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.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.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 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).Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.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.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.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.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 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.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.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)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.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 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.Solvents: Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.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).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.Crystallography: The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.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.Muramidase: A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.Static Electricity: The accumulation of an electric charge on a objectEnzymes: Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.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)Knowledge Bases: Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).Artificial Intelligence: Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.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.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.Protein Stability: The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.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)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.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.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.Myoglobin: A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.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.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Bacterial Proteins: Proteins found in any species of bacterium.X-Ray Diffraction: The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Monte Carlo Method: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.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.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.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.Neural Networks (Computer): A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Solutions: The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)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.Entropy: The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Chemistry, Physical: The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.Physicochemical Phenomena: The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Models, Theoretical: Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.Kinetics: The rate dynamics in chemical or physical systems.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.Automation: Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)Pliability: The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)Spectrophotometry, Infrared: Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Protein Unfolding: Conformational transitions of the shape of a protein to various unfolded states.Cryoelectron Microscopy: Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.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.Mathematical Concepts: Numeric or quantitative entities, descriptions, properties, relationships, operations, and events.Computing Methodologies: Computer-assisted analysis and processing of problems in a particular area.Hydrogen: The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Deuterium Exchange Measurement: A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Biophysical Phenomena: The physical characteristics and processes of biological systems.Biophysics: The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.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.Electrons: Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.Hemerythrin: A non-heme iron protein consisting of eight apparently identical subunits each containing 2 iron atoms. It binds one molecule of oxygen per pair of iron atoms and functions as a respiratory protein.Synchrotrons: Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Normal Distribution: Continuous frequency distribution of infinite range. Its properties are as follows: 1, continuous, symmetrical distribution with both tails extending to infinity; 2, arithmetic mean, mode, and median identical; and 3, shape completely determined by the mean and standard deviation.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.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.Surface Properties: Characteristics or attributes of the outer boundaries of objects, including molecules.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Scattering, Small Angle: Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.Rubredoxins: A class of iron-sulfur proteins that contains one iron coordinated to the sulfur atom of four cysteine residues. (McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Online Systems: Systems where the input data enter the computer directly from the point of origin (usually a terminal or workstation) and/or in which output data are transmitted directly to that terminal point of origin. (Sippl, Computer Dictionary, 4th ed)Quantum Theory: The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Drug Design: The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.Programming Languages: Specific languages used to prepare computer programs.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Spectroscopy, Fourier Transform Infrared: A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.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)Ribonuclease, Pancreatic: An enzyme that catalyzes the endonucleolytic cleavage of pancreatic ribonucleic acids to 3'-phosphomono- and oligonucleotides ending in cytidylic or uridylic acids with 2',3'-cyclic phosphate intermediates. EC 3.1.27.5.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.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Bacteriorhodopsins: Rhodopsins found in the PURPLE MEMBRANE of halophilic archaea such as HALOBACTERIUM HALOBIUM. Bacteriorhodopsins function as an energy transducers, converting light energy into electrochemical energy via PROTON PUMPS.Crown Ethers: Macrocyclic polyethers with the repeating unit of (-CH2-CH2-O)n where n is greater than 2 and some oxygens may be replaced by nitrogen, sulfur or phosphorus. These compounds are useful for coordinating CATIONS. The nomenclature uses a prefix to indicate the size of the ring and a suffix for the number of heteroatoms.Proteome: The protein complement of an organism coded for by its genome.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Amino Acids, Aromatic: Amino acids containing an aromatic side chain.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.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Apoproteins: The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Software Design: Specifications and instructions applied to the software.Drug Stability: The chemical and physical integrity of a pharmaceutical product.Databases as Topic: Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)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).Amides: Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)Fourier Analysis: Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)Software Validation: The act of testing the software for compliance with a standard.Motion: Physical motion, i.e., a change in position of a body or subject as a result of an external force. It is distinguished from MOVEMENT, a process resulting from biological activity.Ions: An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.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.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Multiprotein Complexes: Macromolecular complexes formed from the association of defined protein subunits.Triose-Phosphate Isomerase: An enzyme that catalyzes reversibly the conversion of D-glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. A deficiency in humans causes nonspherocytic hemolytic disease (ANEMIA, HEMOLYTIC, CONGENITAL NONSPHEROCYTIC). EC 5.3.1.1.Biochemistry: The study of the composition, chemical structures, and chemical reactions of living things.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Energy Transfer: The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.Pyrococcus furiosus: A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Metalloproteins: Proteins that have one or more tightly bound metal ions forming part of their structure. (Dorland, 28th 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.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.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Spectrum Analysis, Raman: Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.Lipid Bilayers: Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.National Institute of General Medical Sciences (U.S.): Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports basic biomedical research that is not targeted to specific diseases and funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells and metabolism. It was established in 1962.Data Display: The visual display of data in a man-machine system. An example is when data is called from the computer and transmitted to a CATHODE RAY TUBE DISPLAY or LIQUID CRYSTAL display.Histidine: An essential amino acid that is required for the production of HISTAMINE.Nitrogen Isotopes: Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.Ubiquitin: A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Deuterium: Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.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.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Micelles: Particles consisting of aggregates of molecules held loosely together by secondary bonds. The surface of micelles are usually comprised of amphiphatic compounds that are oriented in a way that minimizes the energy of interaction between the micelle and its environment. Liquids that contain large numbers of suspended micelles are referred to as EMULSIONS.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)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.Torsion, Mechanical: A twisting deformation of a solid body about an axis. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Lactalbumin: A major protein fraction of milk obtained from the WHEY.Protein Footprinting: A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.Mutant Proteins: Proteins produced from GENES that have acquired MUTATIONS.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.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).Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Electron Spin Resonance Spectroscopy: A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.Metals: Electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals. (Grant & Hackh's Chemical Dictionary, 5th ed)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.Molecular Docking Simulation: A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.Probability: The study of chance processes or the relative frequency characterizing a chance process.Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.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.Neutrons: Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.Aspartate Aminotransferase, Mitochondrial: An aspartate aminotransferase found in MITOCHONDRIA.Mathematical Computing: Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem.Heme: The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.Urea: A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.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.Detergents: Purifying or cleansing agents, usually salts of long-chain aliphatic bases or acids, that exert cleansing (oil-dissolving) and antimicrobial effects through a surface action that depends on possessing both hydrophilic and hydrophobic properties.Genetic Variation: Genotypic differences observed among individuals in a population.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.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)

Melatonin biosynthesis: the structure of serotonin N-acetyltransferase at 2.5 A resolution suggests a catalytic mechanism. (1/55031)

Conversion of serotonin to N-acetylserotonin, the precursor of the circadian neurohormone melatonin, is catalyzed by serotonin N-acetyltransferase (AANAT) in a reaction requiring acetyl coenzyme A (AcCoA). AANAT is a globular protein consisting of an eight-stranded beta sheet flanked by five alpha helices; a conserved motif in the center of the beta sheet forms the cofactor binding site. Three polypeptide loops converge above the AcCoA binding site, creating a hydrophobic funnel leading toward the cofactor and serotonin binding sites in the protein interior. Two conserved histidines not found in other NATs are located at the bottom of the funnel in the active site, suggesting a catalytic mechanism for acetylation involving imidazole groups acting as general acid/base catalysts.  (+info)

Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A. (2/55031)

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of activated Rab3A/GTP/Mg2+ bound to the effector domain of rabphilin-3A was solved to 2.6 A resolution. Rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion.  (+info)

Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. (3/55031)

The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F, and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Crystal structures of two Sm protein complexes, D3B and D1D2, show that these proteins have a common fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers superpose closely in their core regions, including the dimer interfaces. The crystal structures suggest that the seven Sm proteins could form a closed ring and the snRNAs may be bound in the positively charged central hole.  (+info)

A viral mechanism for inhibition of p300 and PCAF acetyltransferase activity. (4/55031)

Nucleosomal histone modification is believed to be a critical step in the activation of RNA polymerase II-dependent transcription. p300/CBP and PCAF histone acetyltransferases (HATs) are coactivators for several transcription factors, including nuclear hormone receptors, p53, and Stat1alpha, and participate in transcription by forming an activation complex and by promoting histone acetylation. The adenoviral E1A oncoprotein represses transcriptional signaling by binding to p300/CBP and displacing PCAF and p/CIP proteins from the complex. Here, we show that E1A directly represses the HAT activity of both p300/CBP and PCAF in vitro and p300-dependent transcription in vivo. Additionally, E1A inhibits nucleosomal histone modifications by the PCAF complex and blocks p53 acetylation. These results demonstrate the modulation of HAT activity as a novel mechanism of transcriptional regulation.  (+info)

Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12. (5/55031)

Activation of the type I TGFbeta receptor (TbetaR-I) requires phosphorylation of a regulatory segment known as the GS region, located upstream of the serine/threonine kinase domain in the cytoplasmic portion of the receptor. The crystal structure of a fragment of unphosphorylated TbetaR-I, containing both the GS region and the catalytic domain, has been determined in complex with the FK506-binding protein FKBP12. TbetaR-I adopts an inactive conformation that is maintained by the unphosphorylated GS region. FKBP12 binds to the GS region of the receptor, capping the TbetaR-II phosphorylation sites and further stabilizing the inactive conformation of TbetaR-I. Certain structural features at the catalytic center of TbetaR-I are characteristic of tyrosine kinases rather than Ser/Thr kinases.  (+info)

Crystal structure of wild-type human procathepsin K. (6/55031)

