OrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceHealth Care
ProteinsProtein Structure, SecondaryModels, MolecularProtein ConformationDatabases, ProteinSequence Analysis, ProteinStructural Homology, ProteinProtein Structure, TertiarySoftwareProtein FoldingAlgorithmsComputational BiologySequence AlignmentAmino Acid SequenceInternetComputer SimulationModels, ChemicalMolecular Sequence DataUser-Computer InterfaceNuclear Magnetic Resonance, BiomolecularCrystallography, X-RayHydrogen BondingComputer GraphicsThermodynamicsBinding SitesAmino AcidsEvolution, MolecularSequence Homology, Amino AcidMolecular Dynamics SimulationStructure-Activity RelationshipProtein BindingSolventsHydrophobic and Hydrophilic InteractionsMagnetic Resonance SpectroscopyMolecular StructureCrystallographyProtein Structure, QuaternaryDatabases, FactualProtein DenaturationMuramidaseStatic ElectricityEnzymesLigandsKnowledge BasesArtificial IntelligenceInformation Storage and RetrievalProtein Interaction MappingDatabase Management SystemsProtein EngineeringAmino Acid MotifsProtein StabilityCircular DichroismMutationMembrane ProteinsConserved SequenceMyoglobinProtein Interaction Domains and MotifsWaterBacterial ProteinsX-Ray DiffractionMonte Carlo MethodCrystallizationPattern Recognition, AutomatedModels, StatisticalProteomicsPeptidesCluster AnalysisTemperatureNeural Networks (Computer)GenomicsSolutionsEscherichia coliEntropyReproducibility of ResultsPhylogenyChemistry, PhysicalPhysicochemical PhenomenaBase SequenceModels, TheoreticalDisulfidesKineticsAmino Acid SubstitutionAutomationPliabilitySpectrophotometry, InfraredCatalytic DomainMolecular ConformationProtein UnfoldingCryoelectron MicroscopyCysteineEnzyme StabilityMathematical ConceptsComputing MethodologiesHydrogenMutagenesis, Site-DirectedDeuterium Exchange MeasurementMarkov ChainsBiophysical PhenomenaBiophysicsTryptophanElectronsHemerythrinSynchrotronsMolecular Sequence AnnotationBacteriophage T4Normal DistributionMass SpectrometryPeptide FragmentsCattleSurface PropertiesEscherichia coli ProteinsScattering, Small AngleRubredoxinsSystems IntegrationOnline SystemsQuantum TheoryRecombinant ProteinsDrug DesignProgramming LanguagesSpectrometry, FluorescenceSpectroscopy, Fourier Transform InfraredData Interpretation, StatisticalHydrogen-Ion ConcentrationRibonuclease, PancreaticCloning, MolecularSequence AnalysisBacteriorhodopsinsCrown EthersProteomeDimerizationAmino Acids, AromaticProlineRepetitive Sequences, Amino AcidApoproteinsProtein MultimerizationSoftware DesignDrug StabilityDatabases as TopicDNAAmidesFourier AnalysisSoftware ValidationMotionIonsPoint MutationHot TemperatureMultiprotein ComplexesTriose-Phosphate IsomeraseBiochemistryDatabases, GeneticEnergy TransferPyrococcus furiosusSubstrate SpecificityMetalloproteinsProtonsModels, BiologicalExonsSpectrum Analysis, RamanLipid BilayersNational Institute of General Medical Sciences (U.S.)Data DisplayHistidineNitrogen IsotopesUbiquitinSolubilityCatalysisDeuteriumTrypsinMultigene FamilyDatabases, Nucleic AcidGenomeSpectrophotometryMicellesMutation, MissenseGlycosylationTorsion, MechanicalLactalbuminProtein FootprintingMutant ProteinsSequence Analysis, DNAPeptide LibraryOxidation-ReductionCodonElectron Spin Resonance SpectroscopyMetalsProtein Processing, Post-TranslationalMolecular Docking SimulationProbabilityModels, StructuralElectrophoresis, Polyacrylamide GelAllosteric RegulationNeutronsAspartate Aminotransferase, MitochondrialMathematical ComputingHemeUreaMacromolecular SubstancesDetergentsGenetic VariationPlant ProteinsAsparagine
Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Structural Homology, Protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Solvents: Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Crystallography: The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Muramidase: A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.Static Electricity: The accumulation of an electric charge on a objectEnzymes: Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Knowledge Bases: Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).Artificial Intelligence: Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Protein Engineering: Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Protein Stability: The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Myoglobin: A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.Protein Interaction Domains and Motifs: Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Bacterial Proteins: Proteins found in any species of bacterium.X-Ray Diffraction: The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Monte Carlo Method: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Neural Networks (Computer): A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Solutions: The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Entropy: The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Chemistry, Physical: The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.Physicochemical Phenomena: The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Models, Theoretical: Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.Kinetics: The rate dynamics in chemical or physical systems.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Automation: Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)Pliability: The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)Spectrophotometry, Infrared: Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Protein Unfolding: Conformational transitions of the shape of a protein to various unfolded states.Cryoelectron Microscopy: Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.Mathematical Concepts: Numeric or quantitative entities, descriptions, properties, relationships, operations, and events.Computing Methodologies: Computer-assisted analysis and processing of problems in a particular area.Hydrogen: The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Deuterium Exchange Measurement: A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Biophysical Phenomena: The physical characteristics and processes of biological systems.Biophysics: The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.Electrons: Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.Hemerythrin: A non-heme iron protein consisting of eight apparently identical subunits each containing 2 iron atoms. It binds one molecule of oxygen per pair of iron atoms and functions as a respiratory protein.Synchrotrons: Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Normal Distribution: Continuous frequency distribution of infinite range. Its properties are as follows: 1, continuous, symmetrical distribution with both tails extending to infinity; 2, arithmetic mean, mode, and median identical; and 3, shape completely determined by the mean and standard deviation.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Surface Properties: Characteristics or attributes of the outer boundaries of objects, including molecules.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Scattering, Small Angle: Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.Rubredoxins: A class of iron-sulfur proteins that contains one iron coordinated to the sulfur atom of four cysteine residues. (McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Online Systems: Systems where the input data enter the computer directly from the point of origin (usually a terminal or workstation) and/or in which output data are transmitted directly to that terminal point of origin. (Sippl, Computer Dictionary, 4th ed)Quantum Theory: The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Drug Design: The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.Programming Languages: Specific languages used to prepare computer programs.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Spectroscopy, Fourier Transform Infrared: A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Ribonuclease, Pancreatic: An enzyme that catalyzes the endonucleolytic cleavage of pancreatic ribonucleic acids to 3'-phosphomono- and oligonucleotides ending in cytidylic or uridylic acids with 2',3'-cyclic phosphate intermediates. EC 3.1.27.5.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Bacteriorhodopsins: Rhodopsins found in the PURPLE MEMBRANE of halophilic archaea such as HALOBACTERIUM HALOBIUM. Bacteriorhodopsins function as an energy transducers, converting light energy into electrochemical energy via PROTON PUMPS.Crown Ethers: Macrocyclic polyethers with the repeating unit of (-CH2-CH2-O)n where n is greater than 2 and some oxygens may be replaced by nitrogen, sulfur or phosphorus. These compounds are useful for coordinating CATIONS. The nomenclature uses a prefix to indicate the size of the ring and a suffix for the number of heteroatoms.Proteome: The protein complement of an organism coded for by its genome.