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)

Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. (1/21611)

The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes.  (+info)

Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D. (2/21611)

The crystal structure of profactor D, determined at 2.1 A resolution with an Rfree and an R-factor of 25.1 and 20.4%, respectively, displays highly flexible or disordered conformation for five regions: N-22, 71-76, 143-152, 187-193 and 215-223. A comparison with the structure of its mature serine protease, complement factor D, revealed major conformational changes in the similar regions. Comparisons with the zymogen-active enzyme pairs of chymotrypsinogen, trypsinogen and prethrombin-2 showed a similar distribution of the flexible regions. However, profactor D is the most flexible of the four, and its mature enzyme displays inactive, self-inhibited active site conformation. Examination of the surface properties of the N-terminus-binding pocket indicates that Ile16 may play the initial positioning role for the N-terminus, and Leu17 probably also helps in inducing the required conformational changes. This process, perhaps shared by most chymotrypsinogen-like zymogens, is followed by a factor D-unique step, the re-orientation of an external Arg218 to an internal position for salt-bridging with Asp189, leading to the generation of the self-inhibited factor D.  (+info)

Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. (3/21611)

Amyloid fibrils are assemblies of misfolded proteins and are associated with pathological conditions such as Alzheimer's disease and the spongiform encephalopathies. In the amyloid diseases, a diverse group of normally soluble proteins self-assemble to form insoluble fibrils. X-ray fibre diffraction studies have shown that the protofilament cores of fibrils formed from the various proteins all contain a cross-beta-scaffold, with beta-strands perpendicular and beta-sheets parallel to the fibre axis. We have determined the threedimensional structure of an amyloid fibril, formed by the SH3 domain of phosphatidylinositol-3'-kinase, using cryo-electron microscopy and image processing at 25 A resolution. The structure is a double helix of two protofilament pairs wound around a hollow core, with a helical crossover repeat of approximately 600 A and an axial subunit repeat of approximately 27 A. The native SH3 domain is too compact to fit into the fibril density, and must unfold to adopt a longer, thinner shape in the amyloid form. The 20x40-A protofilaments can only accommodate one pair of flat beta-sheets stacked against each other, with very little inter-strand twist. We propose a model for the polypeptide packing as a basis for understanding the structure of amyloid fibrils in general.  (+info)

RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids. (4/21611)

The RNA-binding/dimerization domain of the NS1 protein of influenza A virus (73 amino acids in length) exhibits a novel dimeric six-helical fold. It is not known how this domain binds to its specific RNA targets, one of which is double-stranded RNA. To elucidate the mode of RNA binding, we introduced single alanine replacements into the NS1 RNA-binding domain at specific positions in the three-dimensional structure. Our results indicate that the dimer structure is essential for RNA binding, because any alanine replacement that causes disruption of the dimer also leads to the loss of RNA-binding activity. Surprisingly, the arginine side chain at position 38, which is in the second helix of each monomer, is the only amino-acid side chain that is absolutely required only for RNA binding and not for dimerization, indicating that this side chain probably interacts directly with the RNA target. This interaction is primarily electrostatic, because replacement of this arginine with lysine had no effect on RNA binding. A second basic amino acid, the lysine at position 41, which is also in helix 2, makes a strong contribution to the affinity of binding. We conclude that helix 2 and helix 2', which are antiparallel and next to each other in the dimer conformation, constitute the interaction face between the NS1 RNA-binding domain and its RNA targets, and that the arginine side chain at position 38 and possibly the lysine side chain at position 41 in each of these antiparallel helices contact the phosphate backbone of the RNA target.  (+info)

Molecular dynamics studies of U1A-RNA complexes. (5/21611)

The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity.  (+info)

Three-dimensional structure of a recombinant gap junction membrane channel. (6/21611)

Gap junction membrane channels mediate electrical and metabolic coupling between adjacent cells. The structure of a recombinant cardiac gap junction channel was determined by electron crystallography at resolutions of 7.5 angstroms in the membrane plane and 21 angstroms in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which is consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. The transmembrane alpha-helical rods contrasted with the double-layered appearance of the extracellular domains. Although not indicative for a particular type of secondary structure, the protein density that formed the extracellular vestibule provided a tight seal to exclude the exchange of substances with the extracellular milieu.  (+info)

Melatonin biosynthesis: the structure of serotonin N-acetyltransferase at 2.5 A resolution suggests a catalytic mechanism. (7/21611)

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)

Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12. (8/21611)

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)

