site, and a range of data delineates a signaling pathway leading from Aβ complexation with PrP C to neuronal impairment. (nih.gov)
  • High-affinity [3H]6-nitroquipazine binding sites in rat brain. (biomedsearch.com)
  • We have characterized the specific binding of [3H]6-nitroquipazine to rat brain membranes at 22 degrees C. The present results indicate the presence of a single saturable high-affinity binding component for [3H]6-nitroquipazine. (biomedsearch.com)
  • The wild-type (wt) protein binds with high affinity to mannose-rich oligosaccharides on the surface of gp120 through two quasi-symmetric sites, located in domains A and B. We recently reported on a mutant of CV-N that contained a single functional mannose-binding site, domain B, showing that multivalent binding to oligomannosides is necessary for antiviral activity. (rcsb.org)
  • Analysis of total binding at 37°C of 125 I-WT apoA-I to the cells and specifically to ABCA1, as determined by covalent cross-linking, revealed saturable high affinity binding in both cases. (ahajournals.org)
  • Conclusions- This study demonstrates that ABCA1 activity creates 2 types of high affinity apoA-I binding sites at the cell surface. (ahajournals.org)
  • An in vivo phosphorylation-dependent change in binding of CREB increases the occupancy of weak binding sites used for transactivation, such as the TATCRE, while high affinity sites may have constitutive binding of transcriptionally active and inactive CREB dimers, as demonstrated by in vivo footprinting at the PEPCK CRE. (uni-muenchen.de)
  • The existence of multiple GABAA receptor subtypes with distinct subunit composition, the contribution of distinct subunit sequences to binding sites of different receptor subtypes, as well as the observation that even subunits not directly contributing to a binding site are able to influence affinity and efficacy of drugs, contribute to a unique pharmacology of each GABAA receptor subtype. (nih.gov)
  • Allosteric binding induces conformational changes that may increase the protein's affinity for substrate. (wikipedia.org)
  • Conversely, allosteric binding that decreases the protein's affinity for substrate is negative modulation. (wikipedia.org)
  • Furthermore, when 125 I -apoA-I was cross-linked to ABCA1-upregulated cells and examined by SDS-PAGE, the major (≈90%) band migrated as monomeric apoA-I. In contrast to WT apoA-I, the C-terminal deletion mutants Δ190 to 243 and Δ223 to 243 that have reduced lipid affinity, exhibited marked reductions (50 and 70%, respectively) in their abilities to bind to the surface of ABCA1-upregulated cells. (ahajournals.org)
  • One class, including the TATCRE, is characterized by asymmetric and weak binding sites (CGTCA), whereas the second class containing symmetrical TGACGTCA sites shows a much higher binding affinity for CREB. (uni-muenchen.de)
  • There were no differences in apparent binding affinity (Kd): 0.046 (0.024-0.062) nM for control and 0.040 (0.027-0.061) nM for Alzheimer. (diva-portal.org)
  • In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. (wikipedia.org)
  • Interestingly, the specificity constant k cat /K M increased with polymer length from HA 5 to HA 7 to a value of 44 mM -1 s -1 , indicating an oligosaccharide binding site with increasing specificity towards a heptasaccharide at the UA domain. (scirp.org)
  • The value of k cat /K M remained moderately constant around 8 mM -1 s -1 for HA 4 , HA 6 , and HA 8 , indicating a binding site with significantly lower binding specificity at the NAc domain than at the UA domain. (scirp.org)
  • Acquisition of Human-Type Receptor Binding Specificity by New H5N1 Influenza Virus Sublineages during Their Emergence in Birds in Egypt. (ebscohost.com)
  • Results: Shape and physico-chemical properties of the PGH2 binding sites of the four prostanoid synthases were analyzed and compared in order to understand the molecular basis of the specificity. (sciweavers.org)
  • Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes . (wikipedia.org)
  • The ribosomal protein S1 binds to adenine sequences upstream of the RBS. (wikipedia.org)
  • We used the expectation-maximization (EM) algorithm to numerically maximize the observed data likelihood with respect to the position weight matrices (PWMs) of the two motifs and the proportions of the sequences containing none (pure "noise"), one or both motif binding sites. (nih.gov)
  • Transcription factor binding to promoter DNA sequences is a stochastic process, and imperfect matches can be sufficient for binding. (bioconductor.org)
  • For species such as yeasts, where genome sequences of numerous related species are available ( 6 ), this approach can allow for the evolutionary comparison of binding sites of conserved TFs across species. (sciencemag.org)
