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.
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 used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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 containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
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.
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.
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.
Sequential operating programs and data which instruct the functioning of a digital computer.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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.
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.
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.
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-based representation of physical systems and phenomena such as chemical processes.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
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.
The portion of an interactive computer program that issues messages to and receives commands from a user.
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.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
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.
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)
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
A computer simulation developed to study the motion of molecules over a period of time.
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.
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.
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)
The thermodynamic interaction between a substance and WATER.
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).
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.
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)
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
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.
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
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
The accumulation of an electric charge on a object
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.
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)
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).
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.
Organized activities related to the storage, location, search, and retrieval of information.
Methods for determining interaction between PROTEINS.
Software designed to store, manipulate, manage, and control data for specific uses.
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.
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.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
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)
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.
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.
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.
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 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.
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)
Proteins found in any species of bacterium.
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)
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)
The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)
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.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
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.
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.
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.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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)
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.
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)
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.
The relationships of groups of organisms as reflected by their genetic makeup.
The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.
The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.
The rate dynamics in chemical or physical systems.
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.
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)
The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)
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)
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
The characteristic three-dimensional shape of a molecule.
Conformational transitions of the shape of a protein to various unfolded states.
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.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
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.
Numeric or quantitative entities, descriptions, properties, relationships, operations, and events.
Computer-assisted analysis and processing of problems in a particular area.
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.
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.
The physical characteristics and processes of biological systems.
The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.
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.
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.
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.
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.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
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.
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.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
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.
Characteristics or attributes of the outer boundaries of objects, including molecules.
Proteins obtained from ESCHERICHIA COLI.
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.
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)
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)
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)
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.
Proteins prepared by recombinant DNA technology.
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.
Specific languages used to prepare computer programs.
Measurement of the intensity and quality of fluorescence.
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.
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
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)
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
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.
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.
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.
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.
The protein complement of an organism coded for by its genome.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Amino acids containing an aromatic side chain.
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.
A sequential pattern of amino acids occurring more than once in the same protein sequence.
The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
Specifications and instructions applied to the software.
The chemical and physical integrity of a pharmaceutical product.
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)
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).
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)
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)
The act of testing the software for compliance with a standard.
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.
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.
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.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
Macromolecular complexes formed from the association of defined protein subunits.
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
The study of the composition, chemical structures, and chemical reactions of living things.
Databases devoted to knowledge about specific genes and gene products.
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.
A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Proteins that have one or more tightly bound metal ions forming part of their structure. (Dorland, 28th ed)
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.
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.
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.
Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.
Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.
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.
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.
An essential amino acid that is required for the production of HISTAMINE.
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.
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.
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)
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.
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
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 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.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.
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.
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)
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.
A twisting deformation of a solid body about an axis. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
A major protein fraction of milk obtained from the WHEY.
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.
Proteins produced from GENES that have acquired MUTATIONS.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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).
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).
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.
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)
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.
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.
The study of chance processes or the relative frequency characterizing a chance process.
A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
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.
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.
An aspartate aminotransferase found in MITOCHONDRIA.
Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem.
The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.
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.
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.
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.
Genotypic differences observed among individuals in a population.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
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)
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.

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)

Domain combinations containing the Carbohydrate-binding domain superfamily in Proterospongia sp. ATCC 50818 . Domain architectures illustrate each occurrence of the Carbohydrate-binding domain superfamily.
Polymerase structure: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment ( PDBid: 2R2U)
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 ...
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers ...
a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers ...
Protein domains are compact regions of a proteins structure that often convey some distinct function. Domain architecture, or order of domains in a protein, is frequently considered as a fundamental level of protein functional complexity [1]. The majority of the protein repertoire is composed of multidomain proteins; two-thirds of the proteins in prokaryotes and about four-fifths eukaryotic ones have two or more domains [2]. Moreover, an organisms complexity relates much better to the number of distinct domain architectures [3] and expansion in particular domain families [4] than to the number of genes in the organism. The prevalence of proteins with more than two domains and the recurrent appearance of the same domain in non-homologues proteins show that functional domains are reused when creating new proteins. Because of this, domains have been likened to Lego bricks that can be recombined in various ways to build proteins with completely new functions [5]. Hence, one way to study evolution ...