This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure types are considered, including
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
A powerful tool used to monitor secondary structure is circular dichroism (CD), which is the differential absorbance of left and right circularly polarized light. Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the proteins secondary structure. This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software.. Protein secondary structure can also be used to monitor protein folding and unfolding. An equilibrium study consists of collection of CD spectra as a function of increasing temperature or chemical denaturant. As the protein unfolds, the CD spectrum reflects this. Fitting data at a single wavelength or the full spectral scans during this denaturation process provides thermodynamic information such as the melting temperature ...
Activation helix orientation of estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations
Quanta will calculate hydrogen bonds and then analyze the secondary structure in its Protein Design Module, but it seems like a rather large investment if all you want to do is determine the secondary structure......... ........Tom Branham ...
Diatoms and sponges use proteins, long chain polyamines, and other biomolecules to assemble silica structures of controlled morphology. Investigated here are biosilicification peptides. Under mild conditions, these peptides produce silica nanoparticles from solutions of silicic acid, whereas harsh methods are currently employed to produce these nanoparticles commercially. Biomimetic precipitation studies have shown that LKα14 (Ac-LKKLLKLLKKLLKL- C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, co-precipitates with silica to form nanospheres. Previous work con- firmed the α-helical secondary structure in both the neat and silica-complexed states of the peptide and suggested that the tetrameric bundles of peptide that are known to form in solution persisted in the silica-complexed form. To further investigate the peptide aggregation, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how the ...
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Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between alpha-helix length and alpha-helix stability, which would be impossible to probe with alpha-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel beta-sheet stability. alpha-Helices become more stable as they grow longer. Our data show that a two-stranded beta-sheet (beta-hairpin) becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further beta-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be
The following is a list of how-to and tutorial content that matched your search term. ProgrammableWebs how-to content comes from two sources; full-blown tutorials that we publish ourselves and other highly relevant tutorials that we find elsewhere on the Web. This list represents on combination of both tutorial types and if you go to ProgrammableWebs API University, youll not only be able to find more, they are organized based on your role (API providers or developers who consumes APIs). If you know of a tutorial that would be of interest to the ProgrammableWeb community, wed like to know about it. Be sure to check our guidelines for making contributions to ProgrammableWeb ...
jay ananth wrote: , I need one help from u... , , search for best tools for the following : , 1.Secondary Structure prediction in RNA , 2.Protein Secondary Structure Prediction. , 3.Prediction of disordered regions in proteins.. , 4.Case Std on Structure-function relationships in proteins , 5.Prediction of transmembrane regions in proteins , 6.Characterization of antigenecity in polypeptides- epitope mapping , , , , Are you looking for computational tools to do the above ? Can you be more specific ? Autodock, Gromacs are some of the tools that you can use for protein structure prediction. -- Deepan http://codeshepherd.com/ http://codeshepherd.blogspot.com/ http://sudoku-solver.net/ ...
In recent years, the nuclear receptors (NR) dynamics have been studied extensively by various approaches. However, the transition path of helix 12 (H12) to an agonist or an antagonist conformation and the exchange pathway between these states is not clear yet. A number of accelerated molecular dynamics (aMD)
Motivation: Transmembrane beta-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few beta-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful. Results: Here, we present tobmodel; a method for generating 3D models of beta-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the beta-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average ...
The DSSP program works by calculating the most likely secondary structure assignment given the 3D structure of a protein. It does this by reading the position of the atoms in a protein (the ATOM records in a PDB file) followed by calculation of the H-bond energy between all atoms. The best two H-bonds for each atom are then used to determine the most likely class of secondary structure for each residue in the protein.. This means you do need to have a full and valid 3D structure for a protein to be able to calculate the secondary structure. Theres no magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you dont have the 3D structure ...
Many proteins are organized into several units. A structural domain is an element of the proteins overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding domain of calmodulin". Because they are self-stabilizing, domains can be "swapped" by genetic engineering between one protein and another to make chimeras. A motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). These elements are often called supersecondary structures. Fold refers to a global type of arrangement, like helix-bundle or beta-barrel. Structure motifs usually consist of just a few elements, e.g. the helix-turn-helix has just ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
This study demonstrates the feasibility of creating structurally complex and catalytically active enzymes by assembling randomized modules that are constructed from a limited set of building blocks and biased toward helical secondary structure by binary patterning. The binary distribution of hydrophilic/hydrophobic residues is inherent in the genetic code (NAN/NTN), and our results support suggestions (9, 26, 27) that modern enzymes could have evolved from primitive precursors constructed from a relatively small number of polar and nonpolar amino acids. There is, nevertheless, a low probability of finding catalysts, even when both position and identity of all critical active site residues are determined in advance. This finding contrasts with the ease of obtaining folded helical proteins through binary patterning (9), underscoring the exacting demands that catalysis places on protein design.. Extrapolating from our data and from modest sequence constraints on interhelical turns (23, 28-30), we ...
