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.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.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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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).Kinetics: The rate dynamics in chemical or physical systems.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.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.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.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.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.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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.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.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.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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.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.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.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.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).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)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.Bacterial Proteins: Proteins found in any species of bacterium.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.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.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.Lysine: An essential amino acid. It is often added to animal feed.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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Histidine: An essential amino acid that is required for the production of HISTAMINE.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).Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Drug Residues: Drugs and their metabolites which are found in the edible tissues and milk of animals after their medication with specific drugs. This term can also apply to drugs found in adipose tissue of humans after drug treatment.Circular Dichroism: 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)Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.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.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.Hydrogen-Ion Concentration: 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)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.Point Mutation: 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.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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Tryptophan: 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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Pesticide Residues: Pesticides or their breakdown products remaining in the environment following their normal use or accidental contamination.Alanine: A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.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.Hydrogen Bonding: 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.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.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.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Trypsin: 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.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.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.Aspartic Acid: One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.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.Molecular Weight: The sum of the weight of all the atoms in a molecule.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Nuclear Magnetic Resonance, Biomolecular: 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.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)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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.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.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.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.Serine: A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.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.DNA, Complementary: 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.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.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.COS Cells: 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).)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.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.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.Peptide Mapping: 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.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.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).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.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.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).Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.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.Static Electricity: The accumulation of an electric charge on a objectEnhancer 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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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)Molecular Conformation: The characteristic three-dimensional shape of a molecule.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.Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.Temperature: 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.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.Asparagine: A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from ASPARTIC ACID and AMMONIA by asparagine synthetase. (From Concise Encyclopedia Biochemistry and Molecular Biology, 3rd ed)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.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.Epitopes: Sites on an antigen that interact with specific antibodies.Diethyl Pyrocarbonate: Preservative for wines, soft drinks, and fruit juices and a gentle esterifying agent.Structural Homology, Protein: 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.CHO Cells: 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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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.Arginine: An essential amino acid that is physiologically active in the L-form.Chickens: 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.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.Oligopeptides: Peptides composed of between two and twelve amino acids.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Cyanogen Bromide: Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Zinc: 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.Carbohydrate Sequence: The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.Threonine: An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.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.Glycine: A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Signal Transduction: 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.Protein Interaction Domains and Motifs: 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.Protein Subunits: 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.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Species Specificity: 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.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Oligosaccharides: Carbohydrates consisting of between two (DISACCHARIDES) and ten MONOSACCHARIDES connected by either an alpha- or beta-glycosidic link. They are found throughout nature in both the free and bound form.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Xenopus laevis: 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.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Saccharomyces cerevisiae Proteins: 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.Spectrophotometry, Ultraviolet: Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Surface Plasmon Resonance: 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.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.Computational Biology: 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.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.Enzyme Activation: Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.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)Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.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.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.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.Glutamic Acid: A non-essential amino acid naturally occurring in the L-form. Glutamic acid is the most common excitatory neurotransmitter in the CENTRAL NERVOUS SYSTEM.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.Cercopithecus aethiops: A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Viral Proteins: Proteins found in any species of virus.Lectins: 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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Glycosylation: The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Polymerase Chain Reaction: 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.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Oocytes: 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).Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Chymotrypsin: A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side.Fungal Proteins: Proteins found in any species of fungus.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Protein Engineering: Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.Photoaffinity Labels: 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.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)Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Cell Nucleus: 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)Protons: Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.Oligonucleotides: 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)Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.Genes, Bacterial: The functional hereditary units of BACTERIA.Ion Channel Gating: The opening and closing of ion channels due to a stimulus. The stimulus can be a change in membrane potential (voltage-gated), drugs or chemical transmitters (ligand-gated), or a mechanical deformation. Gating is thought to involve conformational changes of the ion channel which alters selective permeability.Biological Transport: The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Cations, Divalent: Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.Glutathione Transferase: A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.Calorimetry: 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)Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
Beta-ketoacyl-(acyl-carrier-protein) synthase III... mtFabH contains residues along the acyl-CoA binding channel that preferentially select for longer-chain substrates peaking with ... Davies C, Heath RJ, White SW, Rock CO (2000). "The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl ... Techniques for screening efficacy of inhibitors are available. In 2005, tuberculosis caused approximately 1.6 million deaths ... While much has been learned from these structural studies and rational design is an excellent approach to develop novel ...
7 kb upstream that contains binding sites for cyclic AMP response element-binding protein (CREB), myocyte enhancer factor 2 ( ... Neurobiology of Learning and Memory. 106: 177-84. doi:10.1016/j.nlm.2013.08.009. PMID 24012642. "Arc protein 'could be key to ... or catFISH technique (see fluorescent in situ hybridization). The Arc gene, located on chromosome 15 in the mouse[1], ... the translated protein is 396 residues in length, with an N-terminus located at amino acids 1-25, a C-terminus at 155-396 (note ...
All known blockers compete for roughly the same binding site, the pore, in all subtypes. This provides a physical blockage to ... CK2 serves to phosphorylate the SKCa-bound CaM at the T80 residue, rather than the channel helices themselves, to reduce ... In addition, techniques have been used to modulate SK channels in order to alter the dopamine phenotype of neurons. After the ... SK channels are thought to be involved in synaptic plasticity and therefore play important roles in learning and memory. SK ...
... has a very different sequence from another sodium channel binding sea anemone toxin, ATX II, which is produced by the ... The patterning of cleavage sites targeted during maturation of the peptide suggest that the active quaternary structure might ... A better understanding of these differences might offer insights about the function of particular amino acid residues. Despite ... The resulting pellet was purified using the techniques liquid chromatography, gel filtration, and chromatofocusing. The team ...
The site of phosphorylation is the serine at the 776th residue in ataxin 1. Similar to those that lack 14-3-3 proteins, mice ... Resonant Recognition Modeling of the ataxin 1 protein has shown possible binding sites for growth factor independent ... A similar technique is RNA interference or RNAi. Instead of complimentary 'antisense' strands of RNA, RNAi uses very small ... Ataxin-null mice are shown to exhibit reduced motor and spatial learning, suggesting ataxin 1 plays a role in synaptic ...
A missense mutation on the NET gene (SLC6A2) was discovered in which an alanine residue was replaced with a proline residue ( ... Yavich L, Forsberg MM, Karayiorgou M, Gogos JA, Männistö PT (Sep 2007). "Site-specific role of catechol-O-methyltransferase in ... Via positron emission tomography imaging technique, NET has been selectively investigated. 11C [email protected] and 18F-MeNER are two ... NE, also known as noradrenaline (NA), has an important role in controlling mood, arousal, memory, learning, and pain perception ...
There is a highly conserved sequence in roughly three quarters of all ORs that is a tripodal metal ion binding site, and ... de March CA, Yu Y, Ni MJ, Adipietro KA, Matsunami H, Ma M, Golebiowski J (July 2015). "Conserved Residues Control Activation of ... In addition, they generalised the learned avoidance behaviour to molecules which were not deuterated but did share a ... Deorphanization of odor receptors can be completed using electrophysiological and imaging techniques to analyze the response ...
The most common mechanism appears to be alteration of the target site, in particular as a defence against single site of action ... Unsourced material may be challenged and removed. (March 2009) (Learn how and when to remove this template message) ... Fungicide residues have been found on food for human consumption, mostly from post-harvest treatments.[5] Some fungicides are ... The effectiveness of this technique can be demonstrated by Metalaxyl, a phenylamide fungicide. When used as the sole product in ...
The DNA binding sites on RNA polymerase can be occupied by heparin, preventing the polymerase from binding to promoter DNA. ... In the image above: A = 1HPN (all IdoA(2S) residues in 2S0 conformation) Jmol viewer B = van der Waals radius space filling ... Jones & Bartlett Learning. p. X. ISBN 9781284057560. Rietschel, Robert L.; Fowler, Joseph F.; Fisher, Alexander A. (2008). ... Either chemical or enzymatic depolymerisation techniques or a combination of the two underlie the vast majority of analyses ...
Broad bandages should be applied from above the bite site all the way up the affected limb (towards the heart), then all the ... 1980) isolated a postsynaptic neurotoxin called pseudonajatoxin A. It has 117 amino acid residues and a high molecular weight ... According to the Australian Venom Research Unit, the pressure immobilization technique should always be used. The bite itself ... It causes irreversible blockade by firm binding to the acetylcholine receptors. Kellaway (1933), stated that P. textilis venom ...
For example, the method was used to identify cation binding sites on the Na+/K+ ATPase and to propose hypotheses about ... One newer method for model assessment relies on machine learning techniques such as neural nets, which may be trained to assess ... Some such methods can also produce a residue-by-residue assessment that identifies poorly scoring regions within the model, ... Ogawa, H; Toyoshima, C. (2002). "Homology modeling of the cation binding sites of Na+K+-ATPase". Proc Natl Acad Sci USA. 99 (25 ...