  • 5. The CDODN of claim 1, which stem structure additionally comprises nucleotide sequences capable of binding the DNA-binding domain of two or more transcription factors. (freepatentsonline.com)
  • That is why the knowledge on preferable secondary structural motifs around each of the amino acid residues may be even more helpful for prediction of ion binding sites than the knowledge on the 3D structural motifs for the complete coordination spheres. (hindawi.com)
  • In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions. (mdpi.com)
  • 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. (mdpi.com)
  • 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 different tools, and future directions in protein DNA-binding site prediction. (mdpi.com)
  • Si J, Zhao R, Wu R. An Overview of the Prediction of Protein DNA-Binding Sites. (mdpi.com)
  • We have developed a computational tool, rVISTA, for high-throughput discovery of cis-regulatory elements that combines transcription factor binding site prediction and the analysis of inter-species sequence conservation. (unt.edu)
  • At the catalytic binding site, several different interactions may act upon the substrate. (wikipedia.org)
  • Competitive inhibitors compete with substrate to bind to free enzymes at active sites and thus impede the production of the enzyme-substrate complex upon binding. (wikipedia.org)
  • Uncompetitive inhibitors, alternatively, bind concurrently with substrate at active sites. (wikipedia.org)
  • Upon binding to an enzyme substrate (ES) complex, an enzyme substrate inhibitor (ESI) complex is formed. (wikipedia.org)
  • Lastly, mixed inhibitors are able to bind to both the free enzyme and the enzyme-substrate complex. (wikipedia.org)
  • At the active site, a substrate binds to an enzyme to induce a chemical reaction. (wikipedia.org)
  • Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. (nature.com)
  • Structural alignment studies between PmHAS and glycosyltransferases of the GT-A fold showed significant similarity in the binding of the UDP-sugars and the orientation of the acceptor substrate. (scirp.org)
  • These similarities in substrate orientation in the active site and in essential amino acid residues involved in substrate binding were utilized to localize the two HA oligosaccharide binding sites. (scirp.org)
  • The binding of this substrate with these Synthases is not properly understood. (sciweavers.org)
  • For most of these ligands, however, binding sites are not known. (nih.gov)
  • This report is presented in recognition and tribute for the Armentrout group's long and hugely productive interest in metal-ion binding to gas-phase ligands. (uva.nl)
  • The present results for the larger peptides reconcile this surprising difference, showing that larger peptide ligands revert to the expected CS binding pattern for gas-phase Mg2+. (uva.nl)
  • Electric charge, steric shape and geometry of the site selectively allow for highly specific ligands to bind, activating a particular cascade of cellular interactions the protein is responsible for. (wikipedia.org)
  • Regulatory site ligands can involve homotropic and heterotropic ligands, in which single or multiple types of molecule affects enzyme activity respectively. (wikipedia.org)
  • This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design. (rcsb.org)
  • For molecules containing fluorine, binding results were further validated by direct observations of the bound ligands using (19)F NMR. (uniprot.org)
  • Schering-Plough used the ESRF MXpress service for data collection on crystals of the progesterone-receptor binding domain with bound ligands. (esrf.eu)
  • In this paper, we report a method to automatically generate 3D motifs of protein structure binding sites based on consensus atom positions and evaluate it on a set of adenine based ligands. (sciweavers.org)
  • With remdesivir bound to this domain, the polymerase is effectively prevented from functioning normally. (medscape.com)
  • We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. (rcsb.org)
  • A PCR primer binding site is a site where a polymerase chain reaction (PCR) primer binds, to prime duplication of a complement to an existing DNA or RNA sequence. (wikipedia.org)
  • NEW YORK (Reuters Health) - The antiviral drug remdesivir binds to a newly identified section of a SARS-CoV-2 enzyme that is part of the virus' replication and transcription machinery, according to a structural analysis. (medscape.com)
  • The novel capsid-binding antiviral pleconaril inhibits in vitro replication of most rhinoviruses and entero-viruses. (ebscohost.com)
  • This conserved 9-amino acid motif ((V/A)P(I/L)AXXE(S/D)D) is required for ankyrin-G binding and functions to localise sodium channels to a variety of 'excitable' membrane domains both inside and outside of the nervous system [ PMID: 12716895 ]. (ebi.ac.uk)
  • Identification of a conserved ankyrin-binding motif in the family of sodium channel alpha subunits. (ebi.ac.uk)