Cathepsin K is a lysosomal cysteine protease belonging to the papain superfamily. It has been implicated as a major mediator of osteoclastic bone resorption. Wild-type human procathepsin K has been crystallized in a glycosylated and a deglycosylated form. The latter crystals diffract better, to 3.2 A resolution, and contain four molecules in the asymmetric unit. The structure was solved by molecular replacement and refined to an R-factor of 0.194. The N-terminal fragment of the proregion forms a globular domain while the C-terminal segment is extended and shows substantial flexibility. The proregion interacts with the enzyme along the substrate binding groove and along the proregion binding loop (residues Ser138-Asn156). It binds to the active site in the opposite direction to that of natural substrates. The overall binding mode of the proregion to cathepsin K is similar to that observed in cathepsin L, caricain, and cathepsin B, but there are local differences that likely contribute to the specificity of these proregions for their cognate enzymes. The main observed difference is in the position of the short helix alpha3p (67p-75p), which occupies the S' subsites. As in the other proenzymes, the proregion utilizes the S2 subsite for anchoring by placing a leucine side chain there, according to the specificity of cathepsin K toward its substrate.  (+info)

Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions. (7/55031)

Hydrophobic substitutions at solvent-exposed positions in two alpha-helical regions of the bacteriophage P22 Arc repressor were introduced by combinatorial mutagenesis. In helix A, hydrophobic residues were tolerated individually at each of the five positions examined, but multiple substitutions were poorly tolerated as shown by the finding that mutants with more than two additional hydrophobic residues were biologically inactive. Several inactive helix A variants were purified and found to have reduced thermal stability relative to wild-type Arc, with a rough correlation between the number of polar-to-hydrophobic substitutions and the magnitude of the stability defect. Quite different results were obtained in helix B, where variants with as many as five polar-to-hydrophobic substitutions were found to be biologically active and one variant with three hydrophobic substitutions had a t(m) 6 degrees C higher than wild-type. By contrast, a helix A mutant with three similar polar-to-hydrophobic substitutions was 23 degrees C less stable than wild-type. Also, one set of three polar-to-hydrophobic substitutions in helix B was tolerated when introduced into the wild-type background but not when introduced into an equally active mutant having a nearly identical structure. Context effects occur both when comparing different regions of the same protein and when comparing the same region in two different homologues.  (+info)

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. (8/55031)

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets.  (+info)

*Protein primary structure

However, the complexity of protein folding currently prohibits predicting the tertiary structure of a protein from its sequence ... Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure ... tertiary structure). Protein sequence can be used to predict local features, such as segments of secondary structure, or trans- ... for example a member of the same protein family) allows highly accurate prediction of the tertiary structure by homology ...

*Protein tertiary structure

A number of tertiary structures may fold into a quaternary structure. The science of the tertiary structure of proteins has ... Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide ... The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary ... Contemporary methods are able to determine, without prediction, tertiary structures to within 5 Å (0.5 nm) for small proteins ( ...

*De novo protein structure prediction

... de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its ... Protein structure prediction Protein structure prediction software Protein design "Editorial: So much more to know". Science. ... De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles ... Coarse-grained protein models allow for de novo structure prediction of small proteins, or large protein fragments, in a short ...

*Protein secondary structure

Predicting protein tertiary structure from only its amino acid sequence is a very challenging problem (see protein structure ... The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with ... He had already introduced the concepts of the primary, secondary, and tertiary structure of proteins in the third Lane Lecture ... Accurate secondary-structure prediction is a key element in the prediction of tertiary structure, in all but the simplest ( ...

*Ram Samudrala

Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. ... Ab initio prediction of protein structure using a combined hierarchical approach. Proteins: Structure, Function, and Genetics ... A database of incorrect protein conformations to improve protein structure prediction. Protein Science 9: 1399-1401, 2000. Liu ... Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins: Structure, Function, and ...

*Template modeling score

... modeling score or TM-score is a measure of similarity between two protein structures with different tertiary structures. The TM ... RMSD - a different structure comparison measure GDT - a different structure comparison measure LCS - a different structure ... Proteins. 57 (4): 702-710. doi:10.1002/prot.20264. PMID 15476259. Zhang Y and Skolnick J (2005). "TM-align: a protein structure ... Xu J and Zhang Y (2010). "How significant is a protein structure similarity with TM-score = 0.5?". Bioinformatics. 26 (7): 889- ...

*Globular protein

The spherical structure is induced by the protein's tertiary structure. The molecule's apolar (hydrophobic) amino acids are ... Even in the protein's denatured state, it can be folded into the correct structure. Globular proteins seem to have two ... Globular proteins or spheroproteins are spherical ("globe-like") proteins and are one of the common protein types (the others ... Regulatory roles are also performed by globular proteins rather than fibrous proteins. Structural proteins, e.g., actin and ...

*Beta sheet

Tertiary Protein Structure and Folds: section 4.3.2.1. From Principles of Protein Structure, Comparative Protein Modelling, and ... See sections II B and III C, D in Richardson JS (1981). Anatomy and Taxonomy of Protein Structures. Advances in Protein ... Anatomy & Taxonomy of Protein Structures -survey NetSurfP - Secondary Structure and Surface Accessibility predictor. ... Hutchinson EG, Thornton JM (1990). "HERA--a program to draw schematic diagrams of protein secondary structures". Proteins. 8 (3 ...

*Michael Levitt

Xia, Y.; Huang, E. S.; Levitt, M.; Samudrala, R. (2000). "Ab initio construction of protein tertiary structures using a ... He has also worked on simplified representations of protein structure for analysing folding and packing, as well as developing ... Hinds, D. A.; Levitt, M. (1994). "Exploring conformational space with a simple lattice model for protein structure". Journal of ... Brenner, S. E.; Koehl, P.; Levitt, M. (2000). "The ASTRAL compendium for protein structure and sequence analysis". Nucleic ...

*Citrullination

Thus, arginine's positive charge (at physiological pH) is removed, altering the protein's tertiary structure. The reaction uses ... This increases the hydrophobicity of the protein, which can lead to changes in protein folding, affecting the structure and ... autoantibodies often attack citrullinated proteins. The presence of anti-citrullinated protein antibody is a standard test for ... Citrullinated proteins are also found in the cellular debris accompanying the destruction of cells in alzheimer disease, and ...

*Jeffrey Skolnick

"TASSER: An automated method for the prediction of protein tertiary structures in CASP6". Proteins: Structure, Function, and ... "Protein study suggests drug side effects are inevitable". Drug Discovery Today. May 23, 2013. Zhang, Yang. "Protein structure ... and the exploration of the interplay between protein physics and evolution in determining protein structure and function. ... Skolnick was first to demonstrate that the library of single domain protein structures is likely complete and that the observed ...

*Latisemin

... cysteines not oxidised to cystine and thus not providing disulfide bond support to tertiary protein structure). They are ... "Structure and function of snake venom cysteine-rich secretory proteins". Toxicon. 44 (3): 227-231. doi:10.1016/j.toxicon. ... Other snake venom proteins in the CRISP family: Ablomin from the Japanese Mamushi snake (Gloydius blomhoffi) Ophanin from the ... Latisemin is a cysteine-rich secretory protein that can be isolated from the venom of the Black-banded sea krait, a sea snake ...

*Prion

Effective prion decontamination relies upon protein hydrolysis or reduction or destruction of protein tertiary structure. ... The "protein-only hypothesis" states that a protein structure can replicate without the use of nucleic acids. This was ... One idea, the "Protein X" hypothesis, is that an as-yet unidentified cellular protein (Protein X) enables the conversion of ... disease Prion pseudoknot Protein folding Protein misfolding cyclic amplification Proteopathy Spiroplasma Tertiary structure ...

*Cystine

Lanthionine, similar with mono-sulfide link Protein tertiary structure Sullivan reaction Cystinosis Nelson, D. L.; Cox, M. M.; ... a site of redox reactions and a mechanical linkage that allows proteins to retain their three-dimensional structure. It is ... It was not recognized as being derived of proteins until it was isolated from the horn of a cow in 1899. Human hair and skin ... In cell biology, cystine (found in proteins) can only exist in non-reductive (oxidative) organelles, such as the secretory ...

*Protein structure

Proteins are often thought of as relatively stable structures that have a set tertiary structure and experience conformational ... The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a ... There are four distinct levels of protein structure. The primary structure of a protein refers to the sequence of amino acids ... The generation of a protein sequence is much easier than the determination of a protein structure. However, the structure of a ...

*Conalbumin

Disulfide groups stabilize the tertiary structures of proteins. Transferrins, are iron binding proteins and acute phase ... This process is determined by the structure of the protein backbone and the carbohydrate attachment site. In addition, ... Egg white albumen is composed of multiple proteins and ovotransferrin is the most heat reliable protein of them all. It has a ... Consequently, structurally this protein differs from its serum counterpart because of its glycosylation pattern. These proteins ...

*Lattice protein

The relative positions of the beads in the native state constitute the lattice protein's tertiary structure. Lattice proteins ... Most researchers consider a lattice protein sequence protein-like only if it possesses a single structure with an energetic ... Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding. Because ... some researchers have claimed that they can be extrapolated onto real protein structures which do include secondary structure, ...

*Cysteine

... disulfide bridges between cysteine residues within a polypeptide support the protein's tertiary structure. Insulin is an ... Gorga, Frank R. (1998-2001). "Introduction to Protein Structure--Non-Polar Amino Acids". Archived from the original on 2012-09- ... Disulfide bonds play an important role in the folding and stability of some proteins, usually proteins secreted to the ... Cysteine residues play a valuable role by crosslinking proteins, which increases the rigidity of proteins and also functions to ...