The 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 ...
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 ...
The SCOP classification for the Signal peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
(2004) Luoni et al. FEBS Letters. Type IIB Ca2+-ATPases have a terminal auto-inhibitory, domain the action of which is suppressed by calmodulin (CaM) binding. Here, we show that a peptide (6His-1M-I116) corresponding to the first 116 aminoacids (aa) of At-ACA8, the first cloned isoform of Arabido...
Shop KH homology domain-containing protein ELISA Kit, Recombinant Protein and KH homology domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
cd05046 (PSSM ID: 133178): Conserved Protein Domain Family PTK_CCK4, CCK4, also called protein tyrosine kinase 7 (PTK7), is an orphan receptor PTK (RTK) containing an extracellular region with seven immunoglobulin domains, a transmembrane segment, and an intracellular inactive pseudokinase domain, which shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding
cd07076 (PSSM ID: 132761): Conserved Protein Domain Family NR_LBD_GR, The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily
CSF1R protein domain and mutation schematic. Schematic diagram of the protein domain structure of CSF1R with amino acid numbers provided. Mutations previously r
The selected domain combination is the occurrence of the following superfamily domains in N- to C-Terminal order:. 49899 - Concanavalin A-like lectins/glucanases ...
.cc domain names are short and easy to remember. Join the global community that markets their ideas and organizations with dotcc domain names.
.cc domain names are short and easy to remember. Join the global community that markets their ideas and organizations with dotcc domain names.
Shop Forkhead-associated domain-containing protein ELISA Kit, Recombinant Protein and Forkhead-associated domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Domain architectures containing both Dcp2 domain-like and Nudix in all archaea. Links to architectures containing these domain pairs in other groups of genomes are provided. Domain pairs which are not adjacent can be added/removed.
Transmembrane domain architecture, symmetry and coupling to LBDa, View of the TMD parallel to the membrane. GluN1 subunits are blue and the GluN2B subunits are
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!
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
Tuning the Flexibility of Glycine-Serine Linkers ToAllow Rational Design of Multidomain Proteins Biochemistry DOI: 10.1021/acs.biochem.7b00902 More...
People Era Consulting is an emerging recruitment firm providing end to end Talent Solutions to multifarious industrial segments across the country. Our focus has always been on providing a pool of potential and validated candidates across the level i.e. Senior, Middle and Junior management. We operate through domain specialist providing high quality permanent hiring services.. ...
People Era Consulting is an emerging recruitment firm providing end to end Talent Solutions to multifarious industrial segments across the country. Our focus has always been on providing a pool of potential and validated candidates across the level i.e. Senior, Middle and Junior management. We operate through domain specialist providing high quality permanent hiring services.. ...
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, ...
Homer protein homolog 1 or Homer1 is a neuronal protein that in humans is encoded by the HOMER1 gene. Other names are Vesl and PSD-Zip45. Homer1 protein has an N-terminal EVH1 domain, involved in protein interaction, and a C-terminal coiled-coil domain involved in self association. It consists of two major splice variants, short-form (Homer1a) and long-form (Homer1b and c). Homer1a has only EVH1 domain and is monomeric while Homer1b and 1c have both EVH1 and coiled-coil domains and are tetrameric. The coiled-coil can be further separated into N-terminal half and C-terminal half. The N-terminal half of the coiled-coil domain is predicted to be a parallel dimer while the C-terminus half is a hybrid of dimeric and anti-parallel tetrameric coiled-coil. As a whole, long Homer is predicted to have a dumbbell-like structure where two pairs of EVH1 domains are located on two sides of long (~50 nm) coiled-coil domain. Mammals have Homer2 and Homer3, in addition to Homer1, which have similar domain ...