  • to construct the p53 consensus binding motif. (frontiersin.org)
  • On the other hand, the percentage of Mn 2+ sites with at least one amino acid in the "beta strand-major binder-random coil" motif of secondary structure (77.88%) does not depend on genomic GC-content. (hindawi.com)
  • Well-known EF-hand motif for Ca 2+ binding consists of two alpha helices and a loop between them [ 6 ]. (hindawi.com)
  • The aim of this study was to find out whether there is a secondary structural motif which is characteristic for relatively short parts of polypeptide chains around Mn 2+ binding amino acid residues. (hindawi.com)
  • For example, four from eight 3D structural motifs for Zn 2+ binding include such a secondary structural motif as beta hairpin. (hindawi.com)
  • Cite this: Remdesivir Fits Binding Site in SARS-CoV-2 Enzyme - Medscape - Apr 20, 2020. (medscape.com)
  • Catalase haem-binding site (IPR002226) Catalases are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects. (ebi.ac.uk)
  • Identification of the tariquidar-binding site has been the subject of intensive molecular modeling studies because it is the most potent inhibitor and corrector of P-gp. (mendeley.com)
  • Binding sites incur functional changes in a number of contexts, including enzyme catalysis, molecular pathway signaling, homeostatic regulation, and physiological function. (wikipedia.org)
  • The structure of the complex with dimannose determined at 1.8 A resolution revealed a different conformation of the binding site than previously observed in the NMR structure of wt CV-N. Here, we present the 1.35 A resolution structure of the complex, which traps three different binding conformations of the site and provides experimental support for a locking and gating mechanism in the nanoscale time regime observed by molecular dynamics simulations. (rcsb.org)
  • Determining molecular binding sites on human serum albumin by displacement of oleic acid. (uniprot.org)
  • One of the oligo probes which I am using is described as 'Universal', and it does indeed bind to yeast genomic DNA (as well as mitochondrial, I assume). (bio.net)
  • Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. (frontiersin.org)
  • Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. (bibsys.no)
  • Cyclic AMP treatment of hepatoma cells leads to increased protein binding at the cyclic AMP response element (CRE) of the tyrosine aminotransferase (TAT) gene in vivo, as revealed by genomic footprinting, whereas no increase is observed at the CRE of the phosphoenolpyruvate carboxykinase (PEPCK) gene. (uni-muenchen.de)
  • Beta strands near Mn 2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. (hindawi.com)
  • 1 ], there are three amino acid residues most frequently found in Mn 2+ binding sites: His, Asp, and Glu. (hindawi.com)
  • Histidine has the highest normalized frequency in binding sites, while glutamic acid has the lowest normalized frequency among those three amino acid residues [ 1 ]. (hindawi.com)
  • The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. (mdpi.com)
  • This is especially useful when multiple start codons are situated around the potential start site of the protein coding sequence. (wikipedia.org)
  • Metal ion binding to peptides: oxygen or nitrogen sites? (uva.nl)
  • Compared with solution-phase behavior, the iminol binding mode shown by Mg2+ for the smallest peptides is surprising, since this ion is considered as generally binding in a CS mode in solution. (uva.nl)
  • The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. (nature.com)
  • Phage display, using combinatorial peptide libraries, is a relatively straightforward method for identifying suitable peptides for binding to the antigen-binding site of mAbs (27). (thefreedictionary.com)
  • Binding to protein binding sites is most often reversible (transient and non-covalent), but can also be covalent reversible or irreversible. (wikipedia.org)
  • But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? (bibsys.no)
  • We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. (bibsys.no)
  • Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site (IPR020563) The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. (ebi.ac.uk)
  • Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains gene regulation. (nih.gov)
  • Recreating the mutations that led to binding site loss confirms that these sequence changes affect gene expression in some cases. (nih.gov)
  • This process, known as autoregulation, helps to maintain a so-called "steady-state" system in which a protein positively regulates its own production by binding to a regulatory element of the mRNA for the gene coding it. (ucsd.edu)
  • Using Gene Ontology (GO) and Enrichment analysis, we were able to associate (for each of the TFs studied) the target genes of both types of binding with known biological processes. (ovid.com)
  • Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species. (sciencemag.org)
  • 1. A transgenic mouse, whose genome comprises an indicator gene under the control of a transcriptional regulatory element, wherein said transcriptional regulatory element comprises a MEF2 binding site and said indicator gene is (a) expressed in embryonic cardiac tissue, (b) not expressed in adult cardiac tissue, and (c) expressed in adult cardiac tissue in response to hypertrophic signals. (google.com)
  • Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. (bibsys.no)
  • By integrating public expression quantitative trait locus (eQTL) data, miRNA binding site predictions, small RNA sequencing, and Argonaute crosslinking immunoprecipitation (AGO-CLIP) datasets, we identified genetic variants that can affect gene expression by modulating miRNA binding efficiency. (harvard.edu)
  • Putative receptors for Aβ, their binding sites, and species selectivity. (nih.gov)
  • Over the time, hundreds of compounds from different structural classes have been demonstrated to modulate, directly activate, or inhibit GABAA receptors, and most of these compounds interact with more than one binding site at these receptors. (nih.gov)
  • Due to the high flexibility of GABAA receptors and the existence of multiple drug-binding sites, the unequivocal identification of interaction sites for individual drugs is extremely difficult. (nih.gov)
  • The opiates bind to opiate receptors that are concentrated in areas within the reward system. (drugabuse.gov)
  • Mifepristone also binds to two other receptors within the body, which could have undesirable effects. (esrf.eu)
  • We determined the structure of the CVA24v to 1.40 Ã… resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. (ebscohost.com)
  • KCNQ2/KCNQ3 channels are preferentially localised to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3 [ PMID: 16735477 ]. (ebi.ac.uk)
  • As to Zn 2+ binding 3D structural motifs, Sri Krishna et al. (hindawi.com)
  • A recent alternative has been to detect specific 3D motifs which are often associated to active sites. (sciweavers.org)
  • Fumarate reductase/succinate dehydrogenase, FAD-binding site (IPR003952) In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate : fumarate reductase (Frd) is used in anaerobic growth. (ebi.ac.uk)
  • 2-oxo acid dehydrogenase, lipoyl-binding site (IPR003016) The 2-oxo acid dehydrogenase multienzyme complexes from bacterial and eukaryotic sources catalyze the oxidative decarboxylation of 2-oxo acids to the corresponding acyl-CoA. (ebi.ac.uk)
  • The weaker metal ions generally form charge-solvated (CS) complexes binding amide carbonyl oxygen, while the strongest metal ion, nickel, deprotonates the amide nitrogens, probably through iminol tautomerization, and binds to the amide nitrogens. (uva.nl)
  • He produced crystals of concanavalin A complexes with methyl-glucoside and with methyl-mannoside and participated in solving the structure of this protein binding-site for saccharides. (ebooks.com)
  • Moreover, currently no crystal structure of complexes bound with PGH2 has been reported. (sciweavers.org)
  • We also estimate that there is a high rate of binding site gain, as more than half of experimentally identified S. cerevisiae binding sites are not conserved across species. (nih.gov)
  • The detection of binding sites with chromatin immunoprecipitation and microarray (ChIP-chip) analysis ( 4 , 5 ) offers the ability to globally map TF binding locations experimentally rather than computationally. (sciencemag.org)
  • Wakeboard boots and bindings vary considerably in flex, the way they are attached, and how they fit. (jobesports.com)
  • Active site residues of hexokinase allow for stabilization of the glucose molecule in the active site and spur the onset of an alternative pathway of favorable interactions, decreasing the activation energy. (wikipedia.org)
  • para·tope/ ( par´ah-tōp ) the site on the antibody molecule that attaches to an antigen. (thefreedictionary.com)
  • Francelia Bound was born, it is assumed in Sullivan Co., NY in about 1854. (jansdigs.com)
  • Wholesale FIT supplier Travel Bound has launched a completely revamped web site, www.booktravelbound.com, with new products such as apartments, villas and ryokan inns, private sightseeing tours and transfers, as well as new features including interactive city maps, search filters and hotel hot deals and special offers. (travelagentcentral.com)
  • First it is minimizing total file transferring time by applying a Pincer-Search algorithm of Data mining approach to discover associated distributed replicas sites to share the transferring file process. (techrepublic.com)
  • For UAE and Namibia, we drove thousands of miles across those deserts in search for specific planetary analog sites. (nasa.gov)