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Amino Acids, Aromatic: Amino acids containing an aromatic side chain.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Apoproteins: The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Software Design: Specifications and instructions applied to the software.Drug Stability: The chemical and physical integrity of a pharmaceutical product.Databases as Topic: Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Amides: Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)Fourier Analysis: Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)Software Validation: The act of testing the software for compliance with a standard.Motion: Physical motion, i.e., a change in position of a body or subject as a result of an external force. It is distinguished from MOVEMENT, a process resulting from biological activity.Ions: An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Multiprotein Complexes: Macromolecular complexes formed from the association of defined protein subunits.Triose-Phosphate Isomerase: An enzyme that catalyzes reversibly the conversion of D-glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. A deficiency in humans causes nonspherocytic hemolytic disease (ANEMIA, HEMOLYTIC, CONGENITAL NONSPHEROCYTIC). EC 5.3.1.1.Biochemistry: The study of the composition, chemical structures, and chemical reactions of living things.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Energy Transfer: The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.Pyrococcus furiosus: A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Metalloproteins: Proteins that have one or more tightly bound metal ions forming part of their structure. (Dorland, 28th ed)Protons: Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Spectrum Analysis, Raman: Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.Lipid Bilayers: Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.National Institute of General Medical Sciences (U.S.): Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports basic biomedical research that is not targeted to specific diseases and funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells and metabolism. It was established in 1962.Data Display: The visual display of data in a man-machine system. An example is when data is called from the computer and transmitted to a CATHODE RAY TUBE DISPLAY or LIQUID CRYSTAL display.Histidine: An essential amino acid that is required for the production of HISTAMINE.Nitrogen Isotopes: Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.Ubiquitin: A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Deuterium: Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Micelles: Particles consisting of aggregates of molecules held loosely together by secondary bonds. The surface of micelles are usually comprised of amphiphatic compounds that are oriented in a way that minimizes the energy of interaction between the micelle and its environment. Liquids that contain large numbers of suspended micelles are referred to as EMULSIONS.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Glycosylation: The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.Torsion, Mechanical: A twisting deformation of a solid body about an axis. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Lactalbumin: A major protein fraction of milk obtained from the WHEY.Protein Footprinting: A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.Mutant Proteins: Proteins produced from GENES that have acquired MUTATIONS.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Electron Spin Resonance Spectroscopy: A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.Metals: Electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals. (Grant & Hackh's Chemical Dictionary, 5th ed)Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Molecular Docking Simulation: A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.Probability: The study of chance processes or the relative frequency characterizing a chance process.Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Allosteric Regulation: The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.Neutrons: Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.Aspartate Aminotransferase, Mitochondrial: An aspartate aminotransferase found in MITOCHONDRIA.Mathematical Computing: Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem.Heme: The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.Urea: A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Detergents: Purifying or cleansing agents, usually salts of long-chain aliphatic bases or acids, that exert cleansing (oil-dissolving) and antimicrobial effects through a surface action that depends on possessing both hydrophilic and hydrophobic properties.Genetic Variation: Genotypic differences observed among individuals in a population.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Asparagine: A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from ASPARTIC ACID and AMMONIA by asparagine synthetase. (From Concise Encyclopedia Biochemistry and Molecular Biology, 3rd ed)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Polbase - Structure of polymerase: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed...Polbase - Structure of polymerase: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed...
Polymerase structure: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment ( PDBid: 2R2U)
Genetic Evidence that Transcription Activation by RhaS Involves Specific Amino Acid Contacts with Sigma 70 | Journal of...Genetic Evidence that Transcription Activation by RhaS Involves Specific Amino Acid Contacts with Sigma 70 | Journal of...
Fig. 4. Model of the C-terminal domain of RhaS bound to DNA based on the crystal structure of a MarA-DNA complex (44). (A) "Front" view of RhaS C-terminal domain (white) in a space-filling model with the negatively charged residues highlighted and numbered. DNA is shown in a stick model and is colored cyan. RhaS residues (in red) were defective at both the rhaBAD and therhaT promoters, while residues in orange were either not defective, were defective at only one promoter, or were not tested (D250 and D191). In this view the N-terminal subdomain of RhaS is on the left and the C-terminal subdomain is on the right. The approximate position of the −35 region of the promoter is shown as a gray bar. (B) Same as panel A, except rotated around the vertical axis by approximately 180° to give the "back" view (i.e., the N-terminal subdomain is on the right, and the C-terminal subdomain is on the left). (C) A model of the C-terminal region of ς70(residues 550 to 613, orange, based on the DNA-binding ...
Evolutionary classification of protein domain structuresEvolutionary classification of protein domain structures
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers ...
Evolutionary classification of protein domain structuresEvolutionary classification of protein domain structures
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers ...
The evolution of protein domain families | Biochemical Society TransactionsThe evolution of protein domain families | Biochemical Society Transactions
Protein domains are compact regions of a proteins structure that often convey some distinct function. Domain architecture, or order of domains in a protein, is frequently considered as a fundamental level of protein functional complexity [1]. The majority of the protein repertoire is composed of multidomain proteins; two-thirds of the proteins in prokaryotes and about four-fifths eukaryotic ones have two or more domains [2]. Moreover, an organisms complexity relates much better to the number of distinct domain architectures [3] and expansion in particular domain families [4] than to the number of genes in the organism. The prevalence of proteins with more than two domains and the recurrent appearance of the same domain in non-homologues proteins show that functional domains are reused when creating new proteins. Because of this, domains have been likened to Lego bricks that can be recombined in various ways to build proteins with completely new functions [5]. Hence, one way to study evolution ...
