Consumer Health Information: Information intended for potential users of medical and healthcare services. There is an emphasis on self-care and preventive approaches as well as information for community-wide dissemination and use.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Molecular Sequence Data: 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.Protein Binding: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Amino Acid 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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Kinetics: The rate dynamics in chemical or physical systems.Binding, Competitive: 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.Promoter Regions, Genetic: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Protein Structure, Tertiary: 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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Ligands: 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)Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.DNA: 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).Recombinant Proteins: Proteins prepared by recombinant DNA technology.Mutation: 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.Escherichia coli: 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.Protein Conformation: 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).Structure-Activity Relationship: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Binding Sites, Antibody: 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.Bacterial Proteins: Proteins found in any species of bacterium.Recombinant Fusion Proteins: 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.Gene Expression Regulation: 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.Transfection: 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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Consensus Sequence: 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.Protein Structure, Secondary: 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.Cloning, Molecular: 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.DNA Footprinting: 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)Nuclear Proteins: 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.Sp1 Transcription Factor: 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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Radioligand Assay: Quantitative determination of receptor (binding) proteins in body fluids or tissue using radioactively labeled binding reagents (e.g., antibodies, intracellular receptors, plasma binders).Repressor Proteins: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Receptors, Cell Surface: 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.Macromolecular Substances: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Conserved Sequence: 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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Cells, Cultured: 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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Sequence Alignment: 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.Affinity Labels: 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.Rabbits: 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.Peptides: 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.Molecular Weight: The sum of the weight of all the atoms in a molecule.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Chromatin Immunoprecipitation: 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.Calcium: 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.RNA, Messenger: 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.Amino Acid Motifs: 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.Adenosine Triphosphate: 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.Deoxyribonuclease I: 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.HeLa Cells: 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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.DNA Primers: 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.Magnesium: 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.Proteins: 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.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Electrophoretic Mobility Shift Assay: 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.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Molecular Structure: 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.Magnetic Resonance Spectroscopy: 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).Oligodeoxyribonucleotides: 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.Iodine Radioisotopes: Unstable isotopes of iodine that decay or disintegrate emitting radiation. I atoms with atomic weights 117-139, except I 127, are radioactive iodine isotopes.Plasmids: 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.Models, Biological: 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.Chromatography, Affinity: 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)Thermodynamics: 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)Cattle: 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.Amino Acid Substitution: 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.Membrane Proteins: 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.Tumor Cells, Cultured: 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.Autoradiography: 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)Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Genes, Reporter: 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.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Allosteric Regulation: 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.Sequence Homology, Nucleic Acid: 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.Cross-Linking Reagents: 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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Response Elements: 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.Saccharomyces cerevisiae: 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.
Spelsberg TC, Steggles AW, O'Malley BW (2008). "Progesterone-binding components of chick oviduct. 3. Chromatin acceptor sites ... This article is based on the transcript of an animated course on the Nuclear Receptor Signaling Atlas (NURSA) website entitled ... might bind to these regions and silence receptors in cells. Again, using the yeast two-hybrid screen, two corepressors were ... A comprehensive database of nuclear receptor coregulators can be found at the Nuclear Receptor Signaling Atlas website. The ...
... has built-in web scraping to automatically download metadata information and online artwork from sites like IMDb, Discogs ... Are website terms of use binding contracts?". chillingeffects.org. 20 August 2007. Retrieved 20 August 2007. "Boxee Privacy ... As it stated, Boxee would have loved for the Boxee Box to be open to other software, but ultimately, they were bound by ... Nuu has since discontinued NUU Player development and has removed any mention of it from their web site. As a partially open ...
For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical ... 34 (Web Server issue): W369-373. doi:10.1093/nar/gkl198. PMC 1538909 . PMID 16845028. Weirauch; et al. (2013). "Evaluation of ... "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16-23. doi:10.1093/bioinformatics/16.1.16. PMID ... An example is the N-glycosylation site motif: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by ...
There are two ATP binding sites; a substrate site where the phosphate transfer occurs, and an allosteric site where allosteric ... AMP and ADP are both positive effectors of 1-phosphofructokinase and bind allosterically to activate the reaction. This ... In addition to the catalytic binding sites, there are 4 additional binding sites for allosteric regulation. 1- ... 1-Phosphofructokinase is a tetramer of 4 identical subunits that each have a catalytic site. ...