*Kaj Ulrik Linderstrøm-Lang

... tertiary and quaternary structure. Linderstrøm-Lang devoted himself unstintingly to protein science and trained a whole ... 1992) "Contribution of physical chemistry to an understanding of protein structure and function", Protein Sci., 1, 691-693. ... Linderstrøm-Lang is justly famous for his organization of protein structure into four levels: primary, secondary, tertiary and ... His most notable scientific contributions were the development of sundry physical techniques to study protein structure and ...

*WHAT IF software

... homology modeling of protein tertiary structures and quaternary structures; validating protein structures, notably those ... Hooft, RW; Vriend, G; Sander, C; Abola, EE (23 May 1996). "Errors in protein structures". Nature. 381 (6580): 272. doi:10.1038/ ... correcting protein structures; visualising macromolecules and their interaction partners (for example, lipids, drugs, ions, and ... WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The ...

*Hans Frauenfelder

Within biophysics, he is known for experiment and theory in understanding the dynamical behavior of protein tertiary structure ... and the biophysics of protein folding and motions. In 1992, Frauenfelder moved to the Los Alamos National Laboratory where he ...

*Protein domain

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist ... motif Protein Protein structure Protein structure prediction Protein structure prediction software Protein superfamily Protein ... The overall 3D structure of the polypeptide chain is referred to as the protein's tertiary structure. Domains are the ... However, sequence similarities can be extremely low between proteins that share the same structure. Protein structures may be ...

*List of MeSH codes (G06)

... protein structure, tertiary MeSH G06.184.603.790.709.610.380 --- hmg-box domains MeSH G06.184.603.790.709.610.480 --- kringles ... protein conformation MeSH G06.184.603.790.709.550 --- protein structure, quaternary MeSH G06.184.603.790.709.600 --- protein ... protein processing, post-translational MeSH G06.535.770.871.790.600.400 --- protein isoprenylation MeSH G06.535.770.871.790.600 ... protein MeSH G06.184.842.550 --- sequence homology, nucleic acid MeSH G06.184.842.550.830 --- synteny MeSH G06.184.850.400 --- ...

*Backbone chain

Further interactions between residues of the individual amino acids form the protein's tertiary structure. For this reason, the ... This primary structure leads to folding of the protein into the secondary structure, formed by hydrogen bonding between the ... primary structure of the amino acids in the polypeptide backbone is the map of the final structure of a protein, and it ... The sequence of the amino acids in the polypeptide backbone is known as the primary structure of the protein. ...

*Protein contact map

HB plot offers a simple way of analyzing protein secondary structure and tertiary structure. Hydrogen bonds stabilizing ... The structure of beta-lactoglobulin reveals that the barrel-form structure with the central cavity of the protein has an " ... Contact maps are also used for protein superimposition and to describe similarity between protein structures. They are either ... Knowledge of the relationship between a protein's structure and its dynamic behavior is essential for understanding protein ...