... , In parallel beta sheets, the adjacent polypeptide chains run in the same direction. Typically parallel beta sheets are large structures that usually consist of at least five strands. Parallel beta sheets usually have hydrophobic residues on both sides of the sheet.
C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Lecture 14 Secondary Structure Prediction. Bioinformatics Center IBIVU. Protein structure . Linus Pauling (1951). Slideshow 80412 by LeeJohn
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 ...
Lee, C., L. Kalmar, B. Xue, P. Tompa, G. W. Daughdrill, V. N. Uversky, and K-H. Han, Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins., Biochim Biophys Acta, vol. 1840, issue 3, pp. 993-1003, 2014 Mar. ...
Secondary structure of proteins refers to local and repetitive conformations, such as α‐helices and β‐strands, which occur in protein structures
Synonyms for alpha-helix, alpha-helix in Free Thesaurus. Antonyms for alpha-helix, alpha-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for alpha-helix, alpha-helix?
View Notes - Bio 1A Lect 2 Quiz from BIO 1A at Berkeley. Bio 1A Lect 2 Quiz 50% adenine aldose alpha alpha-helix amino Amino acids antiparallel beta beta-pleated sheets blood flow carbonyl cell
Its not true that the Ramachandran plot will determine the secondary structure of an amino acid. Ramachandran plots show the sterically allowed phi/psi angles of an amino acid. As such nearly all non-glycine amino acids are in alpha/beta spaces. Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense ...
As evidenced by a buried core of hydrophobic residues within globular proteins, hydrophobicity provides essential insights into the folding structure of pr
6. "Helix Propensities of Amino Acid Residues via Thioester Exchange." Fisher, B. F.; Hong, S.H.; Gellman, S.H. J. Am. Chem. Soc. DOI: 10.1021/jacs.7b07930. 5. "Detection and analysis of chimeric tertiary structures by backbone thioester exchange: Packing of an alpha helix against an alpha/beta-peptide helix," Price, J. L.;Hadley,E. B.;Steinkruger,J. D. and Gellman,S. H., Angew.Chem.Int.Ed Engl., 2010, 49, 368-371.. 4. "Preferred Side-chain Constellations at Antiparallel Coiled-coil Interfaces," E. B. Hadley, O. D. Testa, D. N. Woolfson and S. H. Gellman Proc. Natl. Acad. Sci. USA 2008, 105, 530.. 3. "An Antiparallel α-Helical Coiled-Coil Model System for Rapid Assessment of Side Chain Recognition at the Hydrophobic Interface," E. B. Hadley an d S. H. Gellman J. Am. Chem. Soc. 2006, 128, 16444.. 2. "Thermodynamic Analysis of β-Sheet Secondary Structure Via Backbone Thioester Exchange," E. B. Hadley, A. M. Witek, F. Friere, A. J. Peoples and S. H. Gellman Angew. Chem. Int. Ed. 2007, 46, ...
On Sun, 13 May 2007, Rolf Kalbermatter wrote: , Changelog , include/winsvc.h , Fix names of structure elements to match PSDK [...] , diff --git a/include/winsvc.h b/include/winsvc.h , index 7a29e8f..af56d29 100644 , --- a/include/winsvc.h , +++ b/include/winsvc.h , @@ -196,13 +196,13 @@ DECL_WINELIB_TYPE_AW(LPENUM_SERVICE_STATUS) , typedef struct _ENUM_SERVICE_STATUS_PROCESSA { , LPSTR lpServiceName; , LPSTR lpDisplayName; , - SERVICE_STATUS_PROCESS ServiceStatusProcess; , + SERVICE_STATUS_PROCESS ServiceStatus; , } ENUM_SERVICE_STATUS_PROCESSA, *LPENUM_SERVICE_STATUS_PROCESSA; [..] This patch is wrong. This field is really called ServiceStatusProcess in the PSDK. -- Francois Gouget ,fgouget at free.fr, http://fgouget.free.fr/ You can have my guns when you pry them from my kids cold, dead hands ...
Scientists have identified where a four-stranded version of DNA exists within the genome of human cells, and suggest that it may hold a key to developing new, targeted therapies for cancer.
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for "alpha-helix"). {{ pdb }} {{ chain }} ...
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for "alpha-helix"). {{ pdb }} {{ chain }} ...
contains an N-terminal beta-sheet that forms a beta-triangle structure; the remainder is a multihelical array of long and short helices ...
Mental exercise is one way to help prevent Alzheimers. Another means of prevention is to remain physically fit throughout life....
The amino-terminal extremity of the human immunodeficiency virus type 1 transmembrane protein (gp41) is thought to play a pivotal role in the fusion of virus membranes with the plasma membrane of the target cell and in syncytium formation. Peptides with sequences taken from the human immunodeficiency virus type 1 gp41 fusogenic (synthetic peptides SPwt and SP-2) and nonfusogenic (SP-3 and SP-4) glycoproteins adopt mainly a beta-sheet conformation in the absence of lipid, as determined by attenuated total reflection Fourier transform infrared spectroscopy, and after interaction with large unilamellar liposomes, the beta-sheet is partly converted into an alpha-helical conformation. Peptides SPwt and SP-2 but not SP-3 or SP-4 were able to promote lipid mixing as assessed by fluorescence energy transfer assay and dye leakage in a vesicle leakage assay. By using polarized attenuated total reflection Fourier transform infrared spectroscopy, SPwt and SP-2 were found to adopt an oblique orientation in ...
in Journal of Protein Chemistry (1994), 13(1), 77-88. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 ... [more ▼]. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 peptide-lipid complexes was evaluated by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Those peptides belonging to the hydrophobic core domain of apo B-100 when associated with phospholipids were rich in beta sheet structure; a predominant alpha helical conformation was shown to be associated with one peptide located in a surface region of apo B-100. IR dichroic spectra revealed, in the case of the core peptides, that the beta sheet component is the only oriented structure with respect to the ...
In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible.. ...
In this study, hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used to classify blends produced from diesel S500 and different kinds of biodiesel produced by the TDSP methodology. The different kinds of biodiesel studied in this work were produced from three raw materials: soybean oil, waste cooking oil and hydrogenated vegetable oil. Methylic and ethylic routes were employed for the production of biodiesel. HCA and PCA were performed on the data from attenuated total reflectance Fourier transform infrared spectroscopy, showing the separation of the blends into groups according to biodiesel content present in the blends and to the kind of biodiesel used to form the mixtures ...