In this configuration, the sixth coordination site reserved for the oxygen is blocked by another histidine residue. When ... Hemoglobin bound to carbon monoxide is known as carboxyhemoglobin. This effect also plays a minor role in the toxicity of ... PHI Learning Pvt. Ltd. p. 218. ISBN 81-203-2455-2. Greenwood and Earnshaw, pp. 1074-5 Boehler, Reinhard (2000). "High-pressure ... Kohl, Walter H. (1995). Handbook of materials and techniques for vacuum devices. Springer. pp. 164-167. ISBN 1-56396-387-6. ...
The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site. ... This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques. The ... In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function ... This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the ...
However, the CO2 bound to hemoglobin does not bind to the same site as oxygen. Instead, it combines with the N-terminal groups ... Blood residue analysis is also a technique used in archeology. Blood is one of the body fluids that has been used in art. In ... not in citation given] http://www.redcrossblood.org/learn-about-blood/history-blood-transfusion[permanent dead link] Lawlor, ... the binding of CO2 decreases the amount of oxygen that is bound for a given partial pressure of oxygen. The decreased binding ...
The Notch binding allows groups of cells to organize themselves such that, if one cell expresses a given trait, this may be ... Each EGF-like repeat can be modified by O-linked glycans at specific sites. An O-glucose sugar may be added between the first ... A non-canonical branch of the Notch signaling pathway that involves the phosphorylation of STAT3 on the serine residue at amino ... In the past decade, advances in mutation and knockout techniques allowed research on the Notch signaling pathway in mammalian ...
Due to the chemical lability of these phosphorylated residues, special procedures and separation techniques are required for ... Some phosphorylation sites appear to have evolved as conditional "off" switches, blocking the active site of an enzyme, such as ... after which the two bound receptors phosphorylate tyrosine residues in trans. Phosphorylation and activation of the receptor ... Mary Finch, Cengage Learning. pp. 489-491. Ninfa, Alexander; David P. Ballou, David (1998). Fundamental Laboratory Approaches ...
Further information: List of fossil sites. Fossil sites with exceptional preservation-sometimes including preserved soft ... This technique is our only means of giving rocks greater than about 50 million years old an absolute age, and can be accurate ... Stromatolites are layered accretionary structures formed in shallow water by the trapping, binding and cementation of ... "Fossil" - news · newspapers · books · scholar · JSTOR (August 2012) (Learn how and when to remove this template message) ...
Antibodies can be used as powerful tool to detect whether a protein is phosphorylated at a particular site. Antibodies bind to ... a proline residue follows the phosphorylated serine or threonine residue). More recently large-scale mass spectrometry analyses ... These techniques are becoming increasingly important for the systematic analysis of complex phosphorylation networks.[30] They ... Grisham, Reginald H. Garrett, Charles M. (2013). Biochemistry (5th ed.). Belmont, CA: Brooks/Cole, Cengage Learning. ISBN 978- ...
A drug, if present in the urine specimen below its cut-off concentration, will not saturate the binding sites of its specific ... Belmont: Wadsworth Cengage Learning. pp. 163-165. ISBN 9781285070278. .. *^ Pesce, Amadeo; West, Cameron; Egan-City, Kathy; ... The scheme is used as a harm reduction technique so people are more aware of what they are taking and the potential risks.[35][ ... There are also surface drug tests that test for the metabolite of parent drug groups in the residue of drugs left in sweat. ...
... that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues ... Yan, C., Dobbs, D., and Honavar, V. Identifying Protein-Protein Interaction Sites from Surface Residues A Support Vector ... Vasant Honavar at the Mathematics Genealogy Project "NSF 12-499 Core Techniques and Technologies for Big Data". Retrieved 29 ... Walia, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2017). Sequence-based Prediction of RNA-binding Residues in Proteins. ...
... or antigen-binding sites, to exist. This region is known as the hypervariable region. Each of these variants can bind to a ... They have sugar chains (glycans) added to conserved amino acid residues.[4][21] In other words, antibodies are glycoproteins.[4 ... Feldmann M, Maini R (2001). "Anti-TNF alpha therapy of rheumatoid arthritis: what have we learned?". Annu Rev Immunol. 19 (1): ... Rosetta Antibody is a novel antibody FV region structure prediction server, which incorporates sophisticated techniques to ...
Porter, C.T.; G.J Bartlett; J.M. Thornton (2004). "The catalytic site atlas: a resource of catalytic sites and residues ... the 3D structure of a particular motif representing an active site or binding site can be targeted. The Structurally Aligned ... This technique is a computational adaptation of 'wet lab' work from 1996. It was discovered that ascertaining the structure of ... machine learning algorithms have also been developed for predicting and differentiating functions at the isoform level. This ...
... because the substrates can no longer bind to the active site, and because amino acid residues involved in stabilizing ... Many laboratory techniques rely on the ability of nucleic acid strands to separate. By understanding the properties of nucleic ... McGraw-Hill Online Learning Center - Animation: Protein Denaturation. ... Web. 25 Oct. 2016. Richard, C., and A. J. Guttmann. "Poland-Scheraga Models and the DNA Denaturation Transition." Journal of ...
NDMA receptors have multiple binding sites just like ionotropic GABA receptors and can be influenced by co-agonists such the ... was used to isolate the sodium channel protein by binding it using the column chromatography technique for chemical separation ... It is hypothesized that the deposition of amyloid-β peptide (40-42 amino acid residues) in the brain is integral in the ... NMDA receptors are notable for their excitatory mechanisms to affect neuronal plasticity in learning and memory, as well as ...
NO binds reversibly to a specific cysteine residue in globin; the binding depends on the state (R or T) of the hemoglobin. The ... with the iron ion bound in the center.[38] The iron ion, which is the site of oxygen binding, coordinates with the four ... Jones & Bartlett Learning. p. 194. ISBN 978-0867203325.. *^ Ogawa, S; Menon, R. S.; Tank, D. W.; Kim, S. G.; Merkle, H; ... This technique is often used for research in e.g. elite sports training, ergonomics, rehabilitation, patient monitoring, ...
... is consumed both at home and outside the home, often in cafés or tea rooms. Afternoon tea with cakes on fine porcelain is a ... Unsourced material may be challenged and removed. (October 2012) (Learn how and when to remove this template message) ... Tea may be consumed early in the day to heighten calm alertness; it contains L-theanine, theophylline, and bound caffeine[5] ( ... Multiple recent reports have found that most Chinese and Indian teas contain residues of banned toxic pesticides.[106][107][108 ...
Conserved residue clusters at protein-protein interfaces and their use in binding site identification | BMC Bioinformatics |...Protein-protein interaction sites are much larger than small molecule biding sites, but still conserved residues are not ... The potential use of this method for discriminating binding sites (interfaces) versus random surface patches was explored by ... surface patches not involved in binding has important implications for the identification of protein-protein binding sites and ... Almost 60% of experimental hot spot residues (with ΔΔG , 2 kcal/mol) were localized to these conserved residue clusters. An ...
... which are significantly better than that of other widely used machine learning algorithms such as Support Vector Machine, ... Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and ... We propose PredRBR, an effectively computational approach to predict RNA-binding residues. PredRBR is built with gradient tree ... The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree ...
The two nucleotide-binding domains of cystic fibrosis transmembrane conductance regulator (CFTR) have distinct functions in...... technique to study CFTR and variants which contained site-directed mutations in the conserved Walker A motif lysine residues in ... To learn how the NBDs regulate channel function, we used the patch-clamp ... The two nucleotide-binding domains of cystic fibrosis transmembrane conductance regulator (CFTR) have distinct functions in ... These results could not be attributed to altered binding of nucleotide because none of the mutants studied had reduced 8-N3ATP ...
Molecules | Free Full-Text | iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by...... it is critical to develop computational methods for identifying in a timely fashion the protein-protein binding sites (PPBSs) ... Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks ... we have provided a step-by-step guide on how to use the predictors web server (http://www.jci-bioinfo.cn/iPPBS-Opt) to get the ... where R1 represents the 1st amino acid residue of the protein P, R2 the 2nd residue, and so forth. The residue R. i. (. i. =. 1 ...
The binding protein of corticotropin-releasing factor: Ligand-binding site and subunit structure | PNAS... with different mass spectrometric techniques to directly determine contact sites between residues of CRF and its binding ... CRFR1 and -2 mediate opposite effects on learning and anxiety. Learning is enhanced through hippocampal CRFR1, whereas it is ... Identification of the Ligand-Binding Site.. After S-carboxamidomethylation of the Cys residues with iodoacetamide, the ... The binding protein of corticotropin-releasing factor: Ligand-binding site and subunit structure. Olaf Jahn, Klaus Eckart, Olaf ...
Protocols and Video Articles Authored by Brian J. Geiss... analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. ... Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a ... together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding ... Mutational studies also confirm the importance of a specific lysine residue in the GTP binding site for the enzymatic activity ...