SMART: SAM domain annotationSMART: SAM domain annotation
The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo- and hetero-oligomerize and to mediate specific protein-protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C-terminus of more than 40 Eph receptor tyrosine kinases that are involved in the control of axonal pathfinding upon ephrin-induced oligomerization and activation in the event of cell-cell contacts. These SAM domains appear to participate in downstream signaling events via interactions with cytosolic proteins. We determined the solution structure of the EphB2 receptor SAM domain and studied its association behavior. The structure consists of five helices forming a compact structure without binding pockets or exposed conserved aromatic residues. Concentration-dependent chemical ...
SMART: SAM domain annotationSMART: SAM domain annotation
The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo- and hetero-oligomerize and to mediate specific protein-protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C-terminus of more than 40 Eph receptor tyrosine kinases that are involved in the control of axonal pathfinding upon ephrin-induced oligomerization and activation in the event of cell-cell contacts. These SAM domains appear to participate in downstream signaling events via interactions with cytosolic proteins. We determined the solution structure of the EphB2 receptor SAM domain and studied its association behavior. The structure consists of five helices forming a compact structure without binding pockets or exposed conserved aromatic residues. Concentration-dependent chemical ...
Signal peptide-binding domain superfamilySignal peptide-binding domain superfamily
The SCOP classification for the Signal peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
Auto-inhibition of Arabidopsis th... preview & related info | MendeleyAuto-inhibition of Arabidopsis th... preview & related info | Mendeley
(2004) Luoni et al. FEBS Letters. Type IIB Ca2+-ATPases have a terminal auto-inhibitory, domain the action of which is suppressed by calmodulin (CaM) binding. Here, we show that a peptide (6His-1M-I116) corresponding to the first 116 aminoacids (aa) of At-ACA8, the first cloned isoform of Arabido...
KH homology domain-containing protein elisa and antibodyKH homology domain-containing protein elisa and antibody
Shop KH homology domain-containing protein ELISA Kit, Recombinant Protein and KH homology domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
CDD Conserved Protein Domain Family: Tup NCDD Conserved Protein Domain Family: Tup N
pfam08581 (PSSM ID: 369972): Conserved Protein Domain Family Tup_N, The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor
CSF1R protein domain and mutation schematic. Schematic | Open-iCSF1R protein domain and mutation schematic. Schematic | Open-i
CSF1R protein domain and mutation schematic. Schematic diagram of the protein domain structure of CSF1R with amino acid numbers provided. Mutations previously r
CDD Conserved Protein Domain Family: zf-C2H2 2CDD Conserved Protein Domain Family: zf-C2H2 2
pfam12756 (PSSM ID: 372293): Conserved Protein Domain Family zf-C2H2_2, This family contains two copies of a C2H2-like zinc finger domain
Forkhead-associated domain-containing protein elisa and antibodyForkhead-associated domain-containing protein elisa and antibody
Shop Forkhead-associated domain-containing protein ELISA Kit, Recombinant Protein and Forkhead-associated domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Domain combination pairs containing Dcp2 domain-like and Nudix in all archaeaDomain combination pairs containing Dcp2 domain-like and Nudix in all archaea
Domain architectures containing both Dcp2 domain-like and Nudix in all archaea. Links to architectures containing these domain pairs in other groups of genomes are provided. Domain pairs which are not adjacent can be added/removed.
Transmembrane domain architecture, symmetry and couplin | Open-iTransmembrane domain architecture, symmetry and couplin | Open-i
Transmembrane domain architecture, symmetry and coupling to LBDa, View of the TMD parallel to the membrane. GluN1 subunits are blue and the GluN2B subunits are
GTLD Domain Names | New Domain Extensions Available - GoDaddy PHGTLD Domain Names | New Domain Extensions Available - GoDaddy PH
Search new domain extension and be the first to get a new domain from the trusted domain registrar. Browse through our new and coming soon domain extensions!
Method for producing and identifying soluble protein domains - Domainex LimitedMethod for producing and identifying soluble protein domains - Domainex Limited
Methods for producing and identifying fragments of proteins, and more particularly to methods for generating and identifying soluble protein domains are disclosed based on a method for generating a li
Domain combinations for gap ,47576, gap ,48350, gap ,143885 superfamilies in groups of genomesDomain combinations for gap ,47576, gap ,48350, gap ,143885 superfamilies in groups of genomes
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Domain combinations for 52518,52922,52518,54862,53323 superfamilies in groups of genomesDomain combinations for 52518,52922,52518,54862,53323 superfamilies in groups of genomes
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Tuning the Flexibility of Glycine-Serine Linkers ToAllow Rational Design of Multidomain Proteins - BioNMRTuning the Flexibility of Glycine-Serine Linkers ToAllow Rational Design of Multidomain Proteins - BioNMR
Tuning the Flexibility of Glycine-Serine Linkers ToAllow Rational Design of Multidomain Proteins Biochemistry DOI: 10.1021/acs.biochem.7b00902 More...
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http://www.peopleeraconsulting.in/http://www.peopleeraconsulting.in/
People Era Consulting is an emerging recruitment firm providing end to end Talent Solutions to multifarious industrial segments across the country. Our focus has always been on providing a pool of potential and validated candidates across the level i.e. Senior, Middle and Junior management. We operate through domain specialist providing high quality permanent hiring services.. ...