The SCOP classification for the Heat shock protein 70kD (HSP70), peptide-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBIs GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of
Monotopic proteins represent a specialized group of membrane proteins in that they are engaged in biochemical events taking place at the membrane interface. In particular, the monotopic lipid-synthesizing enzymes are able to synthesize amphiphilic lipid products by catalyzing two biochemically distinct molecules (substrates) at the membrane interface. Thus, from an evolutionary point of view, anchoring into the membrane interface enables monotopic enzymes to confer sensitivity to a changing environment by regulating their activities in the lipid biosynthetic pathways in order to maintain a certain membrane homeostasis. We are focused on a plant lipid-synthesizing enzyme DGD2 involved in phosphate shortage stress, and analyzed the potentially important lipid anchoring segments of it, by a set of biochemical and biophysical approaches. A mechanism was proposed to explain how DGD2 adjusts its activity to maintain a proper membrane. In addition, a multivariate-based bioinformatics approach was used ...
Ras is a small GTPase, controlling signal transduction pathways and promoting cell proliferation and survival. KRAS is frequently mutated in cancer. Ras consists of highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ significantly across Ras isoforms. Recent NMR and MD simulations discovered that the HVR of K-Ras4B-GDP extensively interacts with the catalytic domain. However, it weakly interacts with the catalytic domain in the GTP-bound state. Here, using MD simulations we modeled K-Ras4B membrane interaction and dimerization. On the membrane, the catalytic domain takes on multiple orientations, including perpendicular and parallel alignments of the allosteric helices with respect to the membrane normal. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with the farnesyl anchored into the membrane and the HVR unrestrained, the catalytic domain fluctuates reinlessly, exposing its ...
The SCOP classification for the Zn2/Cys6 DNA-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
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 ...
immune Acetylcholine Nicotinic Receptors 220036-08-8 supplier, Rabbit Polyclonal to SP3/4 Herb intracellular immune receptors comprise a large number of multi-domain proteins resembling animal NOD-like receptors (NLRs). show unique functions for the nuclear and cytoplasmic MLA10 pools in disease resistance and cell death signaling and provide evidence for a model uncoupling MLA10 cell death signaling from its disease resistance activity. Our results suggest that herb immune receptors integrate signals from multiple sub-cellular storage compartments to organize effective immune responses against pathogen attack. Introduction Plants defend themselves against pathogens by mounting effective, spatiotemporally fine-tuned immune responses. Two major types of immune receptors are responsible for pathogen acknowledgement and subsequent defense induction [1]. One class comprises membrane-localized pattern acknowledgement receptors that launch PAMP/MAMP-triggered immunity (PTI/MTI) upon detection of ...
Many putative downstream effectors of the small GTPases Cdc42 and Rac contain a GTPase binding domain (GBD), also called p21 binding domain (PBD), which has been shown to specifically bind the GTP bound form of Cdc42 or Rac, with a preference for Cdc42 [1,2]. The most conserved region of GBD/PBD domains is the N-terminal Cdc42/Rac interactive binding motif (CRIB), which consists of about 16 amino acids with the consensus sequence I-S-x-P-x(2,4)-F-x-H-x(2)-H-V-G [3]. Although the CRIB motif is necessary for the binding to Cdc42 and Rac, it is not sufficient to give high-affinity binding [4,5]. A less well conserved inhibitory switch (IS) domain responsible for maintaining the proteins in a basal (autoinhibited) state is located C-terminaly of the CRIB-motif [6,7,8]. GBD domains can adopt related but distinct folds depending on context. Although GBD domains are largely unstructured in the free state, the IS domain forms an N-terminal β hairpin that immediately follows the conserved CRIB motif and ...
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.. ...
Journal Article: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface ...