Download Html Seiten Design Mit Ms Frontpage 2000website: a most stable website. I would try this dialog 6 or 7 professionals if I could, but on journals we bind called to 5, ... I would generate this issue 6 or 7 axioms if I could, but on residues we learn deleted to 5, Now 5 it poses. This has a ... Our Download discusses on techniques to request your religion morality. By reading our biology, you have naturalizing to our ... not, belief of scenario has known upon to learn on the browser between service and site, signaling to both the current ...
These facts reinforce the idea that the pattern of inter-residue distances is an important component of family structural ... CSM generates feature vectors that represent distance patterns between protein residues. These feature vectors are then used as ... Witten IH, Frank E: Data Mining: Practical Machine Learning Tools and Techniques. 2005, Morgan Kaufmann, secondGoogle Scholar. ... Babor M, Gerzon S, Raveh B, Sobolev V, Edelman M: Prediction of transition metal-binding sites from apo protein structures. ...
Diamond Publications - Search ResultsBound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal ... Strategies and techniques for special handling are reported, as well as the typical results and the lessons learned for each of ... Mutations in the hydrophobic cap and in basic residues of the C1?domain of MgcRacGAP prevent association of the protein with ... Both proteins bind to phosphoethanolamine and we show here that, under physiological conditions, phosphoethanolamine is bound ...
Overview of Crosslinking and Protein Modification | Thermo Fisher Scientific - ZALearn about protein structure and the functional groups that crosslinking reagents target, including primary amines, carbonyls ... Each Ig monomer contains two antigen-binding sites and is said to be bivalent. The hinge region is the area of the H chains ... Bioconjugate Techniques is a complete textbook and protocols-manual for life scientists wishing to learn and master ... By reacting the compound to a purified protein, the side chain of lysine residues can be modified to contain a sulfhydryl group ...
Biomedical Engineering with a Year in Industry (05C3) | Undergraduate Programmes 2019 | The University of KentPrediction of binding sites/interfaces with small ligands and with other proteins. Bioinformatics analyses using protein data. ... imaging techniques, radiation detectors); In vitro techniques (Radiation counting techniques and applications); Positron ... Learning outcomes. Knowledge and understanding. You gain knowledge and understanding of:. *Mathematical principles relevant to ... Using sequence data for analysis - sequence searching methods, multiple sequence alignments, residue conservation, Protein ...
Cell cycle kinases predicted from conserved biophysical properties. | ROSTLAB.ORGAs expected, the most informative residues tend to be highly conserved and tend to localize in the ATP binding regions of the ... Machine-learning techniques can classify functionally related proteins where homology-transfer as well as sequence and ... Amino Acid Motifs, Artificial Intelligence, Binding Sites, Cell Cycle, Cell Cycle Proteins, Conserved Sequence, Databases, ... Another observation confirmed that ATP binding regions are typically not found on the surface but in partially buried sites, ...
Interactome-wide prediction of short, disordered protein interaction motifs in humans - Molecular BioSystems (RSC Publishing...... incorporating techniques that explicitly characterise32 or predict such binding sites (e.g. ANCHOR29 or PONDR-RIBS33) could ... The lower panel plots Relative Local Conservation (RLC) and IUPred disorder prediction scores for each residue. Residues ... There are three key lessons to be learnt from the sensitivity of some of the results to losing a few interactors (e.g. the ... with databases specifically focusing on phosphorylation13 and cleavage sites,14,15 in addition to classical ligand-binding ...
The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains... and coimmunoprecipitation experiments are powerful methods for identifying novel proteins that bind to ones favorite protein ... experiments are powerful methods for identifying novel proteins that bind to ones favorite protein for the purpose of learning ... These same techniques, coupled with truncation and mutagenesis experiments, have been used to define the region of interaction ... This review highlights the analysis of those protein-protein interactions that involve proline residues, the biochemistry of ...
NLM Informatics Training Conference 2008: Agenda and AbstractsPrediction of Transcription Factor Binding Sites Using Multiple Linear, Multivariate Regression Techniques. Authors:. Elizabeth ... The nodes of the network are the residues, that are predicted (or known) to interact with residues in another subunit, and the ... Development of a Learning Health System for Inflammatory Bowel Disease Authors:. Marc D Natter1,4,5, Athos Bousvaros2,4, Joshua ... Prediction of Transcription Factor Binding Sites Using Multiple Linear, Multivariate Regression Techniques - Siewert, Colorado ...
Discovery of Protein Interaction Sites: Computer Science & IT Book Chapter | IGI GlobalSince protein-protein interactions are mediated via their interaction sites ... Discovery of Protein Interaction Sites: 10.4018/978-1-60566-010-3.ch106: Physical interactions between proteins are important ... or binding sites in some contexts). Protein interaction sites have unique features that distinguish them from other residues ( ... To determine the interaction sites, many biotechnological techniques have been applied, such as phage display and site-directed ...
KAKEN - Research Projects | Development of a method for predicting functional sites in function-unknown splicing isoforms ...Presentation] Evaluation of functionality of uncharacterized splicing isoforms using machine learning techniques2016. *. Author ... Presentation] A new approach for protein-ligand binding predictions based on matching of vector-represented amino acid residues ... The method we developed showed higher accuracy for predicting small molecule-binding sites than that of our previous method. ... Development of a method for predicting functional sites in function-unknown splicing isoforms. Research Project ...
Synthetic Biology and Organism Engineering | The New York Academy of Sciences... structure-based design techniques are typically much slower but can model diverse molecules in a protein binding site. Our ... We encourage you to learn more about cookies on our site in our Privacy policy and Terms of Use. ... Moreover, careful design at the residue level can lead to enhanced secondary structural stability among the foldamers relative ... The highest-ranked features form a map that is consistent with known tight-binding compounds, and these binding site maps can ...
Mutations that alter structure locally can be distinguished from those that do not through a machine-learning (logistic ... Here, we compare pairs of pentamers (five consecutive residues) that locally change protein three-dimensional structure (3D, ... Usually, this is more likely for structure changes connected to binding sites. For instance, the disruption of hydrophobic ... Ofran Y, Mysore V, Rost B: Prediction of DNA-binding residues from sequence. Bioinformatics. 2007, 23 (13): i347-353. 10.1093/ ...
Cell Signaling Assays Kit Platforms | Sigma-Aldrich... in the sample competes with a fixed amount of the same enzyme-conjugated protein for the constant number of binding sites on ... Techniques based on the use of fluorescent agents (dyes, probes) during the reaction or as a detection method. Fluorescent ... ELISAs for the detection of proteins phosphorylated at a specified residue(s) of serine, tyrosine or threonine. The format is ... a specific antibody or probe is allowed to bind and the presence of bound antibody/probe is then shown by using a coupled ...
PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites... capable of predicting cleavage sites of multiple proteases within a single substrate sequence using machine learning techniques ... with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and ... Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding ... an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four ...
New test detects drug use from a single fingerprint | EurekAlert! Science NewsOften these tests also require analysis off-site.. "The beauty of this method is that, not only is it non-invasive and more ... "We are only bound by the size of the current technology. Companies are already working on miniaturised mass spectrometers, and ... "For our part of the investigations, we sprayed a beam of solvent onto the fingerprint slide (a technique known as Desorption ... and these chemical indicators are present in fingerprint residue," said lead author Dr Melanie Bailey from the University of ...
Xenobiotics in the Soil Environment | SpringerLinkAn Overview of Extraction, Clean-up and Instrumentation Techniques for Quantification of Soil-Bound Xenobiotic Compounds ... HCH and DDT Residues in Indian Soil: Atmospheric Input and Risk Assessment ... metagenomic strategies for assessing contaminated sites; xenobiotics in the food chain; phyto-chemical remediation; ... This service is more advanced with JavaScript available, learn more at http://activatejavascript.org ...
... mtFabH contains residues along the acyl-CoA binding channel that preferentially select for longer-chain substrates peaking with ... Davies C, Heath RJ, White SW, Rock CO (2000). "The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl ... Techniques for screening efficacy of inhibitors are available. In 2005, tuberculosis caused approximately 1.6 million deaths ... While much has been learned from these structural studies and rational design is an excellent approach to develop novel ...
enzyme facts, information, pictures | Encyclopedia.com articles about enzymeThe molecule undergoing reaction (the substrate) binds to a specific active site on the enzyme molecule to form a short-lived ... The side chains of the residues in this particular geometry produce the active site that accounts for the enzymes reactivity. ... Learn more about citation styles Citation styles. Encyclopedia.com gives you the ability to cite reference entries and articles ... amino acid sequences and three-dimensional structure of a significant number have been fully determined through the technique ...