LmrP is an electrogenic H(+)/drug antiporter that extrudes a broad spectrum of antibiotics. Five carboxylic residues are implicated in drug binding (Asp142 and Glu327) and proton motive force-mediated restructuring (Asp68, Asp128 and Asp235). ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) and tryptophan quenching experiments revealed that phosphatidylethanolamine (PE) is required to generate the structural intermediates induced by ionization of carboxylic residues. Surprisingly, no ionization-induced conformational changes were detectable in the absence of PE, suggesting either that carboxylic acid residues do not ionize or that ionization does not lead to any conformational change. The mean pKa of carboxylic residues evaluated by ATR-FTIR spectroscopy was 6.5 for LmrP reconstituted in PE liposomes, whereas the pKa calculated in the absence of PE was 4.6. Considering that 16 of the 19 carboxylic residues are located in the extramembrane loops, the pKa values obtained in the ...
TY - JOUR. T1 - Proton nuclear magnetic resonance assignments and secondary structure determination of the Co1E1 rop (rom) protein. AU - Eberle, W.. AU - Klaus, W.. AU - Cesareni, G.. AU - Sander, C.. AU - Rosch, P.. PY - 1990. Y1 - 1990. N2 - The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy (1H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and 3J(HNα) coupling constants. One 7.2-kDa monomer of the homodimer consists of two antiparallel helices connected by a hairpin loop at residue 31. The C-terminal peptide consisting of amino acids 59-63 shows no stable conformation. The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the X-ray structure.. AB - ...
TY - JOUR. T1 - Salivary molecular spectroscopy. T2 - a sustainable, rapid and non-invasive monitoring tool for diabetes mellitus during insulin treatment. AU - Caixeta, Douglas C.. AU - Aguiar, Emília M. G.. AU - Cardoso-Sousa, Léia. AU - Coelho, Líris M. D.. AU - Oliveira, Stephanie W.. AU - Espindola, Foued S.. AU - Raniero, Leandro. AU - Crosara, Karla T. B.. AU - Baker, Matthew J.. AU - Siqueira, Walter L.. AU - Sabino-Silva, Robinson. PY - 2020/3/17. Y1 - 2020/3/17. N2 - Monitoring of blood glucose is an invasive, painful and costly practice in diabetes. Consequently, the search for a more cost-effective (reagent-free), non-invasive and specific diabetes monitoring method is of great interest. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used in diagnosis of several diseases, however, applications in the monitoring of diabetic treatment are just beginning to emerge. Here, we used ATR-FTIR spectroscopy to evaluate saliva of non-diabetic (ND), ...
Abstract This paper proposes a direct and efficient method to discriminate between counterfeit and authentic Cialis and Viagra samples by combining attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy with multivariate techniques. The chemical profile of 53 commercial samples (Viagra®, Cialis®) and 104 counterfeit samples (Viagra and Cialis) from distinct seizures were obtained from ATR-FTIR…. [...] ...
Looking for online definition of alpha helix conformation in the Medical Dictionary? alpha helix conformation explanation free. What is alpha helix conformation? Meaning of alpha helix conformation medical term. What does alpha helix conformation mean?
Research Corridor has published a new research study titled "Circular Dichroism Spectroscopy Market - Growth, Share, Opportunities, Competitive Analysis and Forecast, 2017 - 2025". The Circular Dichroism Spectroscopy Market report studies current as well as future aspects of the Circular Dichroism Spectroscopy Market based upon factors such as market dynamics, key ongoing trends and segmentation analysis. Apart from the above elements, the Circular Dichroism Spectroscopy Market research report provides a 360-degree view of the Lipstick Packing industry with geographic segmentation, statistical forecast and the competitive landscape.. Browse the complete report at http://www.researchcorridor.com/circular-dichroism-spectroscopy-market/. Geographically, the Circular Dichroism Spectroscopy Market report comprises dedicated sections centering on the regional market revenue and trends. The Circular Dichroism Spectroscopy Market has been segmented on the basis of geographic regions into North America, ...
Transmembrane helix-helix interactions may have at least two major functions: 1) intramolecular helix-helix interactions would serve to stabilize the tertiary structure of the protein in the membrane bilayer, and 2) helix-helix interactions between two or more integral membrane proteins appear to regulate ligand-initiated response systems. X-Ray crystallography of the α1-subunit of Na/K-ATPase (Figure 6) indicates that 5 of the 10 helices (M4, M5, M6, M7 and M8) lie largely within the core of the α1-subunit, whereas the remaining 5 helices (M1, M2, M3 M9 and M10)) are on the periphery. Computer-generated projections of each helix (Figure 7) indicate that helices within the core are disordered whereas peripheral helices are largely ordered. This suggests that the disordered helices contribute to and/or maintain the tertiary structure of the α1-subunit, whereas the peripheral ordered helices are available for interaction with ordered helices of neighboring integral membrane proteins.. In our ...
The model six-residue linear peptide AAGDYY-NH2 from TEM-1 beta -lactamase inhibitor protein and BLIP was predicted to adopt a beta -turn conformation and synthesized in order to elucidate the mechanism of beta -turn formation and stability. Its structural preferences in solution were comprehensively characterized using CD (circular dichroism), FT-IR and H-1-NMR spectroscopy. The set of observed short- and medium-range NOEs, the restrained molecular dynamics simulation, CD and FT-IR spectroscopy were consistent with the formation of beta -turn in solution by the model peptide. The results implicate beta -turn playing an important role in the process of protein folding. ...
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus sigma NS. Here, we compared the abilities of NSP2 and sigma NS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while sigma NS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, ...