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 ...
definition of ILKBP, what does ILKBP mean?, meaning of ILKBP, Integrin-Linked Kinase-Binding Protein, ILKBP stands for Integrin-Linked Kinase-Binding Protein
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.
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
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...
Prof. Dr. Winfried Römer and his research team at the University of Freiburg have recently found that bacterial protein impairs important cellular processes
TY - JOUR. T1 - Purification and aggregation of the amyloid precursor protein intracellular domain. AU - El Ayadi, Amina. AU - Stieren, Emily S.. AU - Barral, José M.. AU - Oberhauser, Andres F.. AU - Boehning, Darren. PY - 2012/8/28. Y1 - 2012/8/28. N2 - Amyloid precursor protein (APP) is a type I transmembrane protein associated with the pathogenesis of Alzheimers disease (AD). APP is characterized by a large extracellular domain and a short cytosolic domain termed the APP intracellular domain (AICD). During maturation through the secretory pathway, APP can be cleaved by proteases termed α, β, and γ-secretases1. Sequential proteolytic cleavage of APP with β and γ-secretases leads to the production of a small proteolytic peptide, termed Aβ, which is amyloidogenic and the core constituent of senile plaques. The AICD is also liberated from the membrane after secretase processing, and through interactions with Fe65 and Tip60, can translocate to the nucleus to participate in transcription ...
TY - JOUR. T1 - CT domain of CCN2/CTGF directly interacts with fibronectin and enhances cell adhesion of chondrocytes through integrin α5β1. AU - Hoshijima, Mitsuhiro. AU - Hattori, Takako. AU - Inoue, Miho. AU - Araki, Daisuke. AU - Hanagata, Hiroshi. AU - Miyauchi, Akira. AU - Takigawa, Masaharu. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2006/2/20. Y1 - 2006/2/20. N2 - Searching for CCN family protein 2/connective tissue growth factor (CCN2/CTGF) interactive proteins by yeast-two-hybrid screening, we identified fibronectin 1 gene product as a major binding partner of CCN2/CTGF in the chondrosarcoma-derived chondrocytic cell line HCS-2/8. Only the CT domain of CCN2/CTGF bound directly to fibronectin (FN). CCN2/CTGF and its CT domain enhanced the adhesion of HCS-2/8 cells to FN in a dose-dependent manner. The CCN2/CTGF-enhancing effect on cell adhesion to FN was abolished by a blocking antibody against α5β1 integrin (α5β1), but not by one against anti-αvβ3 ...
How many ways protein protein interactions are regulated? - posted in Biochemistry: I wonder how many ways protein-protein interactions are regulated. I know a lot of protein protein interactions are modified by phosphorylaton or other modification. Is there other ways that mediate the protein protein interaction? Thanks!
AICD, the C-terminal tail generated from the proteolytic cleavage of the Amyloid Precursor Protein (APP), has been generating interest for its transcriptional modulatory roles. AICD has been hypothesized to have such a function as it is generated by a gamma-secretase-mediated regulated intramembrane proteolysis step, analogous to the generation of Notch intracellular domain (NICD), a well-known transcriptional regulator, from Notch. The AICD/Fe65/Tip60 ternary complex has been proposed as the working transcriptional regulatory complex and some of its target genes have been reported. However, our knowledge of the functions of AICD is still limited due to difficulties in detecting and manipulating the rapidly degraded peptide. Looking at AICD transcription modulation targets from a genome-wide perspective will aid our understanding of the role of AICD tremendously. To this end, AICD chromatin binding sites were investigated from a genome-wide perspective by performing Chromatin Immunoprecipitation ...