ProteinsLigandFunctionally important residuesPeptideSequencePeptidesLysine residuesHydrophobic residuesPredictionSubstratesPutativeCysteine residueMotifMutationsComputationalInteractionStructuralAmino acid compositionAntigenHistidineTypicallySmall moleculeDistinctCharacterizePredictSubunitSerineInteractionsBiologicalSpecificityMoleculesEnzymeLigandsMutagenesisCoupled secondaryAntiparallelCytosineDouble-strandedEnzymesCompositionBiophysicalExperimentalMoleculeEvolutionarilyStructuresExtracellular domainOxidationComplexesNucleotideInteractsLocal environmentsWidelyAtomicPhosphorylation
- Binding surfaces on proteins are subjected to considerable selective pressure to maintain critical interactions with partner molecules throughout the course of evolution, and not surprisingly therefore, the use of residue conservation has been widely adopted in the identification of protein binding sites [ 17 - 20 ]. (biomedcentral.com)
- RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. (biomedcentral.com)
- Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex. (biomedcentral.com)
- 12 ] implement a RF classifier to detect the RNA binding residues in proteins by integrating interaction propensity with other sequence and structural features. (biomedcentral.com)
- A number of techniques for studying the structure and interaction of proteins, as well as for manipulating proteins for use in affinity purification or detection procedures, depend on methods for chemically crosslinking, modifying or labeling proteins. (thermofisher.com)
- Machine-learning techniques can classify functionally related proteins where homology-transfer as well as sequence and structure motifs fail. (rostlab.org)
- First, we identified functionally significant residues in cell cycle proteins through their high sequence conservation and biophysical properties. (rostlab.org)
- We then incorporated these residues and their features into support vector machines (SVM) to identify new kinases and more specifically to differentiate cell cycle kinases from other kinases and other proteins. (rostlab.org)
- Yeast two-hybrid, cDNA expression library screening, and coimmunoprecipitation experiments are powerful methods for identifying novel proteins that bind to one's favorite protein for the purpose of learning more regarding its cellular function. (nih.gov)
- These same techniques, coupled with truncation and mutagenesis experiments, have been used to define the region of interaction between pairs of proteins. (nih.gov)
- Other examples include protein-interaction modules, such as Src homology (SH) 2 and 3 domains, phosphotyrosine binding domains (PTB), postsynaptic density/disc-large/ZO1 (PDZ) domains, WW domains, Eps15 homology (EH) domains, and 14-3-3 proteins that typically recognize linear regions of 3-9 amino acids. (nih.gov)
- ELISAs for the detection of proteins phosphorylated at a specified residue(s) of serine, tyrosine or threonine. (sigmaaldrich.com)
- Approximately 5,000 lysine methylation sites were identified on different proteins, which are set by few dozens of protein lysine methyltransferases. (jove.com)
- Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. (jove.com)
- NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. (jove.com)
- It acts mainly through redox-based modification of cysteine residue(s) of target proteins, called protein S -nitrosylation.In this way NO regulates numerous cellular functions and signaling events in plants. (frontiersin.org)
- Telomeres, the physical ends of linear chromosomes, generally comprise dsDNA with a short repeating species-specific sequence ending in a 3′ single-stranded overhang of variable length plus associated telomere binding proteins, called shelterin in humans ( 1 , 2 ). (pnas.org)
- To perform quantitative studies of membrane bound G protein-coupled receptors (GPCRs) with high-performance microscopy, the proteins must first be labeled with bright and photostable dyes. (leica-microsystems.com)
- Because the reported technique is performed using a commercially available microscope, the approach can be used for the general study of membrane proteins with fluorescence microscopy. (leica-microsystems.com)
- Short linear motifs in proteins (typically 3-12 residues in length) play key roles in protein-protein interactions by frequently binding specifically to peptide binding domains within interacting proteins. (ucd.ie)
- Cleavable or reversible biotinylation reagents enable the specific elution of biotinylated molecules from biotin-binding proteins. (thermofisher.com)
- Although reactive oxygen species are usually promiscuous in their reactivity, Dr. Levine and his colleagues found that this modification was localized to the metal binding sites of proteins that contained them. (nih.gov)
- Counter to the commonly held notion that methionines (which are hydrophobic residues) are typically buried within proteins, many methionine residues lie on the surfaces of proteins. (nih.gov)
- The team found that these proteins, which were already known to play a role in synaptic plasticity, learning, and memory, have surprising properties in their activity. (maxplanckflorida.org)
- Such residues turn out to be often directly involved in binding ligands or interfacing with other proteins. (biomedcentral.com)
- The drug-binding domains of some proteins subtypes are extremely similar to one another. (exposed-skin-care.net)
- Cloning and Proteins Appearance The molecular cloning, appearance, as well as the purification of His-tagged Stat3 and His-tagged Stat3 SH2 site were completed as we've previously reported (27). (exposed-skin-care.net)
- We found that the proteins of mesophilic organisms have more number of binding sites than thermophiles and the binding propensities of amino acid residues are distinct in E. coli , H. sapiens , S. cerevisiae , thermophiles and archaea. (biomedcentral.com)
- Proteins prefer to bind with RNA using a single residue segment in all the organisms while RNA prefers to use a stretch of up to six nucleotides for binding with proteins. (biomedcentral.com)
- The interaction of proteins with RNA has been generally explained using different types of motifs such as Arginine rich motif, RNA recognition motif, GXXG motif, double stranded RNA binding motif, tetra loops (GX[GA]A) in RNA and so on [ 1 ]. (biomedcentral.com)
- The three GRO cDNAs encode 107 amino acid precursor proteins from which the N-terminal 34 amino acid residues are cleaved to generate the mature GROs. (novusbio.com)
- CX-MS crosslinks used to identify mitochondrial-specific ribosomal proteins or confirm their locations (Cα of crosslinked residues shown as spheres). (fei.com)
- This is usually accomplished by antibody immunoprecipitation methods or with methyl-CpG binding domain (MBD) proteins. (activemotif.com.cn)
- Hydrogen-deuterium exchange (HDX) and fast photo-chemical oxidation of proteins (FPOP) are orthogonal exam-ples of protein footprinting techniques that afford information regarding higher-order structure. (springer.com)
- After his PhD in protein crystallography with Tom Blundell in Cambridge, he has focused on methodology and high throughput techniques for crystallography, first in San Diego (academically at JCSG, and industrially at Syrrx, Inc), and since 2004 at the SGC, where his group has to date helped solve over 600 crystal structures of human proteins. (ox.ac.uk)
- Sequestration of iron by host iron-binding proteins, such as hemoglobin, lactoferrin, and transferrin, contributes to its low concentration. (asm.org)
- makeshift optimization proteins are incorporated clarified in this viscosity, with the emotional disease of learning the executive chaotic set so the programme can present possible. (way2goal.com)
- Methylation situate for a chemical modification to the DNA on cytosine bases and histones.That manipulates the way the molecule is shaped and, consequently binds various regulatory proteins that resolves the transcriptional status of the gene. (expertsmind.com)
- Zinc binding proteins play an important role in biological function, many researches focus on the area of zinc-binding sites. (alliedacademies.org)
- By analysis of the human genome, there are up to 3000 proteins participating in binding with zinc [ 3 ]. (alliedacademies.org)
- Then, they presented a better method called zincFinder [ 5 ] based on support vector machines for the identification of zinc-binding sites with human proteins. (alliedacademies.org)
- At its fundamental level, it operates by sampling amino acid residues in proteins to optimize stability and function. (proquest.com)
- In addition, some transcription regulatory proteins bind more easily to their DNA target sites if the nucleosomes associated with those sites are acetylated. (encyclopedia.com)
- intrinsically disordered proteins and regions, physicochemical-based method, machine-learning-based method, template-based method, meta method Introduction Proteins and protein regions without a stable three-dimensional structure are called intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) [1, (deepdyve.com)
- We shall also discuss our futuristic ideas about understanding the hydrophobic effects around a complex molecular surface (e.g. proteins), which seem to play a very important role in various self-assembly, aggregation and binding processes. (tifr.res.in)
- In quest for partners of PSMD9, we perfo rmed C-terminal tetrapeptide screen representing the C-termini of proteins of human proteome to test the ability of these peptides to bind to PSMD9 and consequently demonstrate that proteins harbouring those C-terminal residues interact with PSMD9. (tifr.res.in)
- Although CRFBP was observed to dimerize, at least in part, the ligand was found to be exclusively bound to the monomer-as indicated by photoaffinity labeling. (pnas.org)
- It was, therefore, concluded that the sequence of amino acid residues 23-36 of CRFBP is involved in ligand binding. (pnas.org)
- A detailed knowledge on the ligand-binding site of CRFBP, whose three-dimensional structure has not been elucidated so far, may facilitate the design of new peptidic and nonpeptidic CRFBP inhibitors. (pnas.org)
- We identified, using a photoaffinity label, the ligand-binding site of the rat CRFBP (rCRFBP). (pnas.org)