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Coiled-coil domain-containing protein 187Coiled-coil domain-containing protein 187
MPTLVVGTPPTCLGDTPQPCHKNSQRQGPFSHGAPGRAADWKAVAKPRLCAPAAEDDVAALRWPGPSQQP 1 - 70 DPPWAAPHVVGSDDLKEPGPWGKACSLPMWSTGPEARDGDSSVSSGRLSCSSGGHDVCVSWKERPPQVLG 71 - 140 PQQRPRKSDARLEQLRDKIRAQAWQQGSCASLGTSAPSSASRLHKASTLMLRRKGQEAKNPPPAPECSGF 141 - 210 SILSAAERRVEAKASHGQGRELSRVSQHQVPVLREKPKRVKSSSCKREKTPKLPSPRRAAKDKHKDEDSE 211 - 280 LVGVYAWRKGQALVRSLLGPPPVLRRHHSKDPSRDPALTVDLGDSEKVIAAKCSPVCAQLPDATSAYSDQ 281 - 350 QVSGNTPSLASFDQPATIQTAMAILQDLRQQIQAGLELAQARKGGQELGPSKRRLQDVAGRGCCRDPNAQ 351 - 420 SSFSKSPWAMTERKHSSLERARSVHTWEPWSSSTARESCPQRAWGAQGQDRSFQRPESPHERLGHFSQRP 421 - 490 WSALAGQACSPQRAWGAQRQGPSSQRPGSPPEKRSPFPQQPWSAVATQPCPRRAWTACETWEDPGPRLRN 491 - 560 PLERPSPPAQRPWSSSGVQRAGPQGKGRGIGSPVSAAKHALPRPTGSFPQNPLGKEKDTLRPCPRSRGLL 561 - 630 GPSHSSESLREFMRQKAQARRRQALEEKASALRTRELRSRRLQEVYRQQREAVLGRAVPVVSRTTPGIVT 631 - 700 FVPSSAQSGGLEASGSLESPVLEWSKVTSGMVLGGQEAPGSFCLCLNRAWNHAETLDPPGMGGPQDGRDA 701 - 770 PVLLSASPSLGSLELQDLTTRYLPRGMCIYLDPKEAEHLGTSSSLHLRHKQAQLQALETTAKVLKQRVDS 771 - 840 ...
Coiled-coil domain-containing protein 13Coiled-coil domain-containing protein 13
MAADESSQNTLRLQFKAMQEMQHKRLQKQMEKKREKELSLKSRADDQEEPLEVSDGLSLLHAGEPNSKNS 1 - 70 FEKRVLEDEIEHLRNELRETVDENGRLYKLLKERDFEIKHLKKKIEEDRFAFTGTAGVAGDVVATKIVEL 71 - 140 SKKNRLLMAESEGAKTRVKQLTNRIQELERELQTALTRLSAKGATDAGAKPPRAQMGDRALLETPEVKAL 141 - 210 QDRLVATNLKMSDLRNQIQSVKQELRMAQKVLAREVGEDINVQQLLSSPGTWRGRAQQILVLQSKVQELE 211 - 280 KQLGQARSQSAGTASDELSVYPDPRKLSAQEKNLLRIRSLEREKQEGLEKLASERDVLQRELEELKKKFE 281 - 350 GMRSRNKLLSSEMKTLKSQMGTLVEKGRHDDELIDALMDQLKQLQEILGSLSLQEEKTRVSQHHLDQQLN 351 - 420 SEAQRSNSLVAQLQAMVAEREAKVRQLEMEIGQLNVHYLRNKGVGEGSSGREVSPAYTQFLEDPGLTKSP 421 - 490 ASAGDHVGRLGSSRSVTSLGHTLVESALTRPSLPSPHRTSPRFSDSPEQKGWQAQVSEIKALWQAAEVER 491 - 560 DRLTEFVTVLQKRVEESNSKLLESERKLQEERHRTVVLEQHLEKIRLEPGKASASQRAAPRTKTGLPTSN 561 - 630 NRHNPTGSEKKDPSFAQLSDVPVESQMEELTTRLAIQVEENEMLKAALGSALRGKEEDFRMYHEILGQVK 631 - 700 SVFLQALRQQKTGKQ 701 - 715 ...
3.3.1 Benefits of the new addressing plan3.3.1 Benefits of the new addressing plan
When the improved inter-domain routing protocol is deployed, an immediate decrease in the number routing table entries should occur, followed by a significant reduction in the rate growth of routing table size (for default-free routers). ...
Etk/Bmx, a tyrosine kinase with a pleckstrin-homology domain, is an effector of phosphatidylinositol 3-kinase and is involved...Etk/Bmx, a tyrosine kinase with a pleckstrin-homology domain, is an effector of phosphatidylinositol 3'-kinase and is involved...
TY - JOUR. T1 - Etk/Bmx, a tyrosine kinase with a pleckstrin-homology domain, is an effector of phosphatidylinositol 3-kinase and is involved in interleukin 6- induced neuroendocrine differentiation of prostate cancer cells. AU - Qiu, Y.. AU - Robinson, D.. AU - Pretlow, T. G.. AU - Kung, H. J.. PY - 1998/3/31. Y1 - 1998/3/31. N2 - Etk/Bmx is the newest member of Btk tyrosine kinase family that contains a pleckstrin homology domain, an src homology 3 domain, an src homology 2 domain, and a catalytic domain. Unlike other members of the Btk family kinases, which are mostly hemopoietic cell-specific, Etk/Bmx is preferentially expressed in epithelial and endothelial cells. We first identified this kinase in prostate cancer [Robinson, D., He, F, Pretlow, T. and Kung, H. J. (1996) Proc. Natl. Acad. Sci. USA 93, 5958-5962). Here we report that Etk is engaged in phosphatidylinositol 3-kinase (PI3-kinase) pathway and plays a pivotal role in interleukin 6 (IL-6) signaling in a prostate cancer cell line, ...
NMR paper Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and...NMR paper Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and...
Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark
HOMER1 - WikipediaHOMER1 - Wikipedia
Homer protein homolog 1 or Homer1 is a neuronal protein that in humans is encoded by the HOMER1 gene. Other names are Vesl and PSD-Zip45. Homer1 protein has an N-terminal EVH1 domain, involved in protein interaction, and a C-terminal coiled-coil domain involved in self association. It consists of two major splice variants, short-form (Homer1a) and long-form (Homer1b and c). Homer1a has only EVH1 domain and is monomeric while Homer1b and 1c have both EVH1 and coiled-coil domains and are tetrameric. The coiled-coil can be further separated into N-terminal half and C-terminal half. The N-terminal half of the coiled-coil domain is predicted to be a parallel dimer while the C-terminus half is a hybrid of dimeric and anti-parallel tetrameric coiled-coil. As a whole, long Homer is predicted to have a dumbbell-like structure where two pairs of EVH1 domains are located on two sides of long (~50 nm) coiled-coil domain. Mammals have Homer2 and Homer3, in addition to Homer1, which have similar domain ...
Heat shock protein 70kD (HSP70), peptide-binding domain superfamilyHeat shock protein 70kD (HSP70), peptide-binding domain superfamily
The SCOP classification for the Heat shock protein 70kD (HSP70), peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
Genes | Free Full-Text | Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by...Genes | Free Full-Text | Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by...