9150PRTHomo sapiens 1Val Met Leu Lys Lys Lys Gln Tyr Thr Ser Ile His His Gly Val Val1 5 10 15Glu Val Asp Ala Ala Val Thr Pro Glu Glu Arg His Leu Ser Lys Met 20 25 30Gln Gln Asn Gly Tyr Glu Asn Pro Thr Tyr Lys Phe Phe Glu Gln Met 35 40 45Gln Asn 502134PRTHomo sapiens 2Ala Pro Lys Asn Glu Leu Val Gln Lys Phe Gln Val Tyr Tyr Leu Gly1 5 10 15Asn Val Pro Val Ala Lys Pro Val Gly Val Asp Val Ile Asn Gly Ala 20 25 30Leu Glu Ser Val Leu Ser Ser Ser Ser Arg Glu Gln Trp Thr Pro Ser 35 40 45His Val Ser Val Ala Pro Ala Thr Leu Thr Ile Leu His Gln Gln Thr 50 55 60Glu Ala Val Leu Gly Glu Cys Arg Val Arg Phe Leu Ser Phe Leu Ala65 70 75 80Val Gly Arg Asp Val His Thr Phe Ala Phe Ile Met Ala Ala Gly Pro 85 90 95Ala Ser Phe Cys Cys His Met Phe Trp Cys Glu Pro Asn Ala Ala Ser 100 105 110Leu Ser Glu Ala Val Gln Ala Ala Cys Met Leu Arg Tyr Gln Lys Cys 115 120 125Leu Asp Ala Arg Ser Gln 130325DNAArtificialPrimer APP_C50_F 3gtaccatatg gtgatgctga agaag 25432DNAArtificialPrimer APP_C50_R 4gtacaagctt ctagttctgc atctgctcaa ...
The BAR (Bin/amphiphysin/Rvs) domain is the most conserved feature in amphiphysins from yeast to human and is also found in endophilins and nadrins. We solved the structure of the Drosophila amphiphysin BAR domain. It is a crescent-shaped dimer that binds preferentially to highly curved negatively charged membranes. With its N-terminal amphipathic helix and BAR domain (N-BAR), amphiphysin can drive membrane curvature in vitro and in vivo. The structure is similar to that of arfaptin2, which we find also binds and tubulates membranes. From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module.
The antigen-binding site of antibodies forms at the interface of their two variable domains, VH and VL, making VH-VL domain orientation a factor that codetermines antibody specificity and affinity. Preserving VH-VL domain orientation in the process of antibody engineering is important in order to re …
Eukaryotic cells have evolved an intricate system to resolve DNA damage to prevent its transmission to daughter cells. This system, collectively known as the DNA damage response (DDR) network, includes many proteins that detect DNA damage, promote repair, and coordinate progression through the cell cycle. Because defects in this network can lead to cancer, this network constitutes a barrier against tumorigenesis. The modular BRCA1 carboxyl-terminal (BRCT) domain is frequently present in proteins involved in the DDR, can exist either as an individual domain or as tandem domains (tBRCT), and can bind phosphorylated peptides. We performed a systematic analysis of protein-protein interactions involving tBRCT in the DDR by combining literature curation, yeast two-hybrid screens, and tandem affinity purification coupled to mass spectrometry. We identified 23 proteins containing conserved BRCT domains and generated a human protein-protein interaction network for seven proteins with tBRCT. This study ...
Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, …
A recent study showed that the globular tail of Myo4p is not required for the localization of GFP-MS2-tethered particles to the bud and for the inheritance of ER (Bookwalter et al., 2009). This observation suggested that the globular tail might be dispensable for the localization of endogenous ASH1 mRNA and thus also for inhibition of mating type switching in the daughter cell. It further raised the question of whether the globular tail of Myo4p has any function. Here, we used an experimentally refined, globular tail-lacking Myo4p to confirm the previous findings from Bookwalter et al. (2009) (Fig. S1, A-F).. However, when analyzing mother cell-specific expression of the HO endonuclease in cells expressing a globular tail-lacking Myo4p fragment, we found that this process is impaired (Fig. 2, A and B). The subsequent analysis of ASH1 mRNA localization by in situ hybridization and of Myo4p localization by immunofluorescence staining consistently showed that the globular tail is required for full ...