The cpssp package ------------------------------------------------------------------------------ This package is released under the LaTeX Project Public License v1.3c or later (see http://www.latex-project.org/lppl.txt). The cpssp package allows you to draw a two-dimensional representation of a proteins secondary structure in LaTeX. Besides, it is possible to graphically compare protein secondary structure predictions. One can both compare predictions from a single program for several protein sequences (which have been aligned using any appropriate algorithm) and predictions from several programs for a single protein sequence. Installation: Run cpssp.ins through LaTeX and follow the instructions. -- Wolfgang Skala June 6th, 2009 ...
For the current problem we define a neural network with one input layer, one hidden layer and one output layer. The input layer encodes a sliding window in each input amino acid sequence, and a prediction is made on the structural state of the central residue in the window. We choose a window of size 17 based on the statistical correlation found between the secondary structure of a given residue position and the eight residues on either side of the prediction point [2]. Each window position is encoded using a binary array of size 20, having one element for each amino acid type. In each group of 20 inputs, the element corresponding to the amino acid type in the given position is set to 1, while all other inputs are set to 0. Thus, the input layer consists of R = 17x20 input units, i.e. 17 groups of 20 inputs each.. In the following code, we first determine for each protein sequence all the possible subsequences corresponding to a sliding window of size W by creating a Hankel matrix, where the ith ...
An alpha helix (α-helix) is a twisted part of a protein. It is one of the two most common parts of the secondary structure, or shape, of a protein. The other is the beta sheet. An alpha helix is created by alternating groups of atoms. There is a carbonyl group, created by a carbon atom double bonded to an oxygen atom, and an amine group, created by a nitrogen atom bonded to a hydrogen atom. Each section containing one of each of these groups is called a residue, a general term for a small part of a molecule. Each amine group forms a hydrogen bond with the carbonyl group four residues earlier. A prion is a protein that causes disease by changing the shape of another protein. It does this by changing some of the alpha helices, which are more common in normal cells, to beta sheets, which are more common in prions. The alpha helix consists of 3.6 residues per turn. All hydrogen bonds face in the same direction. If two or more alpha helices come together, they become a tertiary structure. (Ex. Five ...
Synonyms for a-helix in Free Thesaurus. Antonyms for a-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for a-helix?
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). ...
"Continuum secondary structure captures protein flexibility". Structure. 10 (2): 175-184. doi:10.1016/S0969-2126(02)00700-1. ... The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic- ... STRIDE (protein) an alternative algorithm Chris Sander (Scientist) Kabsch W, Sander C (1983). "Dictionary of protein secondary ... where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins. DSSP begins by ...
In protein structure, STRIDE (Structural identification) is an algorithm for the assignment of protein secondary structure ... Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23(4):566-79. doi:10.1002/prot. ... 2005). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol 5 ... from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the Protein ...
Kyngas J, Valjakka J (1998). "Unreliability of the Chou-Fasman parameters in predicting protein secondary structure". Protein ... Chou PY, Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence". Adv Enzymol ... Kabsch W, Sander C (1983). "How good are predictions of protein secondary structure?". FEBS Lett. 155 (2): 179-82. doi:10.1016/ ... The Chou-Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed ...
psipred Protein structure prediction software "JPred4: A Protein Secondary Structure Prediction Server". Retrieved 16 July 2015 ... "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins. 40: 502-11. ... In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The ... Jpred v.4 is the latest version of the popular JPred Protein Secondary Structure Prediction Server which provides predictions ...
Newlove T, Konieczka JH, Cordes MH (April 2004). "Secondary structure switching in Cro protein evolution". Structure. 12 (4): ... The crystal structure of the lambda Cro repressor reveals a HTH DNA-binding protein with an alpha/beta fold that differs from ... Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought ... Ohlendorf DH, Tronrud DE, Matthews BW (July 1998). "Refined structure of Cro repressor protein from bacteriophage lambda ...
Many proteins may adopt a beta sheet as part of their secondary structure. In beta sheets, sections of a single polypeptide may ... "Secondary structure of Proteins". www.chembio.uoguelph.ca. Retrieved 2017-04-01. ... G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures ... Beta sheets can also be either a parallel or anti-parallel secondary structure. However, an anti-parallel beta sheet is ...
Andersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". Structure. 10 (2 ... The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic- ... Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical ... where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins. ...
Sen TZ, Jernigan RL, Garnier J, Kloczkowski A (June 2005). "GOR V server for protein secondary structure prediction". ... This may still provide valuable information, though, on a possible partial structure for this protein. FAM83A is expressed in ... Protein FAM83A (family member with sequence similarity 83) also known as tumor antigen BJ-TSA-9 is a protein that in humans is ... This protein is predicted to contain one domain of unknown function 1669 (DUF1669), which places this protein into the PLDc_ ...
"Combining evolutionary information and neural networks to predict protein secondary structure". Proteins: Structure, Function, ... doi:10.1093/protein/12.2.85. PMID 10195279. "20110621 - Protein Prediction 1 - Protein Structure - Burkhard Rost". 2011. doi: ... Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular ... protein structure and protein function. Examples of research carried out in his lab includes the prediction of enzymatic ...