- This could be especially important given that phosphorylation of mycolate synthesis enzymes is suggested to be critical to regulation and kinase domains are known to have multiple control mechanisms remote from ligand binding and active sites. (wikipedia.org)
- The extraordinary affinity of avidin for biotin is one the strongest known non-covalent interactions of a protein and ligand (Ka=10 15 M -1 ) and allows biotin-containing molecules in a complex mixture to be discretely bound with avidin conjugates. (thermofisher.com)
- Surface model of the α7 nAChR ligand-binding domain. (intechopen.com)
- Only the ligand-binding domain (LBD) is shown. (intechopen.com)
- They have the response element and the ion channel domain within the same molecular entity as the ligand-binding domain that is activated by acetylcholine. (intechopen.com)
- Ligand binding to nAChR usually occurs in the submillisecond range. (intechopen.com)
- Ligand binding selectivity to these subtypes is both dependant on the structural and physicochemical top features of the conserved and non-conserved residues . (exposed-skin-care.net)
- While our typical docking methods hold the protein structure rigid, the flexibility feature in AutoDock Vina allows selected residue side chain conformations to be sampled along with the flexible ligand molecule. (worldcommunitygrid.org)
- This enables the protein pocket to adopt alternate shapes to better model protein-ligand binding and the so-called "induced fit", minimizing the bias of using a rigid target structure. (worldcommunitygrid.org)
- The most common way of quantifying binding mode similarity is Root Mean Square Deviation (RMSD), but Protein Ligand Interaction Fingerprint (PLIF) similarity and shape-based metrics are sometimes used. (ox.ac.uk)
- After binding to a ligand, LXR forms a complex with another receptor and interacts with specific DNA elements to promote expression of target genes. (asbmb.org)
- This study showed that binding of 25HC or a synthetic ligand to LXR inhibited certain viral infections, such as herpes simplex virus type 1, in cell culture. (asbmb.org)
- Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
- Here, we report that PSMD9 interacts with the C-terminal residues of hnRNPA1, S14, a ligand growth hormone and IL6 receptor via its PDZ-like domain. (tifr.res.in)
- In this work, we demonstrated how the exploration of global atomic distributions can be used to indicate functionally important residues. (biomedcentral.com)
- Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity.Nearest neighbour among functionally important residues emerged among the most effective methods.Our results underscore the complexity of TF-DNA recognition, and suggest a rational approach for future analyses of TF families. (nih.gov)
- Nearest neighbour among functionally important residues emerged among the most effective methods. (nih.gov)
- That small peptide is engineered to bind very tightly to the "Large BiT" protein, and together they form a functional, stable, and rather bright luciferase enzyme. (sciencemag.org)
- The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy. (jove.com)
- CORAL GABLES, FL (October 16, 2017) - A probe invented at Rice University that lights up when it binds to a misfolded amyloid beta peptide--the kind suspected of causing Alzheimer's disease--has identified a specific binding site on the protein that could facilitate better drugs to treat the disease. (eurekalert.org)
- The light-switching complex glows when hit with ultraviolet light, but when it binds to the fibril it becomes more than 100 times brighter and causes oxidation of the amyloid peptide. (eurekalert.org)
- The sensor is composed of phospho-Thr binding domain (WW domain), EV linker, ERK substrate peptide and docking site, sREACh with S208F/R223F/V224L mutations, and EGFP. (maxplanckflorida.org)
- ERK phosphorylation triggers the association of the WW domain with the substrate peptide, increasing FRET between EGFP and sREAChet, and the three-residue mutations in sREACh enhanced FRET signal. (maxplanckflorida.org)
- biochemical and biophysical research indicate SPI, like Stat3 binds to cognate pTyr-peptide motifs with an identical affinity. (exposed-skin-care.net)
- Appropriately, SPI blocks the binding of Stat3 (or Stat3 SH2 site) to cognate pTyr peptide motifs, and therefore functions being a selective inhibitor of constitutive Stat3 activation in individual breasts, prostate, pancreatic, and non-small cell lung tumor cells, with antitumor cell results. (exposed-skin-care.net)
- Peptide Synthesis The Stat3 SH2 site peptide series, FISKERERAILSTKPPGTFLLRFSESSK was bought from Peptide 2.0 (Fairfax, VA) at 95% purity. (exposed-skin-care.net)
- In the HLA-A3/Gag20C28 complex, we suggest that Arg at position P1 of the peptide may push the 2 2 helix residue Trp-167 of HLA-A3 and affect mAb recognition. (techuniq.com)
- Crystallographic structure analysis of a series of class I MHC/peptide complexes revealed that peptides carrying specific MHC anchor residues bind in a large-solvent-exposed groove of the heavy chain. (techuniq.com)
- HDX provides structural information down to the region and, with some forms of peptide fragmentation, site-specific protein backbone conformational changes. (springer.com)
- Experimental techniques have characterized thousands of peptide binding events, but conducting experiments can be costly and time-consuming, and their results can be prone to false positives. (proquest.com)
- Structure of MHC class I: Alpha chain and domains, beta-2 microglobulin, peptide in cleft with closed ends, papain cleavage locus, CD8 binding site, secondary structure. (bioinformatics.org)
- Evolutionary conservation of CD8 binding site and residues binding peptide anchor residues and ends. (bioinformatics.org)
- Peptide side chains buried (anchor residues) vs. exposed to T cell surveillance. (bioinformatics.org)
- The analysis of sequence conservation in a protein family is a useful method for identifying residues that are functionally important - for catalytic activity or binding, or responsible for providing stability to the folded structure [ 1 - 10 ]. (biomedcentral.com)
- A series of machine learning methods [ 6 ] such as Naive Bayes, support vector machine (SVM), and random forest (RF), combined with amino acid sequence or protein three-dimensional structural characteristics [ 4 , 7 ], have been proposed to identify RNA-binding residues. (biomedcentral.com)
- 8 ] build a neural network classifier to predict RNA-binding residues based on protein sequence and structural information. (biomedcentral.com)
- Wang and Brown [ 9 ] develop BindN, an efficient online approach that uses amino acid sequence and SVM to predict potential RNA-binding sites. (biomedcentral.com)
- With the avalanche of protein sequences generated in the postgenomic age, it is critical to develop computational methods for identifying in a timely fashion the protein-protein binding sites (PPBSs) based on the sequence information alone because the information obtained by this way can be used for both biomedical research and drug development. (mdpi.com)
- The amino acid residues Arg-23 and Arg-36 of CRFBP were identified as the sites of photoincorporation of monofunctional and bifunctional photoprobes designed on the basis of the amino acid sequence of human/rat CRF 6-33 . (pnas.org)
- Protein-protein interactions are mediated by short sequence of residues among the long stretches of interacting sequences, which are referred to as interaction sites (or binding sites in some contexts). (igi-global.com)
- This constrained sampling process explains the sequence diversity compatible with a given protein three-dimensional (3D) structure: over 50-80% of all residues can be changed without altering structure significantly [ 1 - 3 ]. (biomedcentral.com)
- We compiled a set of structurally superimposed pairs of protein fragments with identical sequence except for one central residue mismatch, and applied machine-learning to predict structural change from sequence. (biomedcentral.com)
- PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. (plos.org)
- To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate sequence using machine learning techniques. (plos.org)
- i) A slippery site with the form of X-XXY-YYZ (the dashes separate in-frame triplets), where XXX can be any homopolymeric sequence, YYY can be either AAA or UUU, and Z can be A, U or C. The slippery sequence allows effective base-pairings between the ribosome-bound tRNAs and mRNA even after frameshifting to XXX-YYY (−1 frame). (hindawi.com)
- The method applies machine learning techniques to predict new motifs based on annotated instances from the Eukaryotic Linear Motif database, as well as structural, biophysical, and biochemical features derived from the protein primary sequence. (ucd.ie)
- and a synaptic activity response element (SARE) sequence at ~7 kb upstream that contains binding sites for cyclic AMP response element-binding protein (CREB), myocyte enhancer factor 2 (MEF2), and SRF. (wikipedia.org)
- For example, while D2 receptor and D3 receptor share high sequence identity in the seven helices regions that define a lot of the binding sites, different compositions from the loop regions affect the contour and topography from the binding pockets and hydrogen bonding sites, which enables subtype selective binding , . (exposed-skin-care.net)
- 25 ] used only protein sequence information to predict PPI, in which a kind of method called PCA-EELM (Principal Component Analysis-Ensemble Extreme Learning Machine) is designed. (hindawi.com)
- The similarities and differences in each set of complexes have been revealed in terms of various sequence and structure based features such as root mean square deviation, sequence homology, propensity of binding site residues, variance, conservation at binding sites, binding segments, binding motifs of amino acid residues and nucleotides, preferred amino acid-nucleotide pairs and influence of neighboring residues for binding. (biomedcentral.com)
- MeDIP techniques are ideal for the enrichment of DNA fragments containing cytosine methylation regardless of the sequence context. (activemotif.com.cn)
- Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. (nih.gov)
- Getting to Yes: What Patent Attorneys Want to Learn from a Sequence Search , Joan Switzer, Merck & Co. Inc. (piug.org)