Protein domain superfamilies in CATH-Gene3D have been subclassified into functional families (or FunFams), which are groups of protein sequences and structures with a high probability of sharing the same function(s). Therefore, the functionally important residues in a family are also expected to be highly conserved.. Information on conserved positions in CATH-Gene3D FunFam alignments is shown through the Alignment tab of the FunFam webpages. Conservation scores have been calculated using Scorecons and columns in the alignment are coloured using a rainbow colour scheme, where the highly conserved residues are shown in red through to positions that are not conserved at all, shown in blue. The conservation scores are also mapped onto a representative protein domain structure.. To investigate putative conserved sites for your protein sequence, run a sequence search against the FunFams and click on the FunFam match Alignment page.. ...
Figure 1. Schematic Representations of the Structure of a CESA Protein and a CSC.. (A) Domain structure of a CESA. The intracellular N-terminal domain contains a Zn binding domain and a variable region and is followed by two transmembrane domains. The large cytoplasmic central catalytic domain is divided into the conserved region, which flanks the plant-specific region on both sides, the variable region(s), which includes the class-specific region, and the conserved region(s). The six subsequent transmembrane domains are followed by the cytoplasmic C-terminal domain. CESA1 phosphorylations on various Ser and Thr residues are indicated (source: PhosPhAt 4.0, Zulawski et al., 2013; and references in the text). Several cysteines in the cytoplasmic loop and within the C-terminal domain that are s-acylated in CESA7 (Kumar 2016b) are depicted in pink. C, cellulose chain; CR1, conserved region 1; CR2, conserved region 2; P-CR, plant-specifc region; S, Ser; T, Thr.. (B) A schematic representation of a ...
The process by which fibronectin (FN), a soluble multidomain protein found in tissue fluids, forms insoluble fibrillar networks in the extracellular matrix is poorly understood. Cryptic sites found in FN type III domains have been hypothesized to function as nucleation points, thereby initiating fibrillogenesis. Exposure of these sites could occur upon tension-mediated mechanical rearrangement of type III domains. Here, we present the solution structures of the second type III domain of human FN ((2)FNIII), and that of an interaction complex between the first two type III domains ((1-2)FNIII). The two domains are connected through a long linker, flexible in solution. A weak but specific interdomain interaction maintains (1-2)FNIII in a closed conformation that associates weakly with the FN N-terminal 30 kDa fragment (FN30 kDa). Disruption of the interdomain interaction by amino-acid substitutions dramatically enhances association with FN30 kDa. Truncation analysis of (1-2)FNIII reveals that the
Cancer arises when genetic mutations in a cell cause abnormal growth that leads to a tumour.. Some cancer drugs exploit this to attack tumour cells by targeting proteins that are mutated from their usual form because of mutations in the genes that encode them.. However, only a fraction of all the mutations that contribute significantly to cancer have been identified.. Thomas Peterson, at the University of Maryland, and colleagues developed a new statistical analysis approach that uses genetic data from cancer patients to find cancer-causing mutations.. Unlike previous studies that focused on mutations in individual genes, the new approach addresses similar mutations shared by families of related proteins.. Specifically, the new method focuses on mutations in sub-components of proteins known as protein domains.. Even though different genes encode them, different proteins can share common protein domains.. The new strategy draws on existing knowledge of protein domain structure and function to ...