... use of this normalized CD is important in studies of protein structure. Methods for estimating secondary structure in polymers ... It may be of interest to note that the protein CD spectra used in secondary structure estimation are related to the π to π* ... That is, for instance, a protein molecule with a helical secondary structure can have a CD that changes with changes in the ... Most notably, UV CD is used to investigate the secondary structure of proteins. UV/Vis CD is used to investigate charge- ...
... and the quartenary structure. Protein secondary structure prediction is a main focus of this subfield as the further protein ... are determined based on the secondary structure. Solving the true structure of a protein is an incredibly expensive and time- ... "Sixty-five years of the long march in protein secondary structure prediction: the final stretch?". Briefings in Bioinformatics ... Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo (December 1, 2015). "Protein secondary structure prediction using deep ...
"Protein Secondary Structure Prediction using logic-based machine learning". Protein Engineering. 5 (7): 647-657. doi:10.1093/ ... Applications included the discovery of rules for protein folding (with Ross King) and drug design as well as systems such as ... Tatjana Zrimec used the system to investigate how playing robots could develop structured knowledge about their world while ... Structured Induction in Expert Systems. Turing Institute Press. ASIN 0201178133. Muggleton, Stephen (1990). Inductive ...
... and predictions of secondary structure". Protein Science. 3 (4): 600-7. doi:10.1002/pro.5560030408. PMC 2142870 . PMID 8003978 ... From crystal structures and kinetic assays, it is believed that FPPS catalyzes the condensation reaction in three concerted ... A notable example of the former is the farnesylation of small G-proteins including Ras, CDC42, Rho, and Rac. The attachment of ... The structure and mechanism of farnesyl pyrophosphate synthase (FPPS), a type of geranyltranstransferase, is well characterized ...
"Exploiting the past and the future in protein secondary structure prediction." Bioinformatics 15.11 (1999): 937-946. Pollastri ... "Porter: a new, accurate server for protein secondary structure prediction." Bioinformatics 21.8 (2005): 1719-1720. [1] ... Translation Handwritten Recognition Protein Structure Prediction Artificial neural network Recurrent neural networks Long short ... The general structure of RNN and BRNN can be depicted in the right diagram. By using two time directions, input information ...
A machine learning approach to the problem of predicting a protein's secondary structure from its primary structure (PROMIS) ( ... "Machine learning approach for the prediction of protein secondary structure". Journal of Molecular Biology. 216 (2): 441-457. ... "Identification and application of the concepts important for accurate and reliable protein secondary structure prediction". ... "Music to my DNA structure". Times Higher Education 2001-05-25. "The Shamen - S2 Translation (S2 Protein)" on YouTube Buckley, ...
Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular ... Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and ... database and the DSSP algorithm for assigning secondary structure to the amino acids of a protein, given the atomic-resolution ... "A database of protein structure families with common folding motifs". Protein Science. 1 (12): 1691-1698. doi:10.1002/pro. ...
Hutchinson EG, Thornton JM (1990). "HERA--a program to draw schematic diagrams of protein secondary structures". Proteins. 8 (3 ... Tertiary Protein Structure and Folds: section 4.3.2.1. From Principles of Protein Structure, Comparative Protein Modelling, and ... "Super Secondary Structure - Part II". Principles of Protein Structure Using the Internet. Retrieved 25 May 2007.. ... The β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins. Beta sheets consist of beta ...
ISBN 978-1-4398-1071-2. Rao ST, Rossmann MG (May 1973). "Comparison of super-secondary structures in proteins". Journal of ... ISBN 978-1-4292-3414-6. Kessel A (2010). Introduction to Proteins: Structure, Function, and Motion. Florida: CRC Press. p. 143 ... The overall tertiary structure of the fold resembles a three-layered sandwich wherein the filling is composed of an extended ... The first three strands are connected by α- helices resulting in a beta-alpha-beta-alpha-beta structure. This pattern is ...
"Comparison of super-secondary structures in proteins". J Mol Biol. 76 (2): 241-56. doi:10.1016/0022-2836(73)90388-4. PMID ... publishing on the structure of an Iresin Diester and a terpenoid, and writing computer programs for analysing structures. ... The title of his thesis was "A Study of Some Organic Crystal Structures". In 1956 he and his family moved to the University of ... Rossmann returned to the UK and to the University of Cambridge in 1958, where he worked with Max Perutz on the structure of ...
Rao ST, Rossmann MG (1973). "Comparison of super-secondary structures in proteins". J Mol Biol. 76 (2): 241-56. doi:10.1016/ ... NAD bound to proteins in the PDB NAD Animation (Flash Required) β-Nicotinamide adenine dinucleotide (NAD+, oxidized) and NADH ( ... However, non-histone proteins can be deacetylated by sirtuins as well. These activities of sirtuins are particularly ... The motif is named after Michael Rossmann who was the first scientist to notice how common this structure is within nucleotide- ...
Methods for predicting both secondary structure and tertiary structure - including homology modeling, protein threading, and ... 2001). EVA: large-scale analysis of secondary structure prediction. Proteins Suppl 5:192-9. PMID 11835497 Eyrich VA, Marti- ... running benchmark project for assessing the quality and value of protein structure prediction and secondary structure ... were compared to results from each week's newly solved protein structures deposited in the Protein Data Bank. The project aims ...
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction. According ... Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, Saviano M (1996). "Discovering protein secondary structures: ... 1981). "The anatomy and taxonomy of protein structure". Adv Protein Chem. 34: 167-339. doi:10.1016/S0065-3233(08)60520-3. PMID ... Richardson, JS (1981). "The anatomy and taxonomy of protein structure". Adv Protein Chem. 34: 167-339. doi:10.1016/s0065-3233( ...
Hirschl D, Bayer P, Müller O (March 1996). "Secondary structure of an armadillo single repeat from the APC protein". FEBS Lett ... Multiple copies of the repeat form what is known as an alpha solenoid structure. Examples of proteins that contain armadillo ... Although β-catenin was previously believed to be a protein involved in linking cadherin cell adhesion proteins to the ... the armadillo repeat is found in a wide range of proteins with other functions. This type of protein domain is important in ...