"Pigment epithelium-derived factor binds to hyaluronan. Mapping of a hyaluronan binding site". The Journal of Biological ... Furthermore, both of these coagulation proteases also contain binding sites (called exosites) for heparin. Heparin, therefore, ... thyroxine-binding globulin, cortisol-binding globulin) and molecular chaperoning (HSP47). The term serpin is used to describe ... The binding event then leads to downstream signalling by the receptor. The S to R transition is therefore used to alert cells ...
The primer binding site (PBS) of this HERV discovered is similar to avian retroviral PBSs, which uses tRNATRP, this HERV was ... and transcription factor binding sites. The 5' U3 region acts as a promoter and the 3' R acts as a poly A signal. It would be ... In fact by doing a Chip-seq analysis of HERV-W LTR's it was found that ¼ of HERV-W LTR's can be bound by transcription factor ... and a primer-binding site (PBS). The pol and gag ORFs are not replication competent due to frame shifts and stop codons but the ...
These binding sites are asymmetric, such that when a Tus-Ter complex (Tus protein bound to a Ter site) is encountered by a ... In E. coli, Tus binds to 10 closely related sites encoded in the chromosome. These sites bind 23 base-pairs. The 10 sites are ... The bound Tus protein effectively halts DNA polymerase movement. Tus helps end DNA replication in prokaryotes. ... Tus, also known as terminus utilization substance, is a protein that binds to terminator sequences and acts as a counter- ...
For example, the binding site of neurosteroids in the GABAA receptor is not known and barbiturates bind at a beta subunit that ... Hosie AM, Wilkins ME, Smart TG (Oct 2007). "Neurosteroid binding sites on GABA(A) receptors". Pharmacology & Therapeutics. 116 ... Benzodiazepines function by binding to the benzodiazepine site on most, but not all, GABAA receptors. GABAA modulation by ... Unlike GABAA receptor agonists, GABAA PAMs do not bind at the same active site as the γ-Aminobutyric acid (GABA) ...
HATs are part of a multiprotein complex that is recruited to chromatin when activators bind to DNA binding sites. Acetylation ... The idea being that whenever the site was methylated, only the methylation insensitive enzyme could cleave at that position. By ... Hypersensitive sites most often represent promoters regions, which require for DNA to be accessible for DNA binding ... "Chromatin patterns at transcription factor binding sites". Nature Encode. ...
Each end of the fork contains an identical antigen binding site. The various regions and domains of a typical IgG are depicted ... Each IgG has two antigen binding sites. Antibodies are major components of humoral immunity. IgG is the main type of antibody ... Given the opposing properties of the IgG subclasses (fixing and failing to fix complement; binding and failing to bind FcR), ... The Fc regions of IgGs bear a highly conserved N-glycosylation site. The N-glycans attached to this site are predominantly core ...
O protein binds the ori site, and P protein binds the DnaB subunit of the host replication machinery as well as binding O. This ... Both operators have three binding sites for cI: OL1, OL2, and OL3 for PL, and OR1, OR2 and OR3 for PR. cI binds most favorably ... N binds to the two Nut (N utilisation) sites, one in the N gene in the PL reading frame, and one in the cro gene in the PR ... It binds DNA in the helix-turn-helix binding motif. It regulates the transcription of the cI protein and the Cro protein. The ...
Snyder, K, et al.. Domain-based small molecule binding site annotation. BMC Bioinformatics 7: 152 (2006) Bader, GD, et al. BIND ... SMID-BLAST is a tool developed to annotate known small-molecule binding sites as well as to predict binding sites in proteins ... In total, 901 taxa were included by September 2004 and BIND has been split up into BIND-Metazoa, BIND-Fungi, and BIND-Taxroot. ... As BIND is a constantly growing database, all components of BIND track updates and changes. BIND is based on a data ...
The other domain is a carboxy-terminal domain that contains the substrate binding site and amino acids that are necessary for ... All three effectors (malate, oxaloacetate and citrate) bind to the same putative allosteric site. Recent studies of ... The active sites in these dimeric proteins are well separated from each other. Because malate dehydrogenase is closely tied to ... Evidence for an allosteric citrate-binding site". The Journal of Biological Chemistry. 257 (22): 13233-9. PMID 7142142. Gelpí ...
Structural aspects of guanine-nucleotide-binding sites". European Journal of Biochemistry / FEBS. 155 (1): 167-71. doi:10.1111/ ... As an elongation factor, it is known to mediate the recruitment of aminoacyl-tRNA to the A-site of the 80S ribosome during ... eEF1A putatively binds actin and microtubules at synapses to modulate the cytoskeleton. In neurons, this ability allows for ... Zhu J, Hayakawa A, Kakegawa T, Kaspar RL (Oct 2001). "Binding of the La autoantigen to the 5' untranslated region of a chimeric ...