  • So you spot-check some Google searches, but that reveals no sign of the website in the search results. (talentzoo.com)
  • You pore through the website and find that the pages that used to bring in tons of targeted Google traffic are now missing altogether, combined with other pages, or buried so deeply in the website's architecture that the search engines no longer find them important. (talentzoo.com)
  • Kupas, K., Ultsch, A. and Klebe, G. (2008) Large Scale Analysis of Protein-Binding Cavities Using Self-Organizing Maps and Wavelet-Based Surface Patches to Describe Functional Properties, Selectivity Discrimination, and Putative Cross-Reactivity. (scirp.org)
  • A competition binding assay was used to assess the selectivity of [ 125 I]-OVTA for peripheral OXTR. (frontiersin.org)
  • Chromatin remodeling, methylation, histone modification, chromosome interaction, distal enhancers, and the cooperative binding of transcription co-factors all play an important role. (bioconductor.org)
  • By means of chromatin immunoprecipitation and DNA microarray analysis, the divergence in the binding sites of the pseudohyphal regulators Ste12 and Tec1 was determined in the yeasts Saccharomyces cerevisiae , S. mikatae , and S. bayanus under pseudohyphal conditions. (sciencemag.org)
  • Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. (bibsys.no)
  • We show that by combining signal intensity with additional data-ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure-we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts. (bibsys.no)
  • Save 10% on the Poppleton In Spring (Turtleback School & Library Binding Edition) (Scholastic Reader: Level 3) by Turtleback at Translate This Website. (translateth.is)
  • A typical ChIP-seq experiment profiles the genome-wide binding of a single transcription factor. (nih.gov)
  • Using genome-wide biochemical methods to look at the set of all RNA molecules across the transcriptome, the researchers found that LIN28 recognizes and binds to a known hairpin-like structure found on the let-7 family of miRNA, but surprisingly, this same structure is also found on mRNAs, allowing LIN28 to directly regulate thousands of targets. (ucsd.edu)
  • The data were obtained from a genome-wide coverage of promoter regions from 8-kb upstream of the transcription start site (TSS) to 2-kb downstream. (ovid.com)
  • Site-directed mutagenesis was used to identify the functional vir box(es) of virB, virC and virD. (unboundmedicine.com)
  • Recent studies have identified the ATP-binding cassette transporter A1 (ABCA1) as a critical factor in the formation of HDL, and lack of a functional ABCA1 leads to cholesterol accumulation in peripheral tissues and low plasma HDL. (ahajournals.org)
  • A primer binding site is a region of a nucleotide sequence where an RNA or DNA single-stranded primer binds to start replication. (wikipedia.org)
  • The primer binding site is on one of the two complementary strands of a double-stranded nucleotide polymer, in the strand which is to be copied, or is within a single-stranded nucleotide polymer sequence. (wikipedia.org)
  • The present invention provides a circular dumbbell oligodeoxynucleotide (CDODN) comprising two loop structures and a stem structure, wherein the stem structure comprises a nucleotide sequence capable of binding the DNA-binding domain of a transcriptional factor. (freepatentsonline.com)
  • The present invention also provides a method for treating and/or preventing a disease or disorder related to such a transcriptional factor, comprising administering to the subject a therapeutically effective amount of a CDODN comprising two loop structures and a stem structure, wherein the stem structure comprises a nucleotide sequence capable of binding the DNA-binding domain of the transcriptional factor. (freepatentsonline.com)
  • 9. The CDODN of claim 6, which stem structure additionally comprises a nucleotide sequence capable of binding the DNA-binding domain of another transcription factor. (freepatentsonline.com)
  • 1991-=-). A PWM assigns a weight to each possible nucleotide at each position of a putative binding site and gives as a site score the sum of these weights. (psu.edu)
  • We find that a significant fraction of functionally constrained binding sites have been lost in a lineage-specific manner among three closely related yeast species. (nih.gov)
  • These multiple DNA-binding sites are known to be the only functionally shared and evolutionarily selected feature among these ICRs. (mendeley.com)
  • With this new technology, one can detect even elusive sites: for instance, scientists managed to detect binding sites concealed in experimental atomic structures or formed by several protein molecules for the ion channel, G protein-coupled receptor, and the epithelial growth factor, one of the most important drug targets. (phys.org)