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBIs GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of
Modulation of Escherichia coli Cell Membrane by a Monotopic Lipid Glycosyltransferase - an Exploration of Potential MechanismsModulation of Escherichia coli Cell Membrane by a Monotopic Lipid Glycosyltransferase - an Exploration of Potential Mechanisms
Monotopic proteins represent a specialized group of membrane proteins in that they are engaged in biochemical events taking place at the membrane interface. In particular, the monotopic lipid-synthesizing enzymes are able to synthesize amphiphilic lipid products by catalyzing two biochemically distinct molecules (substrates) at the membrane interface. Thus, from an evolutionary point of view, anchoring into the membrane interface enables monotopic enzymes to confer sensitivity to a changing environment by regulating their activities in the lipid biosynthetic pathways in order to maintain a certain membrane homeostasis. We are focused on a plant lipid-synthesizing enzyme DGD2 involved in phosphate shortage stress, and analyzed the potentially important lipid anchoring segments of it, by a set of biochemical and biophysical approaches. A mechanism was proposed to explain how DGD2 adjusts its activity to maintain a proper membrane. In addition, a multivariate-based bioinformatics approach was used ...
Mechanisms of membrane interaction and dimerization of K-Ras4B | NIH Research FestivalMechanisms of membrane interaction and dimerization of K-Ras4B | NIH Research Festival
Ras is a small GTPase, controlling signal transduction pathways and promoting cell proliferation and survival. KRAS is frequently mutated in cancer. Ras consists of highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ significantly across Ras isoforms. Recent NMR and MD simulations discovered that the HVR of K-Ras4B-GDP extensively interacts with the catalytic domain. However, it weakly interacts with the catalytic domain in the GTP-bound state. Here, using MD simulations we modeled K-Ras4B membrane interaction and dimerization. On the membrane, the catalytic domain takes on multiple orientations, including perpendicular and parallel alignments of the allosteric helices with respect to the membrane normal. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with the farnesyl anchored into the membrane and the HVR unrestrained, the catalytic domain fluctuates reinlessly, exposing its ...
Zn2/Cys6 DNA-binding domain superfamilyZn2/Cys6 DNA-binding domain superfamily
The SCOP classification for the Zn2/Cys6 DNA-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
ISMB 2006: Fortaleza, Brazil, August 6-10ISMB 2006: Fortaleza, Brazil, August 6-10
Alpha-helical transmembrane proteins constitute about 20% of all proteins encoded by most genomes (Krogh et al. 2001) and are responsible for several vital processes in the cell. In addition, the medical importance of membrane bound receptors, channels, and pumps as targets for drugs is well established. Still, for the large majority of membrane proteins, the structure or even the topology, i.e., the positions and in/out-orientations of all transmembrane helices, is not known experimentally. The continuously growing amount of sequence data, in combination with the limited amount of structural data available, highlight the need for better and more accurate theoretical structure prediction methods, particularly for the annotation of membrane proteins. ,br,,br, Protein domains are modular, independently evolving, and structurally similar amino acid segments, which may exist alone in single-domain proteins, or may combine to form multi-domain proteins. Although covalent combinations between ...
org.Rn.egSF @ dnet 1.1.2org.Rn.egSF @ dnet 1.1.2
An R object that contains domain superfamily information for Rat Entrez Genes. This data is prepared based on SUPERFAMILY database, which provides SCOP domain architecture assignments to all completely sequenced genomes including eukaryotic genomes. The domain architecture for an Entrez gene is the protein product with the longest length of amino acids. Thus, domain superfamily information for Rat Entrez gene is a list of domain superfamilies (excluding unknown gap) appearing in its domain architecture.. ...
Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved...Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved...
Journal Article: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface ...
1ira - Proteopedia, life in 3D1ira - Proteopedia, life in 3D
Inflammation, regardless of whether it is provoked by infection or by tissue damage, starts with the activation of macrophages which initiate a cascade of inflammatory responses by producing the cytokines interleukin-1 (IL-1) and tumour necrosis factor-alpha (ref. 1). Three naturally occurring ligands for the IL-1 receptor (IL1R) exist: the agonists IL-1alpha and IL-1beta and the IL-1-receptor antagonist IL1RA (ref. 2). IL-1 is the only cytokine for which a naturally occurring antagonist is known. Here we describe the crystal structure at 2.7 A resolution of the soluble extracellular part of type-I IL1R complexed with IL1RA. The receptor consists of three immunoglobulin-like domains. Domains 1 and 2 are tightly linked, but domain three is completely separate and connected by a flexible linker. Residues of all three domains contact the antagonist and include the five critical IL1RA residues which were identified by site-directed mutagenesis. A region that is important for biological function in ...
ILKBP Definition: Integrin-Linked Kinase-Binding ProteinILKBP Definition: Integrin-Linked Kinase-Binding Protein
definition of ILKBP, what does ILKBP mean?, meaning of ILKBP, Integrin-Linked Kinase-Binding Protein, ILKBP stands for Integrin-Linked Kinase-Binding Protein
Avoiding Adverse Effects on SEO through Domain Name Ownership History ChecksAvoiding Adverse Effects on SEO through Domain Name Ownership History Checks
In this post, we explored the effects of domain name ownership history on an organizations SEO ranking, and how a simple check using WHOIS History Search can help users avoid related challenges.
SVEP1 Gene - GeneCards | SVEP1 Protein | SVEP1 AntibodySVEP1 Gene - GeneCards | SVEP1 Protein | SVEP1 Antibody
Complete information for SVEP1 gene (Protein Coding), Sushi, Von Willebrand Factor Type A, EGF And Pentraxin Domain Containing 1, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Automated Recommendation of Related Model Elements for Domain Models | SpringerLinkAutomated Recommendation of Related Model Elements for Domain Models | SpringerLink
Domain modeling is an important activity in the early stages of software projects to achieve a common understanding of the problem area among project participants. Domain models describe concepts and...
Bacterial Protein Impairs Important Cellular Processes | The BioScientistBacterial Protein Impairs Important Cellular Processes | The BioScientist
Prof. Dr. Winfried Römer and his research team at the University of Freiburg have recently found that bacterial protein impairs important cellular processes
PHLDB3 (pleckstrin homology like domain family B member 3)PHLDB3 (pleckstrin homology like domain family B member 3)
... , Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
generating terminal truncations of a proteingenerating terminal truncations of a protein
Hi guys, What are the routine methods by which you generate terminal truncations of a protein of interest for subsequent screening for purification, stability and efficient folding for the purposes of crystallization? My protein has 2 known domains and a conserved C-terminal part which is defined as domain by sequence homology with other proteins. We would like to generate different lengths of the protein containing this C-terminus and screen them for expression, solubility, purification, and folding and thus increase our chances for success. appreciate all help Iva ...