This calcium uncovers the actin binding sites. When the muscle no longer needs to contract, the calcium ions are pumped from ... ATP binds to the cross bridges between myosin heads and actin filaments. The release of energy powers the swiveling of the ... detach and then reattach to the nearest active site of the actin filament. This is called a ratchet type drive system. This ... Larger structures along the myosin filament called myosin heads are used to provide attachment points on binding sites for the ...
Because binding to CD4 alone can sometimes result in gp120 shedding, gp120 must next bind to co-receptor CCR5 in order for ... "The BBXB motif of RANTES is the principal site for heparin binding and controls receptor selectivity". The Journal of ... Structural aspects of guanine-nucleotide-binding sites". European Journal of Biochemistry / FEBS. 155 (1): 167-71. doi:10.1111/ ... either through binding to alternative domains of CCR5, or by binding to the receptor at a higher affinity. However, because ...
The FAD and NADP binding sites of the enzyme were predicted by sequence analysis of the enzyme. While the FAD-binding site has ... Adrenodoxin reductase has two domains that bind NADPH and FAD separately. ... that is similar to other Rossmann folds in FAD and NAD binding sites, the NADPH binding site consensus sequence differs from ... Identification of NADP-binding sites in oxidoreductases". European Journal of Biochemistry / FEBS. 180 (2): 479-84. doi:10.1111 ...
Hence these types of binding sites on proteins are generally thought to be undruggable but there has been some progress (by ... Seco J, Luque FJ, Barril X (March 2009). "Binding Site Detection and Druggability Index from First Principles". J. Med. Chem. ... that is known to or is predicted to bind with high affinity to a drug. Furthermore, by definition, the binding of the drug to a ... A high-throughput method for detection of drug binding sites". J. Med. Chem. 53 (15): 5858-67. doi:10.1021/jm100574m. PMID ...
Dutta-Roy, Asim K.; Hoque, Lutful; Paterson, Brian J. (1993). "Prostaglandin-E1-binding sites in rabbit erythrocyte membranes ... "Asim K. Duttaroy- Home Page". [self-published source?] "Provexis- Home Page". O'Kennedy, N; Crosbie, L; Van Lieshout, M; Broom ... "Placental membrane fatty acid-binding protein preferentially binds arachidonic and docosahexaenoic acids". Life Sciences. 63 (4 ... "Placental membrane fatty acid-binding protein preferentially binds arachidonic and docosahexaenoic acids". Life Sciences. 63 (4 ...
... the ratio of the concentration of bound ligand to total antibody concentration and n is the maximum number of binding sites per ... Thus these regions are the paratope, the binding site of an antigen. The rest of the V region between the hypervariable regions ... The strength of an individual interaction between a single binding site on an antibody and its target epitope is termed the ... Since the antibody necessarily has two paratopes, and in many circumstances complex binding occurs, the multiple binding ...
The binding-sites are located on the surface within the loops C1-C3 and C5-C6. Long consecutive arrays of laminin EGF-like ... In muscle, it binds to alpha dystroglycan and integrin alpha7-beta1 via the G domain, and via the other end binds to the ... modules of laminin gamma1 chain harboring the nidogen binding site". Journal of Molecular Biology. 257 (3): 644-57. doi:10.1006 ... Yurchenco PD, Cheng YS (August 1993). "Self-assembly and calcium-binding sites in laminin. A three-arm interaction model". The ...
... 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) and Prediction of Immunoglobulin Structure (PIGS) enables computational ... Since an antibody has at least two paratopes, it can bind more than one antigen by binding identical epitopes carried on the ... A typical human B cell will have 50,000 to 100,000 antibodies bound to its surface. Upon antigen binding, they cluster in large ...
Evidence for cooperative binding through two discrete sites". J. Biol. Chem. 275 (9): 6479-89. doi:10.1074/jbc.275.9.6479. PMID ... Morinaka K, Koyama S, Nakashima S, Hinoi T, Okawa K, Iwamatsu A, Kikuchi A (Dec 1999). "Epsin binds to the EH domain of POB1 ... 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635-48. doi:10.1016/ ... "Entrez Gene: EPN1 epsin 1". Drake MT, Downs MA, Traub LM (2000). "Epsin binds to clathrin by associating directly with the ...