... is an information theory-based method for the prediction of secondary structures in proteins. It was developed in the late ... Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol ... GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266:540-53. Garnier J, ... The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position ...
Predictions of protein secondary structure by Benner and colleagues achieved high accuracy. It became possible to model protein ... "Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure ... The use of multiple sequence information to predict secondary structure of proteins became popular as a result of the work of ... Jones, David T. (1999). "Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices" (PDF). Journal of ...
how community structure, function and stability is determined.[36][37]. Ecological pyramids[edit]. See also: Ecological pyramid ... Aquatic producers, such as planktonic algae or aquatic plants, lack the large accumulation of secondary growth as exists in the ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... Pyramid structure can vary across ecosystems and across time. In some instances biomass pyramids can be inverted. This pattern ...
... This example shows a secondary structure prediction method that ... 1] Rost, B., and Sander, C., "Prediction of protein secondary structure at better than 70% accuracy", Journal of Molecular ... 2] Holley, L.H. and Karplus, M., "Protein secondary structure prediction with a neural network", PNAS, 86(1):152-6, 1989. ... 3] Kabsch, W., and Sander, C., "How good are predictions of protein secondary structure?", FEBS Letters, 155(2):179-82, 1983. ...
A physical basis for protein secondary structure. Rajgopal Srinivasan and George D. Rose ... Residue boundaries in each element of secondary structure element and percentage of the ensemble found in helix (H), strand (S ... The statistical bias toward native secondary structure in helix (red), strand (green), turn (blue), and generalized turn (black ... Percentage of ensemble found in each element of native secondary structure, averaged over 10 independent simulations, together ...
Does anyone know where I can find a database of protein secondary ,structure on-line? Ideally, for each protein in the database ... Database of Protein Secondary Structure Needed. Catherine Letondal letondal at nefertiti.pasteur.fr Tue Sep 19 07:14:20 EST ... I would ,find its amino-acid sequence and *known* (not predicted) secondary ,structure. , , Thanks in advance for any replies, ... More information about the Proteins mailing list. ... Database of Protein Secondary Structure Needed *Next message: ...
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with ... Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary ... Distant relationships between proteins whose primary structures are unalignable can sometimes be found by secondary structure. ... Kihara D (Aug 2005). "The effect of long-range interactions on the secondary structure formation of proteins". Protein Science ...
Availability: The executable program for predicting protein secondary structure is available from the authors free of charge. ... is an important step towards elucidating its three dimensional structure, as well as its function. Presently, the best ... Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) ... dimensional structure protein secondary structure variable long-ranged information correct prediction evolutionary information ...
Prediction of protein secondary structure at better than 70% accuracy.. Rost B1, Sander C. ... neural network on a non-redundant data base of 130 protein chains to predict the secondary structure of water-soluble proteins ... The accuracy in predicting the content of three secondary structure types is comparable to that of circular dichroism ... The inclusion of protein family information in this form increases the prediction accuracy by six to eight percentage points. A ...
The prediction of protein secondary structures is not only of great importance for many biological applications but also ... Machine Learning Techniques for Protein Secondary Structure Prediction:An Overview and Evaluation ... Recent research on secondary structure prediction is mainly based on widely known machine learning techniques, such as ... Keywords: Amino acids encoding; evolutionary information; long-range dependencies; machine learning; protein secondary ...
It is well known that protein secondary-structure information can help the process of performing multiple alignment, in ...
The service predicts secondary protein structures by analyzing amino acid sequences submitted and detecting hydrogen-bonded ... The API returns indicators of hydrogen-bonded residues detected within the input data for use in secondary structure prediction ... Potential for hydrogen bonds is associated with resulting secondary structures, providing a partial indicator that may be used ...
... www.embraceregistry.net/service/gor-i-protein-secondary-structure-prediction-cnrs-ibcp ... API methods support submission of a protein sequence from experimental data. The API returns predictions of secondary sequences ... This collection of three services -- GORI, GORIII, and GORIV -- provide predictions of secondary protein sequences using ... The highest score is taken to indicate the protein conformation. ...
Primary and secondary structure of bovine retinal S antigen (48-kDa protein). T Shinohara, B Dietzschold, C M Craft, G Wistow, ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ...
This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure ...
Protein Data Bank (PDB) STING Schneider, R., de Daruvar, A., & Sander, C. (1997). "The HSSP database of protein structure- ... HSSP is also a database of homology-based implied protein structures. ... This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of ... HSSP is a database that combines structural and sequence information about proteins. ...
... corelation between codon and protein secondary structures *Next message: correlation between codon and protein secondary ... corelation between codon and protein secondary structures *Next message: correlation between codon and protein secondary ... corelation between codon and protein secondary structures. CCoburn CCoburn at pofvax.pnb.sunysb.edu Wed Jan 7 18:58:10 EST 1998 ... Argos P. Title Protein secondary structural types are differentially coded on messenger RNA. Source Protein Science. Vol 5(10 ...