  • What are the important characteristics of the progesterone-receptor binding site? (esrf.eu)
  • the site in the variable region of an antibody or T cell receptor that binds to an epitope of an antigen. (thefreedictionary.com)
  • A ribosome binding site , or ribosomal binding site ( RBS ), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of protein translation . (wikipedia.org)
  • Variations of the 5'-AGGAGG-3' sequence have been found in Archaea as highly conserved 5′-GGTG-3′ regions, 5 basepairs upstream of the start site. (wikipedia.org)
  • We found that for each of the nine TFs the estimated binding site distribution is closely approximated by a mixture of two components: a narrow peak, localized within 300-bp upstream of the TSS, and a distribution of almost uniform density within the tested region. (ovid.com)
  • However, it is not well understood why the imprinting control regions tend to maintain a high density of a particular transcription factor-binding site. (mendeley.com)
  • Intracellular consequences of Aβo binding to PrP C . PrP C and mGluR5 localize to lipid rafts (indicated in orange) in synapses. (nih.gov)
  • In these circumstances, the binding of carbon monoxide induces a conformation change that discourages heme from binding to oxygen, resulting in carbon monoxide poisoning. (wikipedia.org)
  • Surprising details were found for this particular structure where mifepristone was able to bind in the conformation expected for an agonist. (esrf.eu)
  • Distinguishing these RBPs or their binding residues is a major aim of structural biology. (mdpi.com)
  • Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. (mdpi.com)
  • 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. (mdpi.com)
  • The results suggest that tariquidar binds to a site within the drug-binding pocket at the interface between the TM segments of both structural wings. (mendeley.com)
  • The rationale was that a charged residue in the drug-binding pocket would disrupt hydrophobic interaction with tariquidar and inhibit its ability to rescue processing mutants or stimulate ATPase activity. (mendeley.com)
  • The addition of rough-type LPS to SFTPA1 blocked the interaction of SFTPA1 with its binding sites and the activation of MAPK1/3 and PTGS2 by SFTPA1. (bioone.org)
  • The low capacity site formed by direct apoA-I/ABCA1 interaction functions in a regulatory role, whereas the much higher capacity site generated by apoA-I/lipid interactions functions in the assembly of nascent HDL particles. (ahajournals.org)
  • In the current study, we have addressed some of these questions by characterizing the sites to which apoA-I binds during its interaction with ABCA1-expressing cells. (ahajournals.org)
  • Cell surface binding sites activated by this interaction have been studied using engineered variants of apoA-I. Importantly, ABCA1 activity creates 2 binding sites on the cell surface for apoA-I: a low capacity site created by direct apoA-I/ABCA1 interaction and a much higher capacity site that involves apoA-I/lipid interactions. (ahajournals.org)
  • Scatchard analysis revealed an apparent equilibrium dissociation constant (Kd) of 93.0 +/- 2.23 pM, and a maximal number of binding sites (Bmax) of 831.7 +/- 18.7 fmol/mg protein (mean +/- S.D., n = 4). (biomedsearch.com)
  • We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs). (nih.gov)
  • Though in recent years many new kinds of data have become available for identifying transcription factor binding sites (TFBSs) - ChIP-seq and DNase I hypersensitivity regions among them - sequence matching continues to play an important role. (bioconductor.org)
  • The HIV primer binding site is a structured RNA element in the genomes of retroviruses to which tRNA binds to initiate reverse transcription. (wikipedia.org)
  • We will see, however, that even this small collection of co-regulated genes of similar function exhibits considerable regulatory complexity, with (among other things) activators and repressors competing to bind to the same DNA promoter sequence. (bioconductor.org)
  • 4. The transgenic mouse of claim 1 , wherein said transcriptional regulatory element comprises two MEF2 binding sites. (google.com)
  • Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. (frontiersin.org)
  • Multiple YY1 and CTCF binding sites in im. (mendeley.com)
  • Known imprinting control regions (ICRs) contain unusual tandem arrays of DNA-binding sites for transcription factors, including YY1 for the Peg3, Gnas, and Xist/Tsix domains and CTCF for the H19/Igf2 domain. (mendeley.com)
  • Platelet [3H]paroxetine binding to 5-HT uptake sites in Alzheimer's disease. (diva-portal.org)
  • Platelet serotonin (5-hydroxytryptamine, 5-HT) uptake sites were studied in a control group (n = 30) and an Alzheimer group (n = 40) using [3H]paroxetine as radioligand. (diva-portal.org)