... binding site seems essentially localized in neurons but could also be present in glial cells, endothelial cells and/or ... The distribution of BmTx3 binding sites is heterogeneous; a high density is found in the caudate-putamen and accumbens nucleus ... As BmTx3 seems to use both sides to bind to different potassium channels, it might be an evolutionary transient between the two ... Vacher, H. (2001). "A new class of scorpion toxin binding sites related to an A-type K+ channel: pharmacological ...
DTIs that bind to the anion-binding site have shown to inactivate thrombin without disconnecting thrombin from fibrin, which ... Unlike the hirudins, bivalirudin is only partially (about 20%) excreted by the kidneys, other sites such as hepatic metabolism ... The active site is the binding site for the globular amino-terminal domain and exosite 1 is the binding site for the acidic ... It binds to the active site on thrombin. The X-ray crystal structure shows that the piperidine ring binds in the S2 pocket and ...
... or into molecules that bind to receptors or other sites of drug action. Such labelled compounds are known as radiotracers. PET ... The presence of the small on-site cyclotron promises to expand in the future as the cyclotrons shrink in response to the high ... Laruelle, M (2000). "Imaging Synaptic Neurotransmission with in Vivo Binding Competition Techniques: A Critical Review". ... Radioligands that bind to dopamine receptors (D1,[14] D2 receptor,[15][16] reuptake transporter), serotonin receptors (5HT1A, ...
Internal ribosome entry site (IRES)[edit]. Eukaryotic ribosomes are known to bind to transcripts in a mechanism unlike the one ... Bacterial mRNA are usually polycistronic and contain multiple ribosome binding sites. Translation initiation is the most highly ... A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA ... 9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ...
When more than one type of ligand can bind to a binding site, competition ensues. Binding sites also exhibit chemical ... Binding sites on proteins can sometimes recognize other proteins. When a binding site of one protein identifies with another ... A more specific type of binding site is the transcription factor binding site present on DNA. Short, recurring patterns in DNA ... Binding sites also exist on antibodies as specifically coded regions that bind antigens based upon their structure. Several ...
A PCR primer binding site is a site where a polymerase chain reaction (PCR) primer binds, to prime duplication of a complement ... c. 2002). "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites". Biochemistry. New York: W. H. Freeman ... 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 ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... Fumarate reductase/succinate dehydrogenase, FAD-binding site (IPR003952) In bacteria two distinct, membrane-bound, enzyme ... Sites * Active site (132) * Binding site (76) * Conserved site (688) * PTM (17) ... Sulphate/thiosulphate-binding site (IPR034408) Sulphate-binding protein (gene sbp or sbpA) and thiosulphate-binding protein ( ...
... thought you would like to see the PNAS web site. ... we identify show extensive overlap with regions bound by ... 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 ...
We studied a data set of structurally similar interfaces that bind to proteins with different binding-site structures and ... Our multipartner protein interface clusters enable us to address questions like: What makes a given site bind differen... ... We studied a data set of structurally similar interfaces that bind to proteins with different binding-site structures and ... are shared proteins with binding sites capable of transient binding to multipartners, linking higher-order networks. © 2007 ...
However, this type of site characteristic for Ca2+ binding regions [17] was found only once in our data set. There are also ... 1 positions from the Asp residues which bind Mn2+ relatively to those which do not bind that ion. It means that there is ... 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. ...
ABC (ATP-binding cassette) transporters are clinically important because drug pumps like P-glycoprotein (P-gp, ABCB1) confer ... Here, we show through cross-linking studies that tariquidar most likely binds to sites within the transmembrane (TM) segments ... The results suggest that tariquidar binds to a site within the drug-binding pocket at the interface between the TM segments of ... Mapping the binding site of the inhibitor tariquidar that stabilizes the first transmembrane domain of P-glycoprotein. *Loo T ...
We recently reported on a mutant of CV-N that contained a single functional mannose-binding site, domain B, showing that ... protein binds with high affinity to mannose-rich oligosaccharides on the surface of gp120 through two quasi-symmetric sites, ... Five site mutated Cyanovirin-N with Mannose dimer bound. *DOI: 10.2210/pdb2RDK/pdb ... Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox. ...
One may measure the amount of free label versus bound label to determine binding or inhibition of binding. ... This signaling pathway is directed at two MEF2 binding sites in the NGFI-B promoter. There is no change in DNA binding activity ... but did not bring the 32P-labeled DNA binding site into the complex (FIG. 14D). The DNA binding site also was not captured by ... site. GST-HDAC4 interacted with 35S-labeled MEF2C bound to its 32P-labeled site (FIG. 14D). In contrast, there was no ...