- The analysis of a protein, through the evaluation of interactions between the amino acid composing its sequence, is a very challenging problem where pattern recognition techniques based on Hidden Markov Model (HMM) have proved to be the most efficient [ 1 ]. (biomedcentral.com)
- Displacement of CRF from its binding protein may be achieved by CRFBP-selective peptides (CRFBP inhibitors) such as human/rat (h/r)-CRF 6-33 ( 8 , 14 ), a synthetic fragment of h/rCRF. (pnas.org)
- Binding of peptides to rCRFBP was determined in PBS/0.02% Nonidet P-40, using a scintillation proximity assay with [ 125 I-Tyr 0 ]h/rCRF as radioligand ( 17 ). (pnas.org)
- It seemed likely that this is due to the peptides binding too tightly to be substrates for the JmjC KDMs, suggesting that in this context the proposed methodology might not be optimal for KDM substrate identification. (europa.eu)
- However, screening studies with histone peptides, followed by kinetic and structural characterisation, revealed that a site on histone H1.4 lysine 26, is a comparably good substrate for the KDM4 subfamily of histone demethylases as the better studied histone H3K9 site and a better substrate than the H3K36 site. (europa.eu)
- Selections with PADI4 identified tight binding peptides that were also enzyme substrates - target arginine residues within the peptides could be converted to citrulline. (europa.eu)
- Due to their very potent binding these peptides have been pursued as inhibitors of PADI4. (europa.eu)
- When amyloid peptides fold properly, they hide their hydrophobic residues while exposing their hydrophilic (water-attracting) residues to water. (eurekalert.org)
- Polymorphic residues in the groove determine distinct binding pockets from A to F. Bound peptides adopt extended conformations that stretch from the N- to the C-terminal end of the groove, and their PF-3644022 anchor residues, generally at positions P2 and P9/10, interact with pockets B and F, respectively (1C4). (techuniq.com)
- To learn how the NBDs regulate channel function, we used the patch-clamp technique to study CFTR and variants which contained site-directed mutations in the conserved Walker A motif lysine residues in either NBD1 (K464A), NBD2 (K1250A and K1250M), or both NBDs simultaneously (K464A/K1250A). (nih.gov)
- The ubiquitous small protein ubiquitin is stapled onto lysine residues of the protein to be degraded, via a ubiquitin ligase complex, and this serves as a marker for transport to the proteasome. (sciencemag.org)
- But when amyloid beta misfolds, it leaves two hydrophobic residues, known as Valine 18 and Phenylalanine 20, exposed to create the hydrophobic cleft. (eurekalert.org)
- The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree boosting algorithm combined with the optimal selected features. (biomedcentral.com)
- Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. (plos.org)
- Taking into account the advantages of support vector machine, based on the different tools for the prediction of zinc-binding sites, a novel predictor named combZincPred was proposed to integrate these result scores. (alliedacademies.org)
- Recently, there are a lot of tools for the prediction of zinc-binding sites. (alliedacademies.org)
- So far, there are no uniform experimental data sets for the prediction of zinc-binding sites. (alliedacademies.org)
- To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. (plos.org)
- Proteases act as processing enzymes that carry out either highly or moderately selective cleavage of the scissile bond within the cleavage site of their substrates. (plos.org)
- The catalytic activity and substrate specificity of mtFabH has been measured then further probed using crystallographic and directed mutagenesis methods Structures have been determined of ecFabH bound with substrates, (CoA, malonyl CoA, degraded CoA). (wikipedia.org)
- Although there is substantial structural homology among all bacterial FabH enzymes determined thus far, with two channels for binding of acyl-CoA and malonyl-ACP substrates and a conserved catalytic triad (C122, H258, N289 in mtFabH), mtFabH contains residues along the acyl-CoA binding channel that preferentially select for longer-chain substrates peaking with lauroyl-CoA (C12). (wikipedia.org)
- Inhibition strategies based on rational design could include competitive displacement of the substrates or disruption of the catalytic site. (wikipedia.org)
- Identification of S -nitrosylated substrates and their exact target cysteine residue(s) is very important to reveal the molecular mechanisms and regulatory roles of S -nitrosylation. (frontiersin.org)
- This study shows that flies use neural substrates attributed to odor learning and memory , including the mushroom body (MB), for immediate sensory integration and modulation of innate behavior. (sdbonline.org)
- It has recently been shown in protein-DNA interfaces that the most stabilizing residues (putative 'hotspots') are those that form clusters of conserved residues at the interface [ 22 ]. (biomedcentral.com)
- Once transported, the translated protein is 396 residues in length, with an N-terminus located at amino acids 1-25, a C-terminus at 155-396 (note that the spectrin homology located at 228-380 within the C-terminal), and a putative coiled coil domain at amino acids 26-154. (wikipedia.org)
- The putative substrate-binding site of LCC can be subdivided into three subsites (−2, −1, +1), each in contact with the MHET units numbered relative to the scissile ester bond (red triangles). (phys.org)
- Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP. (uniprot.org)
- This chapter reviews both traditional and recent computational methods such as protein-protein docking and motif discovery, as well as new methods on machine learning approaches, for example, interaction classification, domain-domain interactions, and binding motif pair discovery. (igi-global.com)
- We have integrated these data sources and benchmarked the predictive accuracy of the method, and found that it performs equivalently to a predictor of protein binding regions in disordered regions, in addition to having predictive power for other classes of motif sites such as polyproline II helix motifs and short linear motifs lying in ordered regions. (ucd.ie)
- Matrix metalloproteinases (MMPs) are members of the metzincin group of proteases which share the conserved zinc-binding motif in their catalytic active site. (ersjournals.com)
- Functional characterization of residues within the carnitine/acylcarnitine translocase RX2PANAAXF distinct motif. (semanticscholar.org)
- Mutations that alter structure locally can be distinguished from those that do not through a machine-learning (logistic regression) method. (biomedcentral.com)
- We propose PredRBR, an effectively computational approach to predict RNA-binding residues. (biomedcentral.com)
- Developing computational methods to predict RNA-binding sites precisely is becoming increasingly important. (biomedcentral.com)
- Computational methods, including many biological data mining methods, are considered as the major approaches in discovering protein interaction sites in practical applications. (igi-global.com)
- Mutagenesis, crystallographic and computational studies have established that only a few residues determine whether or not KDO8PS requires a metal for function. (jove.com)
- Special focus will be on potential S -nitrosylation motifs, site-specific proteomic analyses, computational predictions using different algorithms, and on structural analysis of cysteine S -nitrosylation. (frontiersin.org)
- Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. (hindawi.com)
- That's where our computational techniques became invaluable," said University of Miami Chemist Rajeev Prabhakar. (eurekalert.org)
- A number of computational methods based on machine learning have been developed to facilitate the identification of novel PPIs. (hindawi.com)
- Please let your prospective employer know that you learned about the job from the Computational Chemistry List Job Listing at http://www.ccl.net/jobs . (ccl.net)
- Using statistical mechanics based computational techniques, we are able to connect the molecular interactions (energetics) to their structural, thermodynamic and kinetic properties. (tifr.res.in)
- Protein-protein interaction sites are much larger than small molecule biding sites, but still conserved residues are not randomly distributed over the whole interface and are distinctly clustered. (biomedcentral.com)
- Residues comprising protein-protein interaction sites are very often found to be more conserved over those residing in the remaining surface [ 11 - 14 ]. (biomedcentral.com)
- The residues in these clusters are more tightly packed than those in the remainder of the interface and analysis of experimental mutational data suggests the existence of cooperative interactions between them (which makes these clusters of conserved residues contribute significantly more towards the stability of the interaction as compared to isolated conserved residues). (biomedcentral.com)
- no single feature can effectively identify protein-RNA interaction residues. (biomedcentral.com)
- Discovery of Protein Interaction Sites. (igi-global.com)
- Since protein-protein interactions are mediated via their interaction sites, identifying these interaction sites can therefore help to discover genome-scale protein interaction map, thereby leading to a better understanding of the organization of living cell. (igi-global.com)
- To date, the experimentally solved protein interaction sites constitute only a tiny proportion among the whole population due to the high cost and low-throughput of currently available techniques. (igi-global.com)
- Protein interaction sites have unique features that distinguish them from other residues (amino acids) in protein surface. (igi-global.com)
- The favored combinations have been repeatedly applied during evolution (Keskin and Nussinov, 2005), which limits the total number of types of interaction sites. (igi-global.com)
- Our proposed method uses a novel data balancing and boosting technique to predict drug-target interaction. (nature.com)
- Should we provide more nAChR-like binding sites as a decoy for Aβ-nAChR interaction? (alzforum.org)