... beta-turn and random-coil regions were predicted for protein protease inhibitors. It appears that in all the inhib ... 11334619 - Amino acid distributions in integral membrane protein structures.. 9466929 - Shear numbers of protein beta-barrels: ... 22544739 - Crystal structure of dnak protein complexed with nucleotide exchange factor grpe in dna.... 19290549 - Reducing ... Next Document: Homology of the predicted secondary structures of the N-terminal fragments of preproteins.. ...
A decision graph explanation of protein secondary structure prediction ... Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level ... Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level ... directly from protein sequence. Therefore, analyzing protein secondary structure is indispensable. In the previous work, ...
Figure 1: Secondary structure distribution around aspartic acid residues binding Mn+2 ions in all the proteins (a); in proteins ... Figure 3: Secondary structure distribution around glutamic acid residues binding Mn+2 ions in all the proteins (a); in proteins ... Figure 2: Secondary structure distribution around histidine residues binding Mn+2 ions in all the proteins (a); in proteins ... for proteins from GC-poor bacteria; % for proteins from bacteria with average genomic G + C; and just % for proteins from GC- ...
1.1 - Protein Surface Accessibility and Secondary Structure Predictions. Version 1.1: Caching system has been implemented. View ... The Z-score is related to the surface prediction, and not the secondary structure.. Instructions Output format Article abstract ... NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method ...
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.. Kabsch W, Sander C ...
Molecular Biology (Protein Secondary Structure) Data Set Download: Data Folder, Data Set Description ... Ning Qian and Terrnece J. Sejnowski (1988), "Predicting the Secondary Structure of Globular Proteins Using Neural Network ... Abstract: From CMU connectionist bench repository; Classifies secondary structure of certain globular proteins ... what secondary structure it is a part of within the protein. There are three choices: alpha-helix, beta-sheet, and random-coil ...
Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Δδ) ... The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. ... Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Δδ) ... Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861 ...
The Secondary Structure of Proteins Biochemistry Lecture Aid by Frieda Reichsman This presentation is designed as an aid in ... teaching material on the secondary structures of proteins. Buttons are intended for the instructors use and are labeled with ...
An encoding scheme for protein folding on lattice models, inspired by parametric L-systems, was proposed. The encoding ... Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. ... Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. In: Talbi EG., Liardet P., ... Secondary Structure Evolutionary Algorithm Encode Scheme Memetic Algorithm Inference Procedure These keywords were added by ...
Protein Secondary Structure Prediction Website Is Open. by wanglj on Tue Mar 30, 2010 10:38 pm ... Based on the described research achievements, now we open the protein secondary structure prediction website, for the aim of ... we have got the leading position in predicting protein secondary structure, and apply the KDTICM and its software ICCKDSS in ... research communication and international technology service in Internet which concludes providing protein secondary structure ...
Loops in globular proteins: a novel category of secondary structure Message Subject. (Your Name) has forwarded a page to you ... The protein loop, a novel category of nonregular secondary structure, is a segment of contiguous polypeptide chain that traces ... A systematic study was made of 67 proteins of known structure revealing 270 omega loops. Although such loops are typically ... Loops are almost invariably situated at the protein surface where they are poised to assume important roles in molecular ...
  • Dandekar, T., Argos, P.: Folding the main chain of small proteins with the genetic algorithm. (springer.com)
  • Using this approach, we demonstrate the applicability of the framework to the problem of reconstructing the overall protein fold for a number of commonly studied small proteins, based on only predicted secondary structure and contact map. (warwick.ac.uk)
  • Detailed consideration of the dynamic behavior or proteins and how they fold to their native structllfcs is deferred until Chapter 9. (coursehero.com)
  • The structure displays the main features of the canonical MH2 fold with two main differences: the addition of an α -helical region and the remodelling of a protein-interaction site that is conserved in the MH2 domain of Smads. (iucr.org)
  • Proteins are chains of amino acids that fold into a three-dimensional shape. (encyclopedia.com)
  • Mutant Escherichia coli strains in which export of the LamB protein (coded for by the lamB gene) to the outer membrane of the cell is prevented have been described previously. (caltech.edu)
  • The mmuM gene product from Escherichia coli is an archetypal HMT family protein and contains a predicted zinc-binding motif in the enzyme active site. (portlandpress.com)
  • Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. (springer.com)
  • We have isolated pseudorevertants that restore export of functional LamB protein to the outer membrane. (caltech.edu)
  • The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni , may play an important role in the adaptation of the organism to various host environments. (asm.org)
  • It was shown that the single-copy cmp locus encoded a protein with characteristics of bacterial outer membrane proteins. (asm.org)
  • Many gram-negative bacteria have one or more predominant outer membrane proteins (OMPs). (asm.org)
  • As the major components of the gram-negative bacterial outer membrane, pore-forming proteins also play a role in bacterial pathogenesis, such as adherence, invasion, and serum resistance ( 35 , 44-46 ). (asm.org)
  • Many times, beta-barrels can be found in proteins that span the membrane. (statpearls.com)
  • The cDNA coding for calf filensin, a membrane-associated protein of the lens fiber cells, has been cloned and sequenced. (elsevier.com)
  • A truncated HIV-1 Tat protein basic domain rapidly translocates through the plasma membrane and accumulates in the cell nucleus. (stackexchange.com)
  • However, this information is not (or rarely) used in phylogenetic studies, even though the structure of dozen thousands of proteins has been elucidated. (cnrs.fr)
  • Humans have tens of thousands of proteins in their bodies at any given moment in time. (statpearls.com)