... looks at an important RNA binding protein called LIN28, which is implicated in pluripotency and reprogramming as well as in ... Home / Newsroom / Releases / Binding Sites for LIN28 Protein Found in Thousands of Human Genes ... "Surprisingly, we discovered that LIN28 not only binds to the non-coding microRNAs, but can also bind directly to thousands of ... "But we now see that LIN28 can, in essence, bypass let-7 and find many, many other binding sites - perhaps with the same adverse ...
PubMed journal article Characterization of the VirG binding site of Agrobacterium tumefacien were found in PRIME PubMed. ... Base SequenceBinding SitesChromosome DeletionChromosomes, BacterialConsensus SequenceDNA Mutational AnalysisDNA, BacterialGene ... The regulatory VirG protein specifically binds to a cis-acting regulatory sequence involved in transcriptional activation of ... Pazour GJ, Das A. Characterization of the VirG Binding Site of Agrobacterium Tumefaciens. Nucleic Acids Res. 1990 Dec 11;18(23 ...
... sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. ... and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding ... The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these ... In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein ...
Your Name) thought you would like to see this page from the Science web site. ... The domains of TFIIB required for binding to the TFIID-promoter complex and for transcription initiation have been determined. ... Transcription factor TFIIB sites important for interaction with promoter-bound TFIID. By S Yamashita, K Hisatake, T Kokubo, K ... Transcription factor TFIIB sites important for interaction with promoter-bound TFIID. By S Yamashita, K Hisatake, T Kokubo, K ...
On native protein blots, hrpZPph bound to a bean protein with similar pI as the protein recognized by the peptide antiserum. ... To localize the peptide-binding site, the hrpZPph gene was mutagenized with randomly placed 15-bp insertions, and the mutant ... Mutations that inhibited peptide-binding localized to the central region of hrpZPph, which is separate from the previously ... Antiserum raised against one of the hrpZPph-binding peptides recognized small proteins in bean, tomato, parsley, and ...
Top20Sites.com is the leading directory of popular Binding Service, Carpet Pullers, Carpet Binding, & Binding Equipment sites. ... Looking for the webs Top Rug Binding Sites? ... Home > Rug Binding Sites > Top Rug Binding Sites. Top Binding ... Select narrow or wide binding and from mitered or squared corners. Bind those pieces of... ... Carpet Binding Sites , Carpet Binding , Binding Equipment Sites , Binding Equipment , Binding Supplies Sites , Binding Supplies ...
Looking for the webs Top Binding Services Sites? Top20Sites.com is the leading directory of popular Bible Bookbinding, Bible ... Home > Binding Services Sites > Top Binding Services Sites. Top Bible Bookbinding Sites , Top Bible Binding Sites , Top Self ... designer book bindings, thesis binding, and an online shop for beautiful handmade gifts and exquisite, traditionally bound one- ... Bible Bookbinding Sites , Bible Bookbinding , Bible Binding Sites , Bible Binding , Self Publishing Sites , Self Publishing , ...
During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and ... HSA, different from BSA also binds directly to the gold surface by particularly flexible protein segments that were identified ... Different binding sites of serum albumins in the protein corona of gold nanoparticles G. P. Szekeres and J. Kneipp, Analyst, ... Different binding sites of serum albumins in the protein corona of gold nanoparticles ...
Inferring binding energies from selected binding sites by Yue Zhao David Granas - PLoS Comput. Biol , 2009 ... as determined by polymerase chain reaction-mediated binding site selection, whereas E-2 would not be predicted to bind these ... 1991-=-). A PWM assigns a weight to each possible nucleotide at each position of a putative binding site and gives as a site ... Mutations at three sites have larger effects in muscle than nonmuscle cells; an AlT-rich site mutation has a pronounced effect ...
These acids are part of the glycoproteins on the cell surface that identify which cells a flu virus will bind to and how easily ... Biochemical studies verified the relevance of the binding site and demonstrated a preference of CVA24v for α2,6-linked glycans ... The novel capsid-binding antiviral pleconaril inhibits in vitro replication of most rhinoviruses and entero-viruses. Oral ... We determined the structure of the CVA24v to 1.40 Å resolution, screened different glycans bearing Neu5Ac for CVA24v binding, ...
Results: Shape and physico-chemical properties of the PGH2 binding sites of the four prostanoid synthases were analyzed and ... Moreover, currently no crystal structure of complexes bound with PGH2 has been reported. Hence, understanding the interactions ... The comparison showed seven physico-chemical features that are common to the four PGH2 binding sites. However this common ... This study provides models with predicted pockets for the binding of PGH2 with PGD, PGE, PGF and PGI Synthases. The results ...