New site in subdirectory better than new domainNew site in subdirectory better than new domain
This is probably amateurish and obvious but I was surprised. I created a new site but under an existing domain that was already getting pretty good traffic. After only a few days the new site including individual pages came up #1 in Google or Yahoo searching with 2 words. I guess because the pages are crawled regularly. Seems like it might be OK to group new smaller sites under a common domain under some circumstances. Cheaper and less hassles too.
RCSB PDB - 4GOD: Crystal structure of the SGTA homodimerization domain Methods Report PageRCSB PDB - 4GOD: Crystal structure of the SGTA homodimerization domain Methods Report Page
4GOD: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface.
anti-SMYD1 antibody | GeneTexanti-SMYD1 antibody | GeneTex
SMYD1 antibody (SET and MYND domain containing 1) for ICC/IF, IHC-P, WB. Anti-SMYD1 pAb (GTX119484) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
Ubxn10 MGI Mouse Gene Detail - MGI:2443123 - UBX domain protein 10Ubxn10 MGI Mouse Gene Detail - MGI:2443123 - UBX domain protein 10
View mouse Ubxn10 Chr4:138709837-138737167 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
What Check Before Buy a New Domain Name - News Web BDWhat Check Before Buy a New Domain Name - News Web BD
Your website should be located at a domain name thats easy to discover, which means you have to opt for an internet address which is easy to remember a new
EH Protein Domain | Cell Signaling TechnologyEH Protein Domain | Cell Signaling Technology
A scientific resource for the EH protein domain containing information on structure, function, and domain binding during endocytosis and vesicle trafficking.
Click to printClick to print
Some of the hardest parts of working towards the ideal of a theorist, at least for me, are: (1) making sure that I engage with problems that can be made interesting to the new domain I enter and not just me; (2) engaging with these problems in a way and using tools that can be…
DOMAIN CONFUSION - TechRepublicDOMAIN CONFUSION - TechRepublic
Heres what happened. I have a domain with the PDC and multiple BDCs. Someone took a BDC and moved it to a new domain. I had to bring ...
How to get off the sinking U.S.S. Titanic - Part 2How to get off the sinking U.S.S. Titanic - Part 2
Oh how sweet the sound of other peoples money! Devoid of the real Truth - Patrick Henry knew that following false hope would lead only to further degradation. The further down the path we are headed the more like beasts we will become.
ConalbuminConalbumin
C20orf96C20orf96
Conformational epitopeConformational epitope
Michael LevittMichael Levitt
C3orf14C3orf14
Electron transferElectron transfer
Multiple Epidermal Growth Factor-like Domains 8Multiple Epidermal Growth Factor-like Domains 8
PRR32PRR32
Joe Betts-LaCroixJoe Betts-LaCroix
TCAIMTCAIM
ThioredoxinThioredoxin
Harry B. GrayHarry B. Gray
C10orf67C10orf67
William Dale PhillipsWilliam Dale Phillips
Predictor@home[email protected]
DestrinDestrin
Jeffrey SkolnickJeffrey Skolnick
CitrullinationCitrullination
Backbone chainBackbone chain
PSMB8PSMB8
PSMB9PSMB9
PhosphoproteomicsPhosphoproteomics
BiochemistryBiochemistry
Swiss-modelSwiss-model
CoroninCoronin
PrionPrion
Circular dichroismCircular dichroism
CystineCystine
High-performance liquid chromatographyHigh-performance liquid chromatography
Extracellular fluidExtracellular fluid
Food webFood web
Lewis Joel GreeneLewis Joel Greene
LeafLeaf
LentilLentil
Alkali metalAlkali metal
Progesterone receptorProgesterone receptor
ReptileReptile
EndosporeEndospore
HistoneHistone
Nuclear magnetic resonance spectroscopy of nucleic acidsNuclear magnetic resonance spectroscopy of nucleic acids
Cold Spring Harbor LaboratoryCold Spring Harbor Laboratory
Glycogen phosphorylaseGlycogen phosphorylase
AmineAmine
DentinDentin
Health in IndiaHealth in India
Kallmann syndromeKallmann syndrome
ProteasomeProteasome
EpistasisEpistasis
PaleontologyPaleontology
David EisenbergDavid Eisenberg
CathelicidinCathelicidin
PRNPPRNP
CASS4CASS4
Food allergyFood allergy
AKR1B1AKR1B1
DomperidoneDomperidone
RiboflavinRiboflavin
CystineCystine
Migration in ChinaMigration in China
ProteinProtein
OrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceHealth Care
ProteinsProtein Structure, SecondaryModels, MolecularProtein ConformationDatabases, ProteinSequence Analysis, ProteinStructural Homology, ProteinProtein Structure, TertiarySoftwareProtein FoldingAlgorithmsComputational BiologySequence AlignmentAmino Acid SequenceInternetComputer SimulationModels, ChemicalMolecular Sequence DataUser-Computer InterfaceNuclear Magnetic Resonance, BiomolecularCrystallography, X-RayHydrogen BondingComputer GraphicsThermodynamicsBinding SitesAmino AcidsEvolution, MolecularSequence Homology, Amino AcidMolecular Dynamics SimulationStructure-Activity RelationshipProtein BindingSolventsHydrophobic and Hydrophilic InteractionsMagnetic Resonance SpectroscopyMolecular StructureCrystallographyProtein Structure, QuaternaryDatabases, FactualProtein DenaturationMuramidaseStatic ElectricityEnzymesLigandsKnowledge BasesArtificial IntelligenceInformation Storage and RetrievalProtein Interaction MappingDatabase Management SystemsProtein EngineeringAmino Acid MotifsProtein StabilityCircular DichroismMutationMembrane ProteinsConserved SequenceMyoglobinProtein Interaction Domains and MotifsWaterBacterial ProteinsX-Ray DiffractionMonte Carlo MethodCrystallizationPattern Recognition, AutomatedModels, StatisticalProteomicsPeptidesCluster AnalysisTemperatureNeural Networks (Computer)GenomicsSolutionsEscherichia