*Prostaglandin-endoperoxide synthase 2

The tertiary and quaternary structures of PTGS1 (COX-1) and PTGS2 (COX-2) enzymes are almost identical. Each subunit has three ... Picot D, Loll PJ, Garavito RM (January 1994). "The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1 ... PTGS (COX, which can be confused with "cytochrome oxidase") enzymes are monotopic membrane proteins; the membrane-binding ... of the protein. The catalytic domain is homologous to mammalian peroxidases such as myeloperoxidase. It has been found that ...
Toll-like receptors (TLRs) act as the first line of defense against bacterial and viral pathogens by initiating critical defense signals upon dimer activation. The contribution of the transmembrane domain in the dimerization and signaling process has heretofore been overlooked in favor of the extracellular and intracellular domains. As mounting evidence suggests that the transmembrane domain is a critical region in several protein families, we hypothesized that this was also the case for Toll-like receptors. Using a combined biochemical and biophysical approach, we investigated the ability of isolated Toll-like receptor transmembrane domains to interact independently of extracellular domain dimerization. Our results showed that the transmembrane domains had a preference for the native dimer partners in bacterial membranes for the entire receptor family. All TLR transmembrane domains showed strong homotypic interaction potential. The TLR2 transmembrane domain demonstrated strong heterotypic interactions
Protein domains are compact regions of a proteins structure that often convey some distinct function. Domain architecture, or order of domains in a protein, is frequently considered as a fundamental level of protein functional complexity [1]. The majority of the protein repertoire is composed of multidomain proteins; two-thirds of the proteins in prokaryotes and about four-fifths eukaryotic ones have two or more domains [2]. Moreover, an organisms complexity relates much better to the number of distinct domain architectures [3] and expansion in particular domain families [4] than to the number of genes in the organism. The prevalence of proteins with more than two domains and the recurrent appearance of the same domain in non-homologues proteins show that functional domains are reused when creating new proteins. Because of this, domains have been likened to Lego bricks that can be recombined in various ways to build proteins with completely new functions [5]. Hence, one way to study evolution ...
The SCOP classification for the Signal peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
(2004) Luoni et al. FEBS Letters. Type IIB Ca2+-ATPases have a terminal auto-inhibitory, domain the action of which is suppressed by calmodulin (CaM) binding. Here, we show that a peptide (6His-1M-I116) corresponding to the first 116 aminoacids (aa) of At-ACA8, the first cloned isoform of Arabido...
Shop KH homology domain-containing protein ELISA Kit, Recombinant Protein and KH homology domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
CSF1R protein domain and mutation schematic. Schematic diagram of the protein domain structure of CSF1R with amino acid numbers provided. Mutations previously r
Shop Forkhead-associated domain-containing protein ELISA Kit, Recombinant Protein and Forkhead-associated domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Domain architectures containing both Dcp2 domain-like and Nudix in all archaea. Links to architectures containing these domain pairs in other groups of genomes are provided. Domain pairs which are not adjacent can be added/removed.
Transmembrane domain architecture, symmetry and coupling to LBDa, View of the TMD parallel to the membrane. GluN1 subunits are blue and the GluN2B subunits are
BACKGROUND: The ferlin gene family possesses a rare and identifying featureconsisting of multiple tandem C2 domains and a C-terminal transmembrane domain.Much currently remains unknown about the fundamental function of this genefamily, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolutionof the ferlin family, providing contextual insight into characteristic featuresthat define the ferlin gene family in its present form in humans. RESULTS: Ferlingenes were detected from all species of representative phyla, with two ferlinsubgroups partitioned within the ferlin phylogenetic tree based on the presenceor absence of a DysF domain. Invertebrates generally possessed two ferlin genes(one with DysF and one without), with six ferlin genes in most vertebrates (threeDysF, three non-DysF). Expansion of the ferlin gene family is ...
2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474) ...
Methods for producing and identifying fragments of proteins, and more particularly to methods for generating and identifying soluble protein domains are disclosed based on a method for generating a li
People Era Consulting is an emerging recruitment firm providing end to end Talent Solutions to multifarious industrial segments across the country. Our focus has always been on providing a pool of potential and validated candidates across the level i.e. Senior, Middle and Junior management. We operate through domain specialist providing high quality permanent hiring services.. ...
People Era Consulting is an emerging recruitment firm providing end to end Talent Solutions to multifarious industrial segments across the country. Our focus has always been on providing a pool of potential and validated candidates across the level i.e. Senior, Middle and Junior management. We operate through domain specialist providing high quality permanent hiring services.. ...
For domaining or for your business needs, get the best aftermarket domain names for sale today! NameJet provides premium and expiring domain names through domain auctions and backorder services.
MAADESSQNTLRLQFKAMQEMQHKRLQKQMEKKREKELSLKSRADDQEEPLEVSDGLSLLHAGEPNSKNS 1 - 70 FEKRVLEDEIEHLRNELRETVDENGRLYKLLKERDFEIKHLKKKIEEDRFAFTGTAGVAGDVVATKIVEL 71 - 140 SKKNRLLMAESEGAKTRVKQLTNRIQELERELQTALTRLSAKGATDAGAKPPRAQMGDRALLETPEVKAL 141 - 210 QDRLVATNLKMSDLRNQIQSVKQELRMAQKVLAREVGEDINVQQLLSSPGTWRGRAQQILVLQSKVQELE 211 - 280 KQLGQARSQSAGTASDELSVYPDPRKLSAQEKNLLRIRSLEREKQEGLEKLASERDVLQRELEELKKKFE 281 - 350 GMRSRNKLLSSEMKTLKSQMGTLVEKGRHDDELIDALMDQLKQLQEILGSLSLQEEKTRVSQHHLDQQLN 351 - 420 SEAQRSNSLVAQLQAMVAEREAKVRQLEMEIGQLNVHYLRNKGVGEGSSGREVSPAYTQFLEDPGLTKSP 421 - 490 ASAGDHVGRLGSSRSVTSLGHTLVESALTRPSLPSPHRTSPRFSDSPEQKGWQAQVSEIKALWQAAEVER 491 - 560 DRLTEFVTVLQKRVEESNSKLLESERKLQEERHRTVVLEQHLEKIRLEPGKASASQRAAPRTKTGLPTSN 561 - 630 NRHNPTGSEKKDPSFAQLSDVPVESQMEELTTRLAIQVEENEMLKAALGSALRGKEEDFRMYHEILGQVK 631 - 700 SVFLQALRQQKTGKQ 701 - 715 ...
MPTLVVGTPPTCLGDTPQPCHKNSQRQGPFSHGAPGRAADWKAVAKPRLCAPAAEDDVAALRWPGPSQQP 1 - 70 DPPWAAPHVVGSDDLKEPGPWGKACSLPMWSTGPEARDGDSSVSSGRLSCSSGGHDVCVSWKERPPQVLG 71 - 140 PQQRPRKSDARLEQLRDKIRAQAWQQGSCASLGTSAPSSASRLHKASTLMLRRKGQEAKNPPPAPECSGF 141 - 210 SILSAAERRVEAKASHGQGRELSRVSQHQVPVLREKPKRVKSSSCKREKTPKLPSPRRAAKDKHKDEDSE 211 - 280 LVGVYAWRKGQALVRSLLGPPPVLRRHHSKDPSRDPALTVDLGDSEKVIAAKCSPVCAQLPDATSAYSDQ 281 - 350 QVSGNTPSLASFDQPATIQTAMAILQDLRQQIQAGLELAQARKGGQELGPSKRRLQDVAGRGCCRDPNAQ 351 - 420 SSFSKSPWAMTERKHSSLERARSVHTWEPWSSSTARESCPQRAWGAQGQDRSFQRPESPHERLGHFSQRP 421 - 490 WSALAGQACSPQRAWGAQRQGPSSQRPGSPPEKRSPFPQQPWSAVATQPCPRRAWTACETWEDPGPRLRN 491 - 560 PLERPSPPAQRPWSSSGVQRAGPQGKGRGIGSPVSAAKHALPRPTGSFPQNPLGKEKDTLRPCPRSRGLL 561 - 630 GPSHSSESLREFMRQKAQARRRQALEEKASALRTRELRSRRLQEVYRQQREAVLGRAVPVVSRTTPGIVT 631 - 700 FVPSSAQSGGLEASGSLESPVLEWSKVTSGMVLGGQEAPGSFCLCLNRAWNHAETLDPPGMGGPQDGRDA 701 - 770 PVLLSASPSLGSLELQDLTTRYLPRGMCIYLDPKEAEHLGTSSSLHLRHKQAQLQALETTAKVLKQRVDS 771 - 840 ...
When the improved inter-domain routing protocol is deployed, an immediate decrease in the number routing table entries should occur, followed by a significant reduction in the rate growth of routing table size (for default-free routers). ...
In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses, however, it is usually ignored that a significant proportion of Metazoan sequences analyzed is mispredicted and that this may seriously affect the validity of the conclusions. To estimate the contribution of errors in gene prediction to differences in DA of predicted proteins, we have used the high quality manually curated UniProtKB/Swiss-Prot database as a reference. For genome-scale analysis of domain architectures of predicted proteins we focused on RefSeq, EnsEMBL and NCBIs GNOMON predicted sequences of Metazoan species with completely sequenced genomes. Comparison of the DA of UniProtKB/Swiss-Prot sequences of worm, fly, zebrafish, frog, chick, mouse, rat and orangutan with those of human Swiss-Prot entries
Homer protein homolog 1 or Homer1 is a neuronal protein that in humans is encoded by the HOMER1 gene. Other names are Vesl and PSD-Zip45. Homer1 protein has an N-terminal EVH1 domain, involved in protein interaction, and a C-terminal coiled-coil domain involved in self association. It consists of two major splice variants, short-form (Homer1a) and long-form (Homer1b and c). Homer1a has only EVH1 domain and is monomeric while Homer1b and 1c have both EVH1 and coiled-coil domains and are tetrameric. The coiled-coil can be further separated into N-terminal half and C-terminal half. The N-terminal half of the coiled-coil domain is predicted to be a parallel dimer while the C-terminus half is a hybrid of dimeric and anti-parallel tetrameric coiled-coil. As a whole, long Homer is predicted to have a dumbbell-like structure where two pairs of EVH1 domains are located on two sides of long (~50 nm) coiled-coil domain. Mammals have Homer2 and Homer3, in addition to Homer1, which have similar domain ...
The crystal structure analysis of the NarL protein provides a first look at interactions between receiver and effector domains of a full-length bacterial response regulator. The N-terminal receiver domain, with 131 amino acids, is folded into a 5-strand beta sheet flanked by 5 alpha helices, as seen in CheY and in the N-terminal domain of NTRC. The C-terminal DNA-binding domain, with 62 amino acids, is a compact bundle of 4 alpha helices, of which the middle 2 form a helix-turn-helix motif closely related to that of Drosophila paired protein and other H-T-H DNA-binding proteins. The 2 domains are connected by an alpha helix of 10 amino acids and a 13-residue flexible tether that is not visible and presumably disordered in the X-ray structure. In this unphosphorylated form of NarL, the C-terminal domain is turned against the receiver domain in a manner that would preclude DNA binding. Activation of NarL via phosphorylation of Asp59 must involve transfer of information to the interdomain interface ...
The SCOP classification for the Heat shock protein 70kD (HSP70), peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBIs GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of
Monotopic proteins represent a specialized group of membrane proteins in that they are engaged in biochemical events taking place at the membrane interface. In particular, the monotopic lipid-synthesizing enzymes are able to synthesize amphiphilic lipid products by catalyzing two biochemically distinct molecules (substrates) at the membrane interface. Thus, from an evolutionary point of view, anchoring into the membrane interface enables monotopic enzymes to confer sensitivity to a changing environment by regulating their activities in the lipid biosynthetic pathways in order to maintain a certain membrane homeostasis. We are focused on a plant lipid-synthesizing enzyme DGD2 involved in phosphate shortage stress, and analyzed the potentially important lipid anchoring segments of it, by a set of biochemical and biophysical approaches. A mechanism was proposed to explain how DGD2 adjusts its activity to maintain a proper membrane. In addition, a multivariate-based bioinformatics approach was used ...
Ras is a small GTPase, controlling signal transduction pathways and promoting cell proliferation and survival. KRAS is frequently mutated in cancer. Ras consists of highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ significantly across Ras isoforms. Recent NMR and MD simulations discovered that the HVR of K-Ras4B-GDP extensively interacts with the catalytic domain. However, it weakly interacts with the catalytic domain in the GTP-bound state. Here, using MD simulations we modeled K-Ras4B membrane interaction and dimerization. On the membrane, the catalytic domain takes on multiple orientations, including perpendicular and parallel alignments of the allosteric helices with respect to the membrane normal. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with the farnesyl anchored into the membrane and the HVR unrestrained, the catalytic domain fluctuates reinlessly, exposing its ...
The SCOP classification for the Zn2/Cys6 DNA-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
pfam00091 (PSSM ID: 333832): Conserved Protein Domain Family Tubulin, This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins
TIGR00493 (PSSM ID: 188055): Conserved Protein Domain Family clpP, This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency
Sequences in Bids N-terminal fragment sequester the proapoptotic BH3 domain. Through this autoinhibitory mechanism, full-length Bid is kept in an inactive state (Chou et al., 1999; Tan et al., 1999). Bid can be converted to its active form by cleavage in its second unstructured loop, such as at D60 by caspase-8/10 and at D75 by granzyme B (Li et al., 1998; Luo et al., 1998; Sutton et al., 2003). Mechanistically, it was unclear why cleavage should lead to Bid activation. Upon Bid cleavage in vitro, the N- and C-terminal fragments remain associated according to both NMR and biochemical analyses (Chou et al., 1999; Zha et al., 2000; Kuwana et al., 2002). Moreover, several investigators have demonstrated that the tBid-N fragment, when expressed independently, can block the proapoptotic activity of the tBid-C fragment (Tan et al., 1999; Kudla et al., 2000; Renshaw et al., 2004). Collectively, these data suggest a critical inhibitory effect of the Bid N terminus upon the C-terminal proapoptotic ...
An R object that contains domain superfamily information for Rat Entrez Genes. This data is prepared based on SUPERFAMILY database, which provides SCOP domain architecture assignments to all completely sequenced genomes including eukaryotic genomes. The domain architecture for an Entrez gene is the protein product with the longest length of amino acids. Thus, domain superfamily information for Rat Entrez gene is a list of domain superfamilies (excluding unknown gap) appearing in its domain architecture.. ...
Several lines of evidence (summarized in [7]) suggest that the majority of BMCs assemble as a series of interacting protein domains that coalesce and are subsequently surrounded by the shell. Given that protein domains are the structural, functional and evolutionary units of proteins, (re-)engineering BMCs and other large multi-protein macromolecular assemblies may be tractable by focusing on domain structures and interactions, leveraging the inherent modularity of proteins for building new subcellular architectures. In this approach, protein domains constitute the architectural vocabulary for constructing new kinds of metabolic compartments. In practice, such a structure-based bioarchitectonic strategy involves surveying encapsulated protein folds in known BMCs to serve as the set of building blocks for engineering catalytic activities. In general, the functions supported by fold families are typically broad; diverse catalytic activities are frequently supported by the same structural scaffold ...
definition of ILKBP, what does ILKBP mean?, meaning of ILKBP, Integrin-Linked Kinase-Binding Protein, ILKBP stands for Integrin-Linked Kinase-Binding Protein