- 2016 ). They modeled the interaction surface of MyD88 TIR domain with full-length MyD88 or with homologous domain of TLR4 and Mal (MyD88-adaptor like protein)/TIRAP (TIR domain containing adaptor protein) using site-directed mutagenesis and in vivo biochemical techniques. (springer.com)
- New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members. (nih.gov)
- Identification by site-directed mutagenesis of a hydrophobic binding site of the mitochondrial carnitine/acylcarnitine carrier involved in the interaction with acyl groups. (semanticscholar.org)
- Both protein stability and function often require a certain degree of structural co-operativity between spatially neighboring residues and it has previously been shown that conserved residues occur clustered together in protein tertiary structures, enzyme active sites and protein-DNA interfaces. (biomedcentral.com)
- These structural cluster(s) comprising conserved residues indicate functionally important regions within the protein-protein interface that can be targeted for further structural and energetic analysis by experimental scanning mutagenesis. (biomedcentral.com)
- We further calculate the feature importance of different feature categories and find that structural neighborhood characteristics are critical in the recognization of RNA binding residues. (biomedcentral.com)
- These facts reinforce the idea that the pattern of inter-residue distances is an important component of family structural signatures. (biomedcentral.com)
- While much has been learned from these structural studies and rational design is an excellent approach to develop novel inhibitors, alternative approaches such as bio-prospecting may reveal unexpected compounds such as an allosteric inhibitor discovered by Daines et al. (wikipedia.org)
- The results obtained from the structural analysis of protein-RNA complexes have been successfully utilized for understanding their recognition mechanism and predicting the binding sites. (biomedcentral.com)
- Recently, Nagarajan and Gromiha (2014) analyzed the performance of various methods for identifying the binding sites in protein-RNA complexes based on protein structural class, fold, family, superfamily, function, RNA structure, and conformation. (biomedcentral.com)
- Solving the structure of large dynamic complexes often requires integrating several complementary techniques, such as biomolecular mass spectrometry (MS) and cryo-electron microscopy (cryo-EM)-an approach known as integrative structural biology. (fei.com)
- Technology developments in mass analyzers are at the forefront of driving the growing number of structural biology studies enabled by increased performance in speed, sensitivity, selectivity and a variety of MS fragmentation techniques. (fei.com)
- SPA is a structural technique wherein 2D transmission electron micrographs of individual, randomly orientated protein complexes or viruses can be mathematically aligned through image processing techniques to generate a 3D volume of the specimen. (fei.com)
- These EM applications benefit from an integrative structural approach with MS techniques, which are equally suitable to perform accurate measurements even with crude and complex sample compositions. (fei.com)
- Zinc binding with protein has a wide variety of biological functions, such as catalysis, structural stability and regulatory roles. (alliedacademies.org)
- Support Vector Machine (SVM) is a new method of classification and pattern recognition, built on the basis of the principle of structural risk minimization, which has a strong learning ability and generalization performance. (alliedacademies.org)
- His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)
- When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. (biomedcentral.com)
- For example, mapping studies and 3-dimensional analyses of antigen-antibody interactions have revealed that epitopes are typically 4-7 residues long (1). (nih.gov)
- Antigen in standards, unknown samples and controls is added and incubated in order to facilitate binding of antigen and antibody. (sigmaaldrich.com)
- Samples, standards, control specimens and unknowns are incubated for two hours and antigen binds to the capture antibody. (sigmaaldrich.com)
- A Fab-antigen complex, a common focus point for the biopharmaceutical industry, was studied with this technique to provide information on regions of the antibody that become more rigid upon antigen binding. (springer.com)
- This antigen-antibody binding is required for the neutralization and clearance of the pathogen from body. (mybiosource.com)
- This region is composed of 110-130 amino acids and shown great variance between different immunoglobulins and also specific for antigen binding. (mybiosource.com)
- The V regions combine to form two identical antigen binding sites. (mybiosource.com)
- The basic mechanism of TCST involves a membrane-bound sensor histidine kinase which, upon stimulation, autophosphorylates a conserved histidine residue in its intracellular catalytic domain. (asm.org)
- Cysteine (CYS), Histidine (HIS), Aspartate (ASP) and Glutamic (GLU) are predominant four binding amino acid residues. (alliedacademies.org)
- Another observation confirmed that ATP binding regions are typically not found on the surface but in partially buried sites, and that this fact is correctly captured by accessibility predictions. (rostlab.org)
- The method we developed showed higher accuracy for predicting small molecule-binding sites than that of our previous method. (nii.ac.jp)
- Now, this is an exciting technique, because wiping out a protein like this can be a very different thing than just blocking some small-molecule binding site it might have. (sciencemag.org)
- Conserved residues occurring in larger interfaces could often be sub-divided into two or more distinct sub-clusters. (biomedcentral.com)
- The two nucleotide-binding domains of cystic fibrosis transmembrane conductance regulator (CFTR) have distinct functions in controlling channel act. (nih.gov)
- The central actions of CRF are mediated through at least two different subtypes of CRF receptors (CRFRs), CRFR1 and CRFR2 ( 4 ), and are modulated by a 37-kDa CRF-binding protein (CRFBP) ( 5 ), which is localized in several distinct brain regions, including the cerebral cortex and the hippocampus ( 6 ). (pnas.org)
- In addition to the conservation of individual interface residues, conservation of interacting residue pairs have also been found to characterize protein-protein binding sites [ 21 ]. (biomedcentral.com)
- Based on the different selections of protein features, some other algorithms have been developed to predict the binding sites [ 9 - 11 ]. (alliedacademies.org)
- Genes with a change in transcript abundance associated with inactivation of ritR included piuB , encoding an Fe permease subunit, and piuA , encoding an Fe carrier-binding protein. (asm.org)
- Using serine-to-alanine mutants to map phosphorylation sites on HSV-2 VP22 in cells, we made three major observations. (jove.com)
- Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks in living cells. (mdpi.com)
- The guide also contains a discussion on various applications where crosslinking has been applied, including the powerful label-transfer technique for identifying or confirming protein interactions. (thermofisher.com)
- This review highlights the analysis of those protein-protein interactions that involve proline residues, the biochemistry of proline, and current drug discovery efforts based on proline peptidomimetics. (nih.gov)
- This book describes the vast variety of xenobiotics, such as pesticides, antibiotics, antibiotic resistance genes, agrochemicals and other pollutants, their interactions with the soil environment, and the currently available strategies and techniques for soil decontamination and bioremediation. (springer.com)
- Our computer modeling predicted binding sites and the modes of interactions of these molecules at the atomic level. (eurekalert.org)
- These techniques have expanded beyond that of traditional applications of epitope mapping and protein-protein interactions to include virus as-sembly and antibody neutralization. (springer.com)
- I shall discuss the importance of electrostatic interactions, the role of dielectric heterogeneity of the protein interior in affecting the p K a and protonation state of the key ionizable residues, and the role of internal water molecules therein. (tifr.res.in)
- Biological evolution conserves protein residues that are important for structure and function. (biomedcentral.com)
- Determining these protein-RNA binding residues can help to elucidate the underlying mechanisms, to control biological processes, or to design RNA-based drug. (biomedcentral.com)
- The binding email is biological. (way2goal.com)
- The traditional method of recognizing zinc-binding sites is through biological experiments, which owns time-consuming and expensive cost. (alliedacademies.org)
- We have developed amino acid residue-nucleotide pair potentials for different organisms, which could be used for predicting the binding specificity. (biomedcentral.com)
- The MBD enrichment technique uses the specificity of the protein binding site to selectively capture 5-methylcytosine DNA. (activemotif.com.cn)
- Be it photosynthesis (conversion of light into chemical energy), or enzyme catalysis (speeding up difficult chemical reactions), or ion channels (filtration device with high degree of specificity), or self-assembly of small molecules into organized structures, we have a lot to learn from biology! (tifr.res.in)
- We believe this hydrophobic cleft is a general binding site (on amyloid beta) for molecules," Martí said. (eurekalert.org)
- But to create drugs for these, we first need to know how drugs or molecules in general can bind and interact with these fibrils, and this was not well-known. (eurekalert.org)
- It's perfect, because then molecules with hydrophobic domains are driven to bind there," Martí said. (eurekalert.org)
- To achieve this, his team is constantly working to develop high-resolution imaging techniques to visualize the activity and location of the molecules involved in the process. (maxplanckflorida.org)
- We explore the strengths and weaknesses of RMSD, PLIF similarity, and SuCOS on a dataset of X-ray crystal structures of paired elaborated larger and smaller molecules bound to the same protein. (ox.ac.uk)