Membrane-bound transcription factor site-2 protease, EC 3.4.24.85 (Endopeptidase S2P) (Sterol regulatory element-binding ... Integrated resource of protein families, domains and functional sites. More...InterProi. View protein in InterPro. IPR001193 ... Membrane-bound transcription factor site-2 proteaseImported. ,p>Information which has been imported from another database using ... tr,B9ZVQ3,B9ZVQ3_HUMAN Membrane-bound transcription factor site-2 protease OS=Homo sapiens OX=9606 GN=MBTPS2 PE=1 SV=1 ...
Binds to DNA replication terminator sequences (terA to terF) to prevent the passage of replication forks. The termination ... Integrated resource of protein families, domains and functional sites. More...InterProi. View protein in InterPro. IPR008865 ... DNA replication terminus site-binding proteinAdd BLAST. 309. Proteomic databases. jPOST - Japan Proteome Standard Repository/ ... DNA replication terminus site-binding proteinUniRule annotation. ,p>Manual validated information which has been generated by ...
These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which ... as opposed to predicting individual binding sites. We explore two implementations of this concept, based on Kolmogorov-Smirnov ... as opposed to predicting individual binding sites. We explore two implementations of this concept, based on Kolmogorov-Smirnov ... These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which ...
... but one receptor that binds leukotriene and sends immune cells to infection sites appears to bind a double ligand. This binds ... Computer Simulation of Receptors Reveals a New Ligand-Binding Site. By Swiss Federal Institute of Technology in Lausanne July ... Scientists at the Swiss Federal Institute of Technology in Lausanne used a computer simulation to discover a novel binding site ... The researchers determined the site can be leveraged pharmacologically to comprehend ligand binding and activation processes, ...
  • These hyperconserved CpG domains largely coincide with domains bound by Polycomb repressive complex 2 in undifferentiated human embryonic stem cells and are almost exclusively present near genes whose products are involved in the regulation of embryonic development. (pnas.org)
  • These hyperconserved CpG domains (HCGDs) we identify show extensive overlap with regions bound by Polycomb repressive complex 2 (PRC2) and are observed almost exclusively at genes related to the regulation of embryonic development. (pnas.org)
  • The discovery of thousands of precise binding sites for LIN28 within human genes offers a novel look at the role this protein plays in development and disease processes. (ucsd.edu)
  • 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)
  • 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)
  • Mangelsdorf, D.J., Umesono, K., Kliewer, S.A., Borgmeyer, U. and Ong, E.S. (1991) Evans RMA Direct Repeat in the Cellular Retinol-Binding Protein Type II Gene Confers Differential Regulation by RXR and RAR. (scirp.org)
  • 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)
  • This is especially useful when multiple start codons are situated around the potential start site of the protein coding sequence. (wikipedia.org)
  • Studying embryonic stem cells and somatic cells stably expressing LIN28, the researchers defined discrete binding sites of LIN28 in 25 percent of human transcripts. (ucsd.edu)
  • Serine hydroxymethyltransferase, pyridoxal phosphate binding site (IPR019798) Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs. (ebi.ac.uk)
  • 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)
  • Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site (IPR001216) Cysteine synthase (CSase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. (ebi.ac.uk)
  • 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 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)
  • A study led by researchers at the UC San Diego Stem Cell Research program and funded by the California Institute for Regenerative Medicine (CIRM) looks at an important RNA binding protein called LIN28, which is implicated in pluripotency and reprogramming as well as in cancer and other diseases. (ucsd.edu)
  • 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)
  • To identify RAR/RXR heterodimer-binding sites in the human genome, we performed a modified yeast one-hybrid assays and identified 193 RAR/RXR heterodimer-binding fragments in the human genome. (scirp.org)
  • 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)
  • In silico docking studies have identified several potential tariquidar-binding sites. (mendeley.com)
  • Here, we show through cross-linking studies that tariquidar most likely binds to sites within the transmembrane (TM) segments located in one wing or at the interface between the two wings (12 TM segments form 2 divergent wings). (mendeley.com)
  • Surprisingly, we discovered that LIN28 not only binds to the non-coding microRNAs, but can also bind directly to thousands of messenger RNAs," said first author Melissa Wilbert, a doctoral student in the UC San Diego Biomedical Sciences graduate program. (ucsd.edu)
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