Complete information for SVEP1 gene (Protein Coding), Sushi, Von Willebrand Factor Type A, EGF And Pentraxin Domain Containing 1, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Hi guys, What are the routine methods by which you generate terminal truncations of a protein of interest for subsequent screening for purification, stability and efficient folding for the purposes of crystallization? My protein has 2 known domains and a conserved C-terminal part which is defined as domain by sequence homology with other proteins. We would like to generate different lengths of the protein containing this C-terminus and screen them for expression, solubility, purification, and folding and thus increase our chances for success. appreciate all help Iva ...
This is probably amateurish and obvious but I was surprised. I created a new site but under an existing domain that was already getting pretty good traffic. After only a few days the new site including individual pages came up #1 in Google or Yahoo searching with 2 words. I guess because the pages are crawled regularly. Seems like it might be OK to group new smaller sites under a common domain under some circumstances. Cheaper and less hassles too.
4GOD: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface.
SMYD1 antibody (SET and MYND domain containing 1) for ICC/IF, IHC-P, WB. Anti-SMYD1 pAb (GTX119484) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
View mouse Ubxn10 Chr4:138709837-138737167 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
Your website should be located at a domain name thats easy to discover, which means you have to opt for an internet address which is easy to remember a new
A scientific resource for the EH protein domain containing information on structure, function, and domain binding during endocytosis and vesicle trafficking.
Some of the hardest parts of working towards the ideal of a theorist, at least for me, are: (1) making sure that I engage with problems that can be made interesting to the new domain I enter and not just me; (2) engaging with these problems in a way and using tools that can be…
Heres what happened. I have a domain with the PDC and multiple BDCs. Someone took a BDC and moved it to a new domain. I had to bring ...
Oh how sweet the sound of other peoples money! Devoid of the real Truth - Patrick Henry knew that following false hope would lead only to further degradation. The further down the path we are headed the more like beasts we will become.
How many ways protein protein interactions are regulated? - posted in Biochemistry: I wonder how many ways protein-protein interactions are regulated. I know a lot of protein protein interactions are modified by phosphorylaton or other modification. Is there other ways that mediate the protein protein interaction? Thanks!
AICD, the C-terminal tail generated from the proteolytic cleavage of the Amyloid Precursor Protein (APP), has been generating interest for its transcriptional modulatory roles. AICD has been hypothesized to have such a function as it is generated by a gamma-secretase-mediated regulated intramembrane proteolysis step, analogous to the generation of Notch intracellular domain (NICD), a well-known transcriptional regulator, from Notch. The AICD/Fe65/Tip60 ternary complex has been proposed as the working transcriptional regulatory complex and some of its target genes have been reported. However, our knowledge of the functions of AICD is still limited due to difficulties in detecting and manipulating the rapidly degraded peptide. Looking at AICD transcription modulation targets from a genome-wide perspective will aid our understanding of the role of AICD tremendously. To this end, AICD chromatin binding sites were investigated from a genome-wide perspective by performing Chromatin Immunoprecipitation ...
9150PRTHomo sapiens 1Val Met Leu Lys Lys Lys Gln Tyr Thr Ser Ile His His Gly Val Val1 5 10 15Glu Val Asp Ala Ala Val Thr Pro Glu Glu Arg His Leu Ser Lys Met 20 25 30Gln Gln Asn Gly Tyr Glu Asn Pro Thr Tyr Lys Phe Phe Glu Gln Met 35 40 45Gln Asn 502134PRTHomo sapiens 2Ala Pro Lys Asn Glu Leu Val Gln Lys Phe Gln Val Tyr Tyr Leu Gly1 5 10 15Asn Val Pro Val Ala Lys Pro Val Gly Val Asp Val Ile Asn Gly Ala 20 25 30Leu Glu Ser Val Leu Ser Ser Ser Ser Arg Glu Gln Trp Thr Pro Ser 35 40 45His Val Ser Val Ala Pro Ala Thr Leu Thr Ile Leu His Gln Gln Thr 50 55 60Glu Ala Val Leu Gly Glu Cys Arg Val Arg Phe Leu Ser Phe Leu Ala65 70 75 80Val Gly Arg Asp Val His Thr Phe Ala Phe Ile Met Ala Ala Gly Pro 85 90 95Ala Ser Phe Cys Cys His Met Phe Trp Cys Glu Pro Asn Ala Ala Ser 100 105 110Leu Ser Glu Ala Val Gln Ala Ala Cys Met Leu Arg Tyr Gln Lys Cys 115 120 125Leu Asp Ala Arg Ser Gln 130325DNAArtificialPrimer APP_C50_F 3gtaccatatg gtgatgctga agaag 25432DNAArtificialPrimer APP_C50_R 4gtacaagctt ctagttctgc atctgctcaa ...
The BAR (Bin/amphiphysin/Rvs) domain is the most conserved feature in amphiphysins from yeast to human and is also found in endophilins and nadrins. We solved the structure of the Drosophila amphiphysin BAR domain. It is a crescent-shaped dimer that binds preferentially to highly curved negatively charged membranes. With its N-terminal amphipathic helix and BAR domain (N-BAR), amphiphysin can drive membrane curvature in vitro and in vivo. The structure is similar to that of arfaptin2, which we find also binds and tubulates membranes. From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module.
Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, …
Eukaryotic cells have evolved an intricate system to resolve DNA damage to prevent its transmission to daughter cells. This system, collectively known as the DNA damage response (DDR) network, includes many proteins that detect DNA damage, promote repair, and coordinate progression through the cell cycle. Because defects in this network can lead to cancer, this network constitutes a barrier against tumorigenesis. The modular BRCA1 carboxyl-terminal (BRCT) domain is frequently present in proteins involved in the DDR, can exist either as an individual domain or as tandem domains (tBRCT), and can bind phosphorylated peptides. We performed a systematic analysis of protein-protein interactions involving tBRCT in the DDR by combining literature curation, yeast two-hybrid screens, and tandem affinity purification coupled to mass spectrometry. We identified 23 proteins containing conserved BRCT domains and generated a human protein-protein interaction network for seven proteins with tBRCT. This study ...
A recent study showed that the globular tail of Myo4p is not required for the localization of GFP-MS2-tethered particles to the bud and for the inheritance of ER (Bookwalter et al., 2009). This observation suggested that the globular tail might be dispensable for the localization of endogenous ASH1 mRNA and thus also for inhibition of mating type switching in the daughter cell. It further raised the question of whether the globular tail of Myo4p has any function. Here, we used an experimentally refined, globular tail-lacking Myo4p to confirm the previous findings from Bookwalter et al. (2009) (Fig. S1, A-F).. However, when analyzing mother cell-specific expression of the HO endonuclease in cells expressing a globular tail-lacking Myo4p fragment, we found that this process is impaired (Fig. 2, A and B). The subsequent analysis of ASH1 mRNA localization by in situ hybridization and of Myo4p localization by immunofluorescence staining consistently showed that the globular tail is required for full ...
Protein domain superfamilies in CATH-Gene3D have been subclassified into functional families (or FunFams), which are groups of protein sequences and structures with a high probability of sharing the same function(s). Therefore, the functionally important residues in a family are also expected to be highly conserved.. Information on conserved positions in CATH-Gene3D FunFam alignments is shown through the Alignment tab of the FunFam webpages. Conservation scores have been calculated using Scorecons and columns in the alignment are coloured using a rainbow colour scheme, where the highly conserved residues are shown in red through to positions that are not conserved at all, shown in blue. The conservation scores are also mapped onto a representative protein domain structure.. To investigate putative conserved sites for your protein sequence, run a sequence search against the FunFams and click on the FunFam match Alignment page.. ...
Domain combinations containing the Periplasmic binding protein-like I superfamily . Domain architectures illustrate each occurrence of the Periplasmic binding protein-like I superfamily.
Domain combinations containing the Ubiquitin-like superfamily in Saccharomyces cerevisiae 69_4. Domain architectures illustrate each occurrence of the Ubiquitin-like superfamily.
The process by which fibronectin (FN), a soluble multidomain protein found in tissue fluids, forms insoluble fibrillar networks in the extracellular matrix is poorly understood. Cryptic sites found in FN type III domains have been hypothesized to function as nucleation points, thereby initiating fibrillogenesis. Exposure of these sites could occur upon tension-mediated mechanical rearrangement of type III domains. Here, we present the solution structures of the second type III domain of human FN ((2)FNIII), and that of an interaction complex between the first two type III domains ((1-2)FNIII). The two domains are connected through a long linker, flexible in solution. A weak but specific interdomain interaction maintains (1-2)FNIII in a closed conformation that associates weakly with the FN N-terminal 30 kDa fragment (FN30 kDa). Disruption of the interdomain interaction by amino-acid substitutions dramatically enhances association with FN30 kDa. Truncation analysis of (1-2)FNIII reveals that the
Cancer arises when genetic mutations in a cell cause abnormal growth that leads to a tumour.. Some cancer drugs exploit this to attack tumour cells by targeting proteins that are mutated from their usual form because of mutations in the genes that encode them.. However, only a fraction of all the mutations that contribute significantly to cancer have been identified.. Thomas Peterson, at the University of Maryland, and colleagues developed a new statistical analysis approach that uses genetic data from cancer patients to find cancer-causing mutations.. Unlike previous studies that focused on mutations in individual genes, the new approach addresses similar mutations shared by families of related proteins.. Specifically, the new method focuses on mutations in sub-components of proteins known as protein domains.. Even though different genes encode them, different proteins can share common protein domains.. The new strategy draws on existing knowledge of protein domain structure and function to ...
The M2 protein of the influenza A virus is a homotetrameric transmembrane proton channel implicated in several stages of the viral replication process. Each of its 97-residue monomers is known to include a transmembrane α-helix. but the structures of the N- and C-terminal domains have not yet been solved. A significant barrier to an atomic level understanding of the M2 protein is the difficulty associated with expression and purification of the full-length protein, which has primarily been studied in the form of truncated constructs covering the amphipathic helix and a short C-terminal segment. This C-terminal segment, which includes residues 46-62, has been shown for a truncated version of the protein to consist of an amphipathic helix lying on the membrane surface. Here, we present SDSL-EPR structural studies using full-length M2 constructs to examine sites 50-54 in the proposed amphipathic helix region of M2. Using power saturation data for the protein reconstituted into vesicles and CW ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
When DArcy Wentworth Thompsons On Growth and Form was published 100 years ago, it raised the question of how biological forms arise during development and across evolution. In light of the advances in molecular and cellular biology since then, a succinct modern view of the question states: how do genes encode geometry? Our new special issue is packed with articles that use mathematical and physical approaches to gain insights into cell and tissue patterning, morphogenesis and dynamics, and that provide a physical framework to capture these processes operating across scales.. Read the Editorial by guest editors Thomas Lecuit and L. Mahadevan, as they provide a perspective on the influence of DArcy Thompsons work and an overview of the articles in this issue.. ...
Looking for online definition of AT-rich interactive domain-containing protein 3C in the Medical Dictionary? AT-rich interactive domain-containing protein 3C explanation free. What is AT-rich interactive domain-containing protein 3C? Meaning of AT-rich interactive domain-containing protein 3C medical term. What does AT-rich interactive domain-containing protein 3C mean?
Looking for online definition of G patch domain-containing protein 7 in the Medical Dictionary? G patch domain-containing protein 7 explanation free. What is G patch domain-containing protein 7? Meaning of G patch domain-containing protein 7 medical term. What does G patch domain-containing protein 7 mean?
Hinge region predictor (H-Predictor) predicts putative hinge regions involved in protein oligomerization via the domain-swapping mechanism. Domain swapping is an important mechanism for protein oligomerization, in which a fragment of a protein exchanges with a corresponding fragment of another like protein. The segment of polypeptide chain that links the swapped domain and the main protein is the hinge region. In most experimentally observed domain-swapped oligomers, the swapped domains correspond to one or several secondary structural elements from either the N- or C-termini. Only in some rare instances the swapped domains are positioned in the middle of the protein. The domain-swapped oligomeric structures are, therefore, mainly determined by the location and the properties of the hinge region.. Using a simple contact-based potential for enthalpy and graph theory- based estimation for entropy, H-Predictor quantifies for each residue the propensity as the hinge region. Physically, the ...
Many large coiled-coil proteins are being found associated peripherally with the cytoplasmic face of the organelles of the secretory pathway. Various roles have been proposed for these proteins, including the docking of donor vesicles or organelles to an acceptor organelle prior to fusion, and, in the case of the Golgi apparatus, the stacking of the cisternae [1] [2] [3] [4] [5]. Such critical roles require accurate recruitment to the correct organelle. For the endosomal coiled-coil protein EEA1, targeting requires a carboxy-terminal FYVE domain, which interacts with Rab5 and phosphatidylinositol 3-phosphate (PI(3)P), whereas the Golgi protein GM130 interacts with Golgi membranes via the protein GRASP65 [3] [6] [7]. In this paper, we show that two other mammalian Golgi coiled-coil proteins, golgin-245/p230 and golgin-97, have a conserved domain of about 50 amino acids at their carboxyl termini. This GRIP domain is also found at the carboxyl terminus of several other large coiled-coiled ...