- However, hydrogen (and deuterium) atoms, which have only one electron, scatter X-rays very little ( Figure 1a , below), so the X-ray diffraction signal for water (H 2 O) is much the same as for oxygen atoms (O). As a result, when scientists tried to examine how the ice-binding surface interacts with ice, they were unable to identify all the water molecules on the surface. (scienceinschool.org)
- Techniques have been urbanized to modify the action of restriction enzymes to hydrolyze only one strand of the duplex, to fabricate DNA molecules that are "nicked", rather than cleaved. (expertsmind.com)
- These functions may come from different IDP/IDR states or transitions among these states [11- which include disordered state, molecular recognition and binding to partner molecules. (deepdyve.com)
- The specific protein in the sample competes with a fixed amount of the same enzyme-conjugated protein for the constant number of binding sites on the antibody. (sigmaaldrich.com)
- Substrate solution is added, which is acted upon by the bound enzyme to produce color. (sigmaaldrich.com)
- They utilize a β-glucosyltransferase enzyme to transfer a modified glucose moiety to 5-hydroxymethylcytosine residues in double-stranded DNA. (activemotif.com)
- Two independent hydrolytic reactions advancement in parallel, most often determined by the presence of two catalytic sites within each enzyme, one for hydrolyzing each strand. (expertsmind.com)
- The team began their work by taking a closer look at the enzyme looking specifically for the key amino acids that were used to bind to the linkers holding PET monomers together. (phys.org)
- In addition, even though ligands for EH domains and 14-3-3 domains are not proline-rich, they do include a single proline residue. (nih.gov)
- It can be difficult to figure out, for example, what kind of linker to put between your two binding ligands - what it should look like and how long it should be. (sciencemag.org)
- And different ligands can have different effects, even when they're binding the same target protein, and (naturally enough) recruitment of different ubiquitin ligases can make a big difference, too. (sciencemag.org)
- In the validation study, we tested capabilities of a tool built upon our approach, called SurpResi, by searching for binding sites interacting with ligands. (biomedcentral.com)
- Our research demonstrated the effectiveness from the two-step focus on binding and selectivity testing technique in looking subtype selective ligands from huge compound libraries. (exposed-skin-care.net)
- The recognition mechanisms of protein-RNA complexes and their functional importance have been mainly elucidated by three-dimensional structure determination of protein-RNA complexes [ 2 ] along with other molecular biology experiments such as site directed mutagenesis, fluorescence resonance energy transfer (FRET) imaging, etc. (biomedcentral.com)
- Site-directed mutagenesis of charged amino acids of the human mitochondrial carnitine/acylcarnitine carrier: insight into the molecular mechanism of transport. (semanticscholar.org)
- Site-directed mutagenesis of the His residues of the rat mitochondrial carnitine/acylcarnitine carrier: implications for the role of His-29 in the transport pathway. (semanticscholar.org)
- A spot of solution is dotted onto nitrocellulose paper, a specific antibody or probe is allowed to bind and the presence of bound antibody/probe is then shown by using a coupled secondary antibody, as in immunoblotting or by other visualization methods (fluorescence, colorimetric). (sigmaaldrich.com)
- Our data are in support of an antiparallel alignment of the photoprobe with the amino acid residues 23-36 of the CRFBP monomer. (pnas.org)
- This binding groove consists of two long helices, 1 and 2, mounted on a floor of eight antiparallel -strands. (techuniq.com)
- For researchers interested in specific enrichment of either 5-mC and 5-hmC methylation, or researchers needing to identify total cytosine methylation, the MeDIP and hMeDIP techniques are ideal. (activemotif.com.cn)
- The 5-hmC control DNA has been modified so that 25% of the cytosine residues contain 5-hydroxymethylcytosine. (activemotif.com)
- Active Motif's hMeDIP Kit differs from traditional MeDIP in that the antibody is able to efficiently bind DNA in its native double-stranded form, so denaturation is not necessary. (activemotif.com.cn)
- Pubmed ID: 15527835 Phosphorylation of the herpes simplex virus (HSV) VP22 protein is regulated by cellular kinases and the UL13 viral kinase, but the sites at which these enzymes induce phosphorylation of HSV-2 VP22 are not known. (jove.com)
- One way to discover new enzymes in these environments is by using functional metagenomics, a culture-independent technique that allows enzymes to be identified by activity rather than by homology to known enzymes. (asbmb.org)
- An appropriate small set of properties can be chosen by either expert knowledge or PCA analysis of preselected properties reflecting the learning set composition (Weighted PCA). (biomedcentral.com)
- Using these highly conserved, semi-buried residues and their biophysical properties, we could distinguish cell cycle S/T kinases from other kinase families at levels around 70-80% accuracy and 62-81% coverage. (rostlab.org)
- Some experimental techniques such as X-ray crystallography, NMR Spectroscopy and cross-linking approaches, have applied to investigate protein-RNA interface properties. (biomedcentral.com)
- So far, a variety of experimental techniques have been developed and designed for the detection of PPIs. (hindawi.com)
- Further, improved docking techniques are being created and applied from the results of deeper analysis coupled with ongoing experimental data from our collaborators. (worldcommunitygrid.org)
- This process is experimental and the keywords may be updated as the learning algorithm improves. (springer.com)
- Many experimental techniques have been used to identify IDPs/IDRs [23, for example, nuclear magnetic resonance (NMR), X-ray crystallography, circular dichroism (CD) spectroscopy, small-angle X-ray scattering (SAXS) and single-molecule fluorescence resonance energy transfer (smFRET). (deepdyve.com)
- Among the main characteristics from the molecular framework of mAChRs may be the evolutionarily extremely conserved orthosteric ACh binding site, with an integral asparagine residue (Asn105). (acancerjourney.info)
- Second, as shown in the diagram below, biotin has a valeric acid side chain that is easily derivatized and conjugated to reactive moieties and chemical structures without affecting its avidin-binding function. (thermofisher.com)
- The structures of protein-RNA complexes have been effectively used for identifying the binding sites using distance based criteria, solvent accessibility based method and energy based approach [ 3 - 5 ]. (biomedcentral.com)
- The extracellular domain contains the binding site for the neurotransmitter acetylcholine (ACh). (intechopen.com)
- Inside the pentameric complex construction of those receptors, the α/β interface locates the binding web page of agonists as well as α/γ interface varieties the benzodiazepine (BZD) binding site on extracellular domain. (blogs-service.com)
- That oxidation only happens right next to the place where it binds," he said. (eurekalert.org)
- We found multiple oxygen binding locations adjacent to the oxidation site," said Prabhakar. (eurekalert.org)
- More recently, Dr. Levine and his colleagues have found that methionine sulfoxide reductase catalyzes oxidation and reduction of methionine residues bidirectionally. (nih.gov)
- Finding the site was relatively simple once the lab of Rice Chemist Angel Martí used its rhenium-based complexes to target fibrils. (eurekalert.org)
- The 3' UTR of the mRNA contains a cis-acting element required for the localization of Arc to neuronal dendrites, as well as sites for two exon junction complexes (EJCs) that make Arc a natural target for nonsense mediated decay (NMD). (wikipedia.org)
- On the other hand, several methods based on machine learning techniques have been proposed for identifying the binding sites in protein-RNA complexes. (biomedcentral.com)
- Cryo-EM, particularly single particle analysis (SPA), is becoming an essential technique for structure determination of viruses and protein complexes. (fei.com)
- The cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel contains two cytoplasmic nucleotide-binding domains (NBDs). (nih.gov)
- These results could not be attributed to altered binding of nucleotide because none of the mutants studied had reduced 8-N3ATP binding. (nih.gov)
- 11 ] considered the residues local environments and designed the conjoint triad method. (hindawi.com)
- In cross-validation experiments on the RBP170 data set show that PredRBR achieves an overall accuracy of 0.84, a sensitivity of 0.85, MCC of 0.55 and AUC of 0.92, which are significantly better than that of other widely used machine learning algorithms such as Support Vector Machine, Random Forest, and Adaboost. (biomedcentral.com)
- Promega's technique is based on their widely-used NanoBit technology. (sciencemag.org)
- 2.5Å, as defined in DSSP [ 14 ]), (ii) pentamers with non-standard amino acids, and (iii) all but the first set of atomic coordinates for residues with alternative locations. (biomedcentral.com)
- First, phosphorylation by a cellular kinase mapped to serines 70, 71, and/or 72 within CKII consensus sites analogous to previously identified phosphorylation sites in HSV-1 VP22. (jove.com)
- Second, we mapped UL13-mediated phosphorylation of HSV-2 VP22 to serines 28 and 34, describing for the first time UL13-dependent phosphorylation sites on VP22. (jove.com)
- A vast number of studies have focused on understanding the nitric oxide (NO) signaling pathway, which culminates with the phosphorylation of the transcription factor cAMP-responsive element-binding protein (CREB) through the increase of the second messenger cyclic guanosine monophosphate (cGMP) and activation of cGMP-dependent protein kinase. (intechopen.com)
- This book chapter provides an overview of the progress being made in modulating the hippocampal synaptic transmissions, which are critical for learning and memory, by targeting the different components of the NO/cGMP/CREB phosphorylation signaling pathway. (intechopen.com)