coliEntropyReproducibility of ResultsPhylogenyChemistry, PhysicalPhysicochemical PhenomenaBase SequenceModels, TheoreticalDisulfidesKineticsAmino Acid SubstitutionAutomationPliabilitySpectrophotometry, InfraredCatalytic DomainMolecular ConformationProtein UnfoldingCryoelectron MicroscopyCysteineEnzyme StabilityMathematical ConceptsComputing MethodologiesHydrogenMutagenesis, Site-DirectedDeuterium Exchange MeasurementMarkov ChainsBiophysical PhenomenaBiophysicsTryptophanElectronsHemerythrinSynchrotronsMolecular Sequence AnnotationBacteriophage T4Normal DistributionMass SpectrometryPeptide FragmentsCattleSurface PropertiesEscherichia coli ProteinsScattering, Small AngleRubredoxinsSystems IntegrationOnline SystemsQuantum TheoryRecombinant ProteinsDrug DesignProgramming LanguagesSpectrometry, FluorescenceSpectroscopy, Fourier Transform InfraredData Interpretation, StatisticalHydrogen-Ion ConcentrationRibonuclease, PancreaticCloning, MolecularSequence AnalysisBacteriorhodopsinsCrown EthersProteomeDimerizationAmino Acids, AromaticProlineRepetitive Sequences, Amino AcidApoproteinsProtein MultimerizationSoftware DesignDrug StabilityDatabases as TopicDNAAmidesFourier AnalysisSoftware ValidationMotionIonsPoint MutationHot TemperatureMultiprotein ComplexesTriose-Phosphate IsomeraseBiochemistryDatabases, GeneticEnergy TransferPyrococcus furiosusSubstrate SpecificityMetalloproteinsProtonsModels, BiologicalExonsSpectrum Analysis, RamanLipid BilayersNational Institute of General Medical Sciences (U.S.)Data DisplayHistidineNitrogen IsotopesUbiquitinSolubilityCatalysisDeuteriumTrypsinMultigene FamilyDatabases, Nucleic AcidGenomeSpectrophotometryMicellesMutation, MissenseGlycosylationTorsion, MechanicalLactalbuminProtein FootprintingMutant ProteinsSequence Analysis, DNAPeptide LibraryOxidation-ReductionCodonElectron Spin Resonance SpectroscopyMetalsProtein Processing, Post-TranslationalMolecular Docking SimulationProbabilityModels, StructuralElectrophoresis, Polyacrylamide GelAllosteric RegulationNeutronsAspartate Aminotransferase, MitochondrialMathematical ComputingHemeUreaMacromolecular SubstancesDetergentsGenetic VariationPlant ProteinsAsparagine
Protein tertiary structure - WikipediaProtein tertiary structure - Wikipedia
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. - PubMed - NCBISWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. - PubMed - NCBI
Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of ProteinsPrediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins
Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction | SpringerLinkModelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction | SpringerLink
Protein Structure, Tertiary | Eukaryotic CellProtein Structure, Tertiary | Eukaryotic Cell
Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. - PubMed - NCBIGene triplication deduced from the tertiary structure of a muscle calcium binding protein. - PubMed - NCBI
FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction
FORCASP • View topic - Please Help: Tertiary Protein Structure PredictionFORCASP • View topic - Please Help: Tertiary Protein Structure Prediction
Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments | SpringerLinkQuantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments | SpringerLink
Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...
Going Beyond Lamarckism in Protein Tertiary Structure PredictionGoing Beyond 'Lamarckism' in Protein Tertiary Structure Prediction
De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure - CaltechAUTHORSDe novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure - CaltechAUTHORS
Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane...Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane...
ROSALIND | Glossary | Protein tertiary structureROSALIND | Glossary | Protein tertiary structure
TCP: a tool for designing chimera proteins based on the tertiary structure information | BMC Bioinformatics | Full TextTCP: a tool for designing chimera proteins based on the tertiary structure information | BMC Bioinformatics | Full Text
Protein Structure, TertiaryProtein Structure, Tertiary
GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary StructuresGP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures
Specific recognition in the tertiary structure of beta-sheets of proteins. - Semantic ScholarSpecific recognition in the tertiary structure of beta-sheets of proteins. - Semantic Scholar
What is protein tertiary structure?What is protein tertiary structure?
Protein Structure, Tertiary | Profiles RNSProtein Structure, Tertiary | Profiles RNS
Protein Structure, Tertiary | The Chopra LibraryProtein Structure, Tertiary | The Chopra Library
Structural Biochemistry/Proteins/Structures - Wikibooks, open books for an open worldStructural Biochemistry/Proteins/Structures - Wikibooks, open books for an open world
Protein Structure: Proteins are organized in tertiary StructureProtein Structure: Proteins are organized in tertiary Structure
Secondary and Tertiary Protein Structure | Life Sciences | SGS BangladeshSecondary and Tertiary Protein Structure | Life Sciences | SGS Bangladesh
Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters | GeneticsRapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters | Genetics
Protein | Encyclopedia.comProtein | Encyclopedia.com
Difference Between Primary Secondary and Tertiary Structure of Protein - Pediaa.ComDifference Between Primary Secondary and Tertiary Structure of Protein - Pediaa.Com
Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs<...Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs<...