The role of domains in defining the equilibrium and kinetic folding properties of dihydrofolate reductase (DHFR) from Escherichia coli was probed by examining the thermodynamic and kinetic properties of a set of variants in which the chain connectivity in the discontinuous loop domain (DLD) and the adenosine-binding domain (ABD) was altered by permutation. To test the concept that chain cleavage can selectively destabilize the domain in which the N- and C-termini are resident, permutations were introduced at one position within the ABD, one within the DLD and one at a boundary between the domains. The results demonstrated that a continuous ABD is required for a stable thermal intermediate and a continuous DLD is required for a stable urea intermediate. The permutation at the domain interface had both a thermal and urea intermediate. Strikingly, the observable kinetic folding responses of all three permuted proteins were very similar to the wild-type protein. These results demonstrate a crucial role for
In this work the affinity maturation of the murine anti c-myc-peptide antibody 9E10 was analysed. Therefore Fab fragments with reversed mutations directed towards germline genes were genetically produced and characterised for their binding to the human c-myc peptide. The epitope recognized by 9E10 consists of the amino acid sequence EQKLISEEDLLRKR of which the key positions LISEXXL are very selectively recognized. The maturation of 9E10 leads to a 3300-fold higher affinity, which is achieved by a faster association as well as by a slower dissociation of the complex. For the gain in affinity formation of additional contacts to the peptide is less important than conformational and/or flexibility changes of the CDRs which are involved in binding. The exceptionally long CDR-H3 contributes essentially to the affinity maturation. The variable light domain serves thereby with its long CDR-L1 and -L3 as a binding platform for the flexible CDR-H3. Changes in specificity of 9E10 are primarily due to ...
4F2hc is a type-II glycoprotein that form covalently-bound heterodimers with several described light chains and whose main function is the transport of amino acids. Likewise, the heavy chain interacts with β-integrins mediating integrin-dependent events such as survival, proliferation, migration and even transformation. Its large C-terminal domain resembles α-amylases structure, but lacking catalytic residues and thus enzymatic activity. In fact, this ectodomain contains the N-terminal domain A, a TIM barrel, connected by 6 residues in α-helix to the C-terminal domain C, comprised of a β-sandwich. Spectroscopic/structural characterization of recombinant 4F2hc-ED shows that its structure in solution is quite similar to that of the crystal, being compact and thermally stable. Moreover, this ectodomain is unable to homodimerize by itself, remaining monomeric in solution. According to the data obtained, the folding/unfolding mechanism of 4F2hc-ED may occur following a 4-state model with 2 ...
2LOU: Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking.
It has been suggested [4] that these transport proteins have evolved from the duplication of an ancestral protein with six transmembrane regions, this hypothesis is based on the conservation of two G-R-[KR] motifs. The first one is located between the second and third transmembrane domains and the second one between transmembrane domains 8 and 9. We have developed two patterns to detect this family of proteins. The first pattern is based on the G-R-[KR] motif; but because this motif is too short to be specific to this family of proteins, we have derived a pattern from a larger region centered on the second copy of this motif. The second pattern is based on a number of conserved residues which are located at the end of the fourth transmembrane segment and in the short loop region between the fourth and fifth segments. Last update: April 2006 / Patterns revised. ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
... , Q5VRH9, AS13 2728, U-box domain-containing protein 12antibody, rice, Oryza sativa, developmental biology
Furuya, F., Poitelea, M., Guo, L., Caspari, T. and Carr, A. M. (2004) Chk1 activation requires Rad9 S/TQ-site phosphorylation to promote association with C-terminal BRCT domains of Rad4TOPBP1. Genes and Development, 18. pp. 1154-1164. ISSN 0890-9369 Full text not available from this repository ...
If you have the timestamp of one of the changed files, then that gives you an exact minute to look at in the access logs, so you just need to look for activity during that minute. You also need to find out if they are only changing files that are writable by the webserver or if they are changing other files as well. If they are changing other files, then its probably being done by FTP, domain control panel or some other server exploit. I just worked on another one of these problems that turned out to be a domain control panel issue ...
Histone H2A H2B H3 H4 H2AX Peptides Biotinylated acetylated methylated phosphorylated for use in enzyme assays, histone binding and pulldown experiments
In order to launch a new website what is better for Google? What will be the best solution to be noticed by Google asap? - Use an old domain name already online for 5/7 years (even if the name is not using the keyword you want) - Use a brand new domain name (with the keyword you need inside) Old domain name vs. new domain with a keyword. What is the best solution?
Rubicon (RUN domain protein as Beclin1 interacting and cysteine-rich containing) protein has recently been identified as a novel Beclin1-binding autophagy prote...
multihelical; 3-helical bundle similar to one half of the DEATH domain fold is flanked by two alpha-hairpins forming a four-helical bundle; the axes of the three-helical and four-helical bundles are aproximately orthogonal to each other ...
View mouse Ccdc47 Chr11:106197408-106216344 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
Get your own Web Address from iDotz.net! Its Cool Domains @ Great Prices. Register a New Domain Name or Transfer your existing name and start saving today! Offering domain.... ...
Last year we created a new domain and we use Citrix for our external users to be able to run the hosted app. However, there is three use...
eIF4G1兔多克隆抗体(ab80003)可与人样本反应并经ELISA, IHC实验严格验证。中国75%以上现货,所有产品均提供质保服务,可通过电话、电邮或微信获得本地专属技术支持。
PTGIS兔多克隆抗体(ab79846)可与小鼠, 人样本反应并经WB, ELISA实验严格验证,被1篇文献引用。所有产品均提供质保服务,中国75%以上现货。
Планета Королёва - информационный ресурс, посвященный достижениям в области отечественной пилотируемой космонавтики. Социальный информационно-просветительский проект, способствующий развитию научных идей в области космических технологий и расширению масштаба их применения в социально-экономической сфере общества.
Phosphoinositide lipids recruit proteins to the plasma membrane involved in the regulation of cytoskeleton organization and in signalling pathways that control cell polarity and growth. Among those, Rgd1p is a yeast GTPase-activating protein (GAP) specific for Rho3p and Rho4p GTPases, which control actin polymerization and stress signalling pathways. Phosphoinositides not only bind Rgd1p, but also stimulate its GAP activity on the membrane-anchored form of Rho4p. Both F-BAR (F-BAR FCH, and BAR) and RhoGAP domains of Rgd1p are involved in lipid interactions. In the Rgd1p-F-BAR domain, a phosphoinositide-binding site has been recently characterized. We report here the X-ray structure of the Rgd1p-RhoGAP domain, identify by NMR spectroscopy and confirm by docking simulations, a new but cryptic phosphoinositide-binding site, comprising contiguous A1, A1′ and B helices. The addition of helix A1′, unusual among RhoGAP domains, seems to be crucial for lipid interactions. Such a site was totally ...
Background The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain Royal Family, which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. Methodology/Principal Findings The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other Royal Family members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak
0025] In certain other embodiments, the VSV vector of the immunogenic composition comprises a G.sub.(ct) mutation and a M.sub.(ncp) mutation. In another embodiment, the G protein encoded by the truncated G gene has a cytoplasmic tail domain consisting of one amino acid (G.sub.(ct-1)) or a cytoplasmic tail domain consisting of nine amino acids (G.sub.(ct-9)). In another embodiment, the M.sub.(ncp) mutation is a mutation of methionine to alanine at position 33 (M33A) and a mutation of methionine to alanine at position 51 (M51A) of the M protein. In one particular embodiment, the immunogenic composition comprises a mutated VSV genome of 3-NPM.sub.(ncp)G.sub.(ct-1)L-5 or 3-NPM.sub.(ncp)G.sub.(ct-9)L-5. In yet other embodiments, the VSV vector of the immunogenic composition further comprises a third class of mutation in its genome, wherein the mutation is a ts mutation, a point mutation, a gene shuffling mutation, a G-stem mutation, an ambisense RNA mutation, a G gene insertion mutation and a ...
Interactions between GPCRs and their cognate G proteins are known to involve several different domains on both the receptor and the G protein heterotrimer. Within Gα, the best characterized GPCR contact site is the extreme C terminus where residues at positions -3 and -4 are particularly important for specific receptor recognition (Conklin et al., 1993, 1996; Kostenis et al., 1997c; Bahia et al., 1998; Blahos et al., 1998; Liu et al., 2002). We have recently demonstrated the importance of the linker I region of Gαq proteins in constraining the fidelity of receptor recognition. A highly conserved glycine residue in linker I (glycine 66) regulates coupling selectivity indirectly by playing a role in the specificity of nucleotide exchange within Gαq induced by ligand-activated GPCRs (Heydorn et al., 2004). Here, we analyzed 1) the relationship between the linker I region and the extreme C terminus of Gα in determining selective GPCR coupling and 2) whether different GPCRs use different Gα ...
The functional characterization of BAR-domain-containing proteins has expanded quite rapidly over the past few years. Recently, Guerrier and colleagues found that the F-BAR domain of srGAP2 shares the functional properties of I-BAR domain activity (Guerrier et al., 2009), such as those contained in IRSp53 and missing in metastasis (MIM) (Mattila et al., 2007; Millard et al., 2007; Saarikangas et al., 2009) by inducing membrane protrusions, rather than making invaginations as observed with canonical F-BAR proteins (Frost et al., 2007; Itoh et al., 2005). Recent reports (Carlson et al., 2011) and reviews (Heath and Insall, 2008) describing the subclasses of F-BAR-domain-containing proteins categorize srGAP family members into one functionally uniform subgroup; however, our work demonstrates that there are discrete roles and intricate differences between each srGAP family member.. Although the F-BAR domains of the srGAP family are all able to induce filopodia-like membrane protrusions to a greater ...
The non‐conservation in ETS proteins of the hydrophobic residues necessary for stabilization of the putative helix 1 as well as the insertion observed in that region for some ETS proteins, together with our secondary structure prediction, suggest that this region is unlikely to fold as an α‐helix. In the absence of experimental data about the structure adopted by this domain in either a monomeric or oligomeric state, its description as an HLH domain clearly appears to be premature.. The conserved fold of the amino‐terminal domain of ETS proteins is likely to underlie a conserved function. Our results show, however, that the conserved amino‐terminal domains of ETS‐1, ERG‐2 and GABPα are not homotypic oligomerization domains since they failed to replace the conserved amino‐terminal domain of TEL in inducing oligomerization when analyzed in an identical setting (Figure 6). These data are in accordance with other experimental approaches which have led to the conclusion that ETS‐1 ...
The epidermal growth factor receptor (EGFR) is activated by dimerization, but activation also generates higher-order multimers, whose nature and function are poorly understood. We have characterized ligand-induced dimerization and multimerization of EGFR using single-molecule analysis, and show that multimerization can be blocked by mutations in a specific region of Domain IV of the extracellular module. These mutations reduce autophosphorylation of the C-terminal tail of EGFR and attenuate phosphorylation of phosphatidyl inositol 3-kinase, which is recruited by EGFR. The catalytic activity of EGFR is switched on through allosteric activation of one kinase domain by another, and we show that if this is restricted to dimers, then sites in the tail that are proximal to the kinase domain are phosphorylated in only one subunit. We propose a structural model for EGFR multimerization through self-association of ligand-bound dimers, in which the majority of kinase domains are activated cooperatively, ...
In the reverse cholesterol transport pathway, high density lipoprotein (HDL) carries cholesterol from peripheral tissues to the liver for excretion via bile formation following interaction of HDL with its receptor, scavenger receptor BI (SR-BI). Due to the absence of a high-resolution structure of SR-BI, our understanding of receptor-ligand interactions between SR-BI and HDL that lead to whole body cholesterol removal remain limited. Our laboratory has demonstrated that oligomerization of SR-BI, likely mediated by its C-terminal transmembrane domain (C-TMD), facilitates delivery of HDL-cholesterol into cells. In this study, we describe the use of novel nuclear magnetic resonance (NMR) strategies to determine the structure and dimerization properties of SR-BI(405-475), a peptide that encompasses residues 405-475 and includes a portion of the extracellular domain, as well as the entire C-TMD of SR-BI. [U-15N,13C]-SR-BI(405-475) was bacterially expressed and purified, and alpha-helical secondary ...
Phosphorylation-dependent protein-protein interactions provide the foundation for a multitude of intracellular signal transduction pathways. One of the goals of signal transduction research is to more precisely understand the nature of these phosphorylation-dependent interactions. Here, we describe a bacterial two-hybrid assay that allows for the rapid, efficient analysis of phosphorylation-dependent protein-protein interactions. In this system, the interacting protein domains are provided as fusion proteins in Escherichia coli. cells that contain a eukaryotic kinase. Specific phosphorylation of one of the fused protein domains results in a protein-protein interaction that can be detected as a change in the expression of a reporter gene. We also describe how this system can be modified to permit the use of cDNA libraries to identify either novel binding partners for a phosphorylated substrate or novel kinases that can induce a specific protein-protein interaction. ...
Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that
Purified Rho Guanine Nucleotide Exchange Factor 7 from Creative Biomart. ARHGEF7(ARHGEF7, Rho guanine nucleotide exchange factor (GEF) 7) can be used for N/A.
Aggregation of misfolded proteins and the associated loss of neurons are considered as a hallmark of numerous neurodegenerative diseases. Optineurin is present in protein inclusions observed in various neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Huntingtons disease, Alzheimers disease, Parkinsons disease, Creutzfeld-Jacob disease and Picks disease. Optineurin deletion mutations have also been described in ALS patients. However, the role of optineurin in mechanisms of protein aggregation remains unclear. In this report, we demonstrate that optineurin recognized various protein aggregates via its C-terminal coiled-coil domain in a ubiquitin-independent manner. We also show that optineurin depletion significantly increase protein aggregation in HeLa cells and morpholino-silencing of the optineurin ortholog in zebrafish causes the motor axonopathy phenotype similar to a zebrafish model of ALS. A more severe phenotype is observed when optineurin is depleted in ...

FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction

structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. Posted: Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. Posted: Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
more infohttp://www.predictioncenter.org/forcasp/viewtopic.php?f=24&t=245&start=0&st=0&sk=t&sd=a&sid=814bbe4b50d137a36988f51418f96b39&view=print

FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction

structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. by AlexanderSimmons on Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. by Proteinglow on Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
more infohttp://predictioncenter.org/forcasp/viewtopic.php?f=24&t=245&sid=5fc727954500b828c87ca1dd3d1e4a39&p=643

FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction

structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. by AlexanderSimmons on Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. by Proteinglow on Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
more infohttp://predictioncenter.org/forcasp/viewtopic.php?f=24&t=245&sid=e7d8215b1a84f39fe3bfa8ff6afa6c21&p=643

FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction

structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. by AlexanderSimmons on Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. by Proteinglow on Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
more infohttp://www.predictioncenter.org/forcasp/viewtopic.php?f=24&t=245&start=0&st=0&sk=t&sd=a

Protein tertiary structure - WikipediaProtein tertiary structure - Wikipedia

A number of tertiary structures may fold into a quaternary structure. The science of the tertiary structure of proteins has ... Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide ... The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary ... Contemporary methods are able to determine, without prediction, tertiary structures to within 5 Å (0.5 nm) for small proteins ( ...
more infohttps://en.wikipedia.org/wiki/Protein_tertiary_structure

Protein Structure, TertiaryProtein Structure, Tertiary

Crystal structure of theLeishmania majorMIX protein: A scaffold protein that mediates protein-protein interactions Academic ... BH3-only proteins: a 20-year stock-take Academic Article * Bax Crystal Structures Reveal How BH3 Domains Activate Bax and ... Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1 Academic Article ... Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body ...
more infohttps://scholars.latrobe.edu.au/display/vocab-mesh-protein-structure-tertiary

Protein Structure, Tertiary | Profiles RNSProtein Structure, Tertiary | Profiles RNS

"Protein Structure, Tertiary" by people in this website by year, and whether "Protein Structure, Tertiary" was a major or minor ... The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions ... "Protein Structure, Tertiary" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ( ... Protein Structure, Tertiary*Protein Structure, Tertiary. *Tertiary Protein Structure. *Protein Structures, Tertiary ...
more infohttps://profiles.uchicago.edu/profiles/display/22839

Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction | SpringerLinkModelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction | SpringerLink

... a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. This approach ... Given some similarity in sequence between two proteins, ... Modelling Protein Structure from Remote Sequence Similarity: An ... Taylor W.R. (1994) Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction. ... Taylor, W. R. and Orengo, C. A. (1989b). Protein structure alignment. J. Molec. Biol., 208:1-22.CrossRefGoogle Scholar ...
more infohttps://link.springer.com/chapter/10.1007/978-1-4615-2451-9_13

Secondary and Tertiary Protein Structure | Life Sciences | SGS BangladeshSecondary and Tertiary Protein Structure | Life Sciences | SGS Bangladesh

Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
more infohttps://www.sgsgroup.com.bd/en/life-sciences/contract-laboratory-services/biopharmaceutical-characterization-services/secondary-and-tertiary-protein-structure

Secondary and Tertiary Protein Structure | Life Sciences | SGS USASecondary and Tertiary Protein Structure | Life Sciences | SGS USA

Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
more infohttps://www.sgsgroup.us.com/en/life-sciences/contract-laboratory-services/biopharmaceutical-characterization-services/secondary-and-tertiary-protein-structure

Secondary and Tertiary Protein Structure | Life Sciences | SGS IndiaSecondary and Tertiary Protein Structure | Life Sciences | SGS India

Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
more infohttps://www.sgsgroup.in/en-gb/life-sciences/contract-laboratory-services/biopharmaceutical-characterization-services/secondary-and-tertiary-protein-structure

ROSALIND | Glossary | Protein tertiary structureROSALIND | Glossary | Protein tertiary structure

Protein tertiary structure. The tertiary structure of a polypeptide (or protein containing only one polypeptide) refers to its ... inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide ... the polypeptides tertiary structure follows uniquely from its primary structure (i.e., the order of amino acids). As a result ... The tertiary structure of a polypeptide will determine its chemical properties on a larger scale; however, ...
more infohttp://rosalind.info/glossary/protein-tertiary-structure/

Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of ProteinsPrediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

... Shambhu Malleshappa Gowder,1 Jhinuk ... The analysis of protein structures provides plenty of information about the factors governing the folding and stability of ... It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using ... the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so ...
more infohttps://www.hindawi.com/journals/tswj/2014/971258/abs/

Protein Structure: Proteins are organized in tertiary StructureProtein Structure: Proteins are organized in tertiary Structure

This chapter explains the basics of tertiary organization of Proteins, It includes myoglobin ... Protein Structure-Proteins are organized in tertiary Structure- ... Protein Structure: How the Proteins are organized in tertiary ... Basic points on Tertiary Structure of Proteins:. The folding of a protein is connects to the Genomic function ... The best example of Tertiary Structure of Proteins are Myoglobin (Muscle Respiratory Pigment) and Ribunuclease. (RNA digestive ...
more infohttps://www.biochemden.com/protein-structure-how-proteins-are/

Going  Beyond Lamarckism in Protein Tertiary Structure PredictionGoing Beyond 'Lamarckism' in Protein Tertiary Structure Prediction

... more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures ... Several novel techniques are employed for protein tertiary structure prediction, but the ... in Protein Tertiary Structure Prediction Several novel techniques are employed for protein tertiary structure prediction, but ... Critical assessment of methods of protein structure prediction (CASP) - round IX. Proteins, Structure, Function & ...
more infohttps://www.jbsdonline.com/going-beyond-lamarckism-protein-tertiary-structure-prediction-p18678.html

Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments | SpringerLinkQuantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments | SpringerLink

The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is ... possible for many protein sequence segments to exhibit multiple 3D... ... Multi-structural segments protein structure protein structure comparison protein structure conservation URMSD ... Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments. ...
more infohttps://link.springer.com/article/10.1007%2Fs10930-006-9016-5

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.  - PubMed - NCBISWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. - PubMed - NCBI

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.. Biasini M1, Bienert S1, ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/24782522?dopt=Abstract

What is protein tertiary structure?What is protein tertiary structure?

The tertiary structure is determined by four interactions: hydrogen bonding,... ... The three-dimensional conformation of a polypeptide chain of a globular protein in its native folded state. ... What is protein tertiary structure?. 4 years ago by Pozzter Q&A 0 replies, read ~321197 times ... polypeptide chain of a globular protein in its. native folded state. The tertiary structure is. determined by four interactions ...
more infohttps://pozzter.com/post/what-is-protein-tertiary-structure-LMVFYHO

Online Analysis Tools - Protein Tertiary StructureOnline Analysis Tools - Protein Tertiary Structure

PROTEIN TERTIARY STRUCTURE Sites are offered for calculating and displaying the 3-D structure of oligosaccharides and proteins ... Structures derived from NMR coordinates:. GeNMR (GEnerate NMR structure) - generates 3D protein structures using NOE-derived ... 3D-Match - Comparing 3D structures of two proteins (Softberry). iPBA - is a tool for comparison of protein structures based on ... With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology ...
more infohttp://www.molbiol-tools.ca/Protein_tertiary_structure.htm

Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...

Assessment of template based protein structure predictions in CASP9, Proteins: Structure, Function, and Bioinformatics, 2011, ... Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method†. Authors. *. ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ...
more infohttp://onlinelibrary.wiley.com/doi/10.1002/prot.23120/abstract?globalMessage=0

GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary StructuresGP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures

GP4Rate is a C++ program which combines Gaussian processes and phylogenetics to infer conserved sites in protein tertiary ... Protein Protein Sequence Protein Structure RNA RNA-Seq Secondary Structure Sequence Sequencing Simulation SNP Structure Tool ... Posted by admin at 4:30 pm Tagged with: GP4Rate, Important Region, Protein Tertiary Structures 71 views. Sorry, the comment ... GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures. 3D molecular model ...
more infohttp://www.mybiosoftware.com/rate4site-1-0-0-inference-of-functionally-important-regions-in-protein-tertiary-structures.html

Probing Secondary, Tertiary, and Quaternary Structure along with
Protein−Cofactor Interactions for a Helical Transmembrane...Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane...

... and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane Protein Complex through 1H Spin ... Helical Transmembrane Protein Complex 1 H Spin Diffusion magic angle Quaternary Structure helical transmembrane model protein ... Probing secondary, tertiary, and quaternary structure along with protein−cofactor interactions through ,sup,1,/sup,H spin ... Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane ...
more infohttps://figshare.com/articles/Probing_Secondary_Tertiary_and_Quaternary_Structure_along_with_Protein_Cofactor_Interactions_for_a_Helical_Transmembrane_Protein_Complex_through_sup_1_sup_H_Spin_Diffusion_with_MAS_NMR_Spectroscopy/3026887/1

Gene triplication deduced from the tertiary structure of a muscle calcium binding protein.  - PubMed - NCBIGene triplication deduced from the tertiary structure of a muscle calcium binding protein. - PubMed - NCBI

Gene triplication deduced from the tertiary structure of a muscle calcium binding protein.. Kretsinger RH. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/0004508374

Difference Between Primary Secondary and Tertiary Structure of Protein - Pediaa.ComDifference Between Primary Secondary and Tertiary Structure of Protein - Pediaa.Com

... a protein is linear and the secondary structure of a protein can be either an α-helix or β-sheet whereas the tertiary structure ... The main difference between primary secondary and tertiary structure of protein is that the primary structure of ... What is the Tertiary Structure of protein. The tertiary structure of protein is the folded structure of the polypeptide chain ... 2. What is the Secondary Structure of Protein. - Definition, Structure, Bonds. 3. What is the Tertiary Structure of Protein. - ...
more infohttp://pediaa.com/difference-between-primary-secondary-and-tertiary-structure-of-protein/

List of protein structure prediction software - WikipediaList of protein structure prediction software - Wikipedia

Protein tertiary structure predictions. server Selvita Protein Modeling Platform Package of tools for protein modeling. Free ... On-line server for peptide structure prediction. Server Secondary structure prediction[edit]. Main article: Protein structure ... This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, ... Commercial protein structure prediction application. Home page I-TASSER Threading fragment structure reassembly. On-line server ...
more infohttps://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
  • H spin diffusion with MAS NMR is demonstrated for a helical transmembrane model protein complex. (figshare.com)
  • The structure contains six transmembrane helices. (biomedsearch.com)
  • The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. (biomedsearch.com)
  • A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. (biomedsearch.com)
  • Comparison of predicted and X -ray crystal structures of retroviral proteases. (springer.com)
  • The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family. (biomedsearch.com)
  • Also, ionic bonds called salt bridges form between positively- and negatively-charged side-chains of amino acids, further stabilizing the tertiary structure. (pediaa.com)
  • A pronounced absorption band in the near-UV CD region, arising from immobilized aromatic side-chains, showed that the artificial protein is folded in solution. (caltech.edu)
  • It is quite apparent that efforts in tertiary structure prediction have saturated to a level where there is an immediate need for methodological innovations - beyond templates of folds to avoid falling into a trap of Lamarckism in protein folding. (jbsdonline.com)
  • To this end, this paper presents statistical analysis of uniqueness of the 3D-structure of all possible protein sequence segments stored in the Protein Data Bank (PDB, Jan. of 2003, release 103) that occur at least twice and whose lengths are greater than 10 amino acids (AAs). (springer.com)
  • Since two of the structure changing operations concern negligible number of segment and the third one is found not to have impact on the structure, we conclude that the 3D-structure of proteins is conserved statistically for more than 98% of the segments. (springer.com)