  • Thus even though several previous studies have demonstrated marked atrophy of 5-HT containing neurites and 5-HT uptake sites in Alzheimer's disease, these findings are not found in the periphery on platelets. (diva-portal.org)
  • However, in contrast to competitive and uncompetitive inhibitors, mixed inhibitors bind to the allosteric site. (wikipedia.org)
  • Substrates, transition states, and products can bind to the active site, as well as any competitive inhibitors. (wikipedia.org)
  • Binding sites for Aβ monomers or oligomers are indicated with arrows when specific sites are known to mediate binding or with brackets when less information is available. (nih.gov)
  • How you choose to bind or map a user interface is specific, based on your technology such as web forms, MVC, WinForms, etc. (codeproject.com)
  • published 20 years ago already contained evidence for the involvement of transposable elements in spreading species-specific p53 binding sites. (frontiersin.org)
  • Find support for a specific problem on the support section of our website. (mdpi.com)
  • The questions asked on the site are specific and ones that students really care about, says Gannett. (edweek.org)
  • Side reactions are also discouraged by this specific binding. (wikipedia.org)
  • Closed toe bindings are usually meant for a specific rider or for riders with the same size foot. (jobesports.com)
  • In fact, their binding is more specific and differs from factor to factor (e.g., cf. (psu.edu)
  • We hypothesized that polymorphisms in microRNA (miRNA) response elements (MRE-SNPs) that either disrupt a miRNA binding site or create a new miRNA binding site can affect the allele-specific expression of target genes. (harvard.edu)
  • An NMR method was developed for determining binding sites of small molecules on human serum albumin (HSA) by competitive displacement of (13)C-labeled oleic acid. (uniprot.org)
  • The optimal distance between the RBS and the start codon is variable - it depends on the portion of the SD sequence encoded in the actual RBS and its distance to the start site of a consensus SD sequence. (wikipedia.org)
  • The identification of RBSs is used to determine the site of translation initiation in an unannotated sequence. (wikipedia.org)
  • Halgren, T. (2007) New Method for Fast and Accurate Binding-Site Identification and Analysis. (scirp.org)
  • Jalencas, X. and Mestres, J. (2013) Identification of Similar Binding Sites to Detect Distant Polypharmacology. (scirp.org)
  • These data indicate that particular evolutionary patterns and distinct sequence properties on scales much larger than standard transcription factor-binding sites may play an important role in Polycomb recruitment and transcriptional regulation of key developmental genes. (pnas.org)
  • A Java application that reuires a local installation of a database that provides binding site information (eg the Public Transfac 6.0 data). (warwick.ac.uk)
  • We will see how to create prompts and validators, as well as bind data to controls in a compile-time checked manner. (codeproject.com)
  • We developed a method for estimating the positional distribution of transcription factor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs: OCT4, SOX2, NANOG, HNF1A, HNF4A, HNF6, FOXA2, USF1 and CREB1. (ovid.com)
  • Message Body (Your Name) thought you would like to see the PNAS web site. (pnas.org)
  • When Aβo bind PrP C , signaling through mGluR5 causes increased intracellular calcium, increased phosphorylation of eEF2, changes in NMDAR activity and trafficking, and increased phosphorylation of Fyn. (nih.gov)
  • Transcription factor binding sites have therefore diverged substantially faster than ortholog content. (sciencemag.org)
  • This site uses cookies to help personalise content, tailor your experience and to keep you logged in if you register. (cpanel.net)
  • This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. (rcsb.org)
  • The 3 crystal systems differ in binding-cavity geometry, due to the conformational flexibility of the light and heavy chains. (springer.com)
  • The binding event is often, but not always, accompanied by a conformational change that alters the protein's function. (wikipedia.org)
  • For example, in the context of protein function, the binding of calcium to troponin in muscle cells can induce a conformational change in troponin. (wikipedia.org)
  • In our collection we have a diverse range of open toe bindings and closed toe bindings for every type and level of rider. (jobesports.com)
  • Eukaryotic ribosomes are known to bind to transcripts in a mechanism unlike the one involving the 5' cap, at a sequence called the internal ribosome entry site . (wikipedia.org)
  • Coenzyme A transferase binding site (IPR004163) Coenzyme A (CoA) transferases belong to an evolutionary conserved family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. (ebi.ac.uk)