Rhys Baker on HubPagesRhys Baker on HubPages
CiteSeerX - Citation Query TL: Comparative protein modelling by satisfaction of spatial restraintsCiteSeerX - Citation Query TL: Comparative protein modelling by satisfaction of spatial restraints
OrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceHealth Care
ProteinsProtein Structure, SecondaryModels, MolecularProtein ConformationDatabases, ProteinSequence Analysis, ProteinStructural Homology, ProteinProtein Structure, TertiarySoftwareProtein FoldingAlgorithmsComputational BiologySequence AlignmentAmino Acid SequenceInternetComputer SimulationModels, ChemicalMolecular Sequence DataUser-Computer InterfaceNuclear Magnetic Resonance, BiomolecularCrystallography, X-RayHydrogen BondingComputer GraphicsThermodynamicsBinding SitesAmino AcidsEvolution, MolecularSequence Homology, Amino AcidMolecular Dynamics SimulationStructure-Activity RelationshipProtein BindingSolventsHydrophobic and Hydrophilic InteractionsMagnetic Resonance SpectroscopyMolecular StructureCrystallographyProtein Structure, QuaternaryDatabases, FactualProtein DenaturationMuramidaseStatic ElectricityEnzymesLigandsKnowledge BasesArtificial IntelligenceInformation Storage and RetrievalProtein Interaction MappingDatabase Management SystemsProtein EngineeringAmino Acid MotifsProtein StabilityCircular DichroismMutationMembrane ProteinsConserved SequenceMyoglobinProtein Interaction Domains and MotifsWaterBacterial ProteinsX-Ray DiffractionMonte Carlo MethodCrystallizationPattern Recognition, AutomatedModels, StatisticalProteomicsPeptidesCluster AnalysisTemperatureNeural Networks (Computer)GenomicsSolutionsEscherichia coliEntropyReproducibility of ResultsPhylogenyChemistry, PhysicalPhysicochemical PhenomenaBase SequenceModels, TheoreticalDisulfidesKineticsAmino Acid SubstitutionAutomationPliabilitySpectrophotometry, InfraredCatalytic DomainMolecular ConformationProtein UnfoldingCryoelectron MicroscopyCysteineEnzyme StabilityMathematical ConceptsComputing MethodologiesHydrogenMutagenesis, Site-DirectedDeuterium Exchange MeasurementMarkov ChainsBiophysical PhenomenaBiophysicsTryptophanElectronsHemerythrinSynchrotronsMolecular Sequence AnnotationBacteriophage T4Normal DistributionMass SpectrometryPeptide FragmentsCattleSurface PropertiesEscherichia coli ProteinsScattering, Small AngleRubredoxinsSystems IntegrationOnline SystemsQuantum TheoryRecombinant ProteinsDrug DesignProgramming LanguagesSpectrometry, FluorescenceSpectroscopy, Fourier Transform InfraredData Interpretation, StatisticalHydrogen-Ion ConcentrationRibonuclease, PancreaticCloning, MolecularSequence AnalysisBacteriorhodopsinsCrown EthersProteomeDimerizationAmino Acids, AromaticProlineRepetitive Sequences, Amino AcidApoproteinsProtein MultimerizationSoftware DesignDrug StabilityDatabases as TopicDNAAmidesFourier AnalysisSoftware ValidationMotionIonsPoint MutationHot TemperatureMultiprotein ComplexesTriose-Phosphate IsomeraseBiochemistryDatabases, GeneticEnergy TransferPyrococcus furiosusSubstrate SpecificityMetalloproteinsProtonsModels, BiologicalExonsSpectrum Analysis, RamanLipid BilayersNational Institute of General Medical Sciences (U.S.)Data DisplayHistidineNitrogen IsotopesUbiquitinSolubilityCatalysisDeuteriumTrypsinMultigene FamilyDatabases, Nucleic AcidGenomeSpectrophotometryMicellesMutation, MissenseGlycosylationTorsion, MechanicalLactalbuminProtein FootprintingMutant ProteinsSequence Analysis, DNAPeptide LibraryOxidation-ReductionCodonElectron Spin Resonance SpectroscopyMetalsProtein Processing, Post-TranslationalMolecular Docking SimulationProbabilityModels, StructuralElectrophoresis, Polyacrylamide GelAllosteric RegulationNeutronsAspartate Aminotransferase, MitochondrialMathematical ComputingHemeUreaMacromolecular SubstancesDetergentsGenetic VariationPlant ProteinsAsparagine
Nucleic AcidsQuaternary structuresInteractionsLipidsPolypeptide chainsChemistrySequencesHomologyBioinformaticsFoldGeneHydrophobicMembrane proteinsConformationDisulfideResiduesMetabolismPEPTIDE BONDNuclear MagneticPolypeptidesGlobular proteinSmall proteinsRecombinant proteinsGenesStructural ClassifiBiologicalSingle polypeptideHelicalSide chainsSecondary structuresAmino Acids and ProteinsConsistFunctions of ProteinsMutationDenaturationPredictPeptidesCrystallographyPolymersMethodsPrimary structureBiosynthesisMonomericSubunitsAlgorithmsHydrogen bondsMyoglobinProtein'sRegionsSequence-similarityFoldsEnzymesStableSolventMonomersFunctional proteins
Nucleic Acids4
Quaternary structures4
Interactions24
Lipids5
Polypeptide chains3
Chemistry6
Sequences21
Homology7
Bioinformatics4
Fold17
Gene21
Hydrophobic9
Membrane proteins2
Conformation10
Disulfide5
Residues9
Metabolism3
PEPTIDE BOND1
Nuclear Magnetic3
Polypeptides4
Globular protein2
Small proteins3
Recombinant proteins1
Genes4
Structural Classifi1
Biological5
Single polypeptide4
Helical3
Side chains3
  • A pronounced absorption band in the near-UV CD region, arising from immobilized aromatic side-chains, showed that the artificial protein is folded in solution. (caltech.edu)
  • The process whereby water-fearing protein side chains interact more favorably with themselves than with water to create a hydrophilic exterior. (sparknotes.com)
  • Also, ionic bonds called salt bridges form between positively- and negatively-charged side-chains of amino acids, further stabilizing the tertiary structure. (pediaa.com)
Secondary structures4
Amino Acids and Proteins1
Consist4
Functions of Proteins2
Mutation1
Denaturation3
Predict4
Peptides3
  • Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. (ucy.ac.cy)
  • TatC captures substrate proteins by binding their signal peptides. (biomedsearch.com)
  • The present invention provides peptides related to agouti signaling protein and agouti related protein which are useful in modulating the activity of the melanocortin 3 and melanocortin 4 receptors. (google.com)
Crystallography3
Polymers2
Methods10
Primary structure14
Biosynthesis1
Monomeric3
Subunits2
Algorithms1
Hydrogen bonds5
Myoglobin1
Protein's3
Regions8
Sequence-similarity1
Folds2
Enzymes6
Stable4
  • Taken together, the results indicate that the de novo designed α/β-barrel protein adopts a stable three-dimensional structure in solution. (caltech.edu)
  • Indeed, they have their own and are stable tertiary structure independently of the rest of the polypeptide chain. (biochemden.com)
  • The components of the assay include (1) construction of test vectors that drive expression of epitope-tagged PpCESA5 carrying engineered mutations, (2) transformation of a ppcesa5 knockout line that fails to produce gametophores with test and control vectors, (3) scoring the stable transformants for gametophore production, (4) statistical analysis comparing complementation rates for test vectors to positive and negative control vectors, and (5) analysis of transgenic protein expression by Western blotting. (osti.gov)
  • Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . (wikipedia.org)
Solvent1
Monomers2
Functional proteins1
  • The assay distinguished mutations that generate fully functional, nonfunctional, and partially functional proteins. (osti.gov)