The M2 protein of the influenza A virus is a homotetrameric transmembrane proton channel implicated in several stages of the viral replication process. Each of its 97-residue monomers is known to include a transmembrane α-helix. but the structures of the N- and C-terminal domains have not yet been solved. A significant barrier to an atomic level understanding of the M2 protein is the difficulty associated with expression and purification of the full-length protein, which has primarily been studied in the form of truncated constructs covering the amphipathic helix and a short C-terminal segment. This C-terminal segment, which includes residues 46-62, has been shown for a truncated version of the protein to consist of an amphipathic helix lying on the membrane surface. Here, we present SDSL-EPR structural studies using full-length M2 constructs to examine sites 50-54 in the proposed amphipathic helix region of M2. Using power saturation data for the protein reconstituted into vesicles and CW ...
p,Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein-DNA, protein-RNA and other protein-ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here, we introduce an approach to identify per-domain-position interaction frequencies by aggregating protein co-complex structures by domain and ascertaining how often residues mapping to each domain position interact with ligands. We perform this domain-based analysis on ∼91000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions or small molecules across 4128 domains, which we refer to collectively as the InteracDome. Cross-validation testing ...
C. elegans NAB-1 protein; contains similarity to Pfam domains PF07647 (SAM domain (Sterile alpha motif)), PF00595 (PDZ domain (Also known as DHR or GLGF)), PF00536 (SAM domain (Sterile alpha motif))contains similarity to Interpro domains IPR001660 (Sterile alpha motif SAM), IPR001478 (PDZ/DHR/GLGF ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
When DArcy Wentworth Thompsons On Growth and Form was published 100 years ago, it raised the question of how biological forms arise during development and across evolution. In light of the advances in molecular and cellular biology since then, a succinct modern view of the question states: how do genes encode geometry? Our new special issue is packed with articles that use mathematical and physical approaches to gain insights into cell and tissue patterning, morphogenesis and dynamics, and that provide a physical framework to capture these processes operating across scales.. Read the Editorial by guest editors Thomas Lecuit and L. Mahadevan, as they provide a perspective on the influence of DArcy Thompsons work and an overview of the articles in this issue.. ...
Structure determination. Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can ... which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all ... Protein structure prediction. Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally ... Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one ...
The secondary and tertiary structures of destrin are similar to the gelsolin family which is another actin-regulating protein ... Structure[edit]. The tertiary structure of destrin was determined by the use of triple-resonance multidimensional nuclear ... "Tertiary structure of destrin and structural similarity between two actin-regulating protein families". Cell. 85 (7): 1047-55. ... Nuclear magnetic resonance determined configuration of the tertiary structure of Destrin.[1] ...
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). ... Protein folding also generates stable conformational isomers which can be observed. The Karplus equation relates the dihedral ... The equation aids in the elucidation of protein folding as well as the conformations of other rigid aliphatic molecules.[13] ...
The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell. 1995 Dec 15;83(6):1047-58. PMID 8521505. ... Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science. 1995 Nov 10;270(5238):954-60. PMID ... GAIP and RGS4 are GTPase-activating proteins for the Gi subfamily of G protein alpha subunits. Cell. 1996 Aug 9;86(3):445-52. ... Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis. Science. 1994 Sep 2;265(5177):1405-12. ...
The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell. 1995 Dec 15;83(6):1047-58. PMID 8521505. ... Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science. 1995 Nov 10;270(5238):954-60. PMID ... GAIP and RGS4 are GTPase-activating proteins for the Gi subfamily of G protein alpha subunits. Cell. 1996 Aug 9;86(3):445-52. ... Authors' summary on the structure (Science) (Retrieved on 26 Nov. 2007). Referências. *↑ «Dallas Nobel Laureate Dr. Alfred G. ...
... disulfide bridges between cysteine residues within a polypeptide support the protein's tertiary structure. Insulin is an ... Roles in protein structure[edit]. In the translation of messenger RNA molecules to produce polypeptides, cysteine is coded for ... "The primary structure of proteins is the amino acid sequence". The Microbial World. University of Wisconsin-Madison ... Cysteine residues play a valuable role by crosslinking proteins, which increases the rigidity of proteins and also functions to ...
... disulfide bridges between cysteine residues within a polypeptide support the protein's tertiary structure. Insulin is an ... Roles in protein structure[edit]. In the translation of messenger RNA molecules to produce polypeptides, cysteine is coded for ... "The primary structure of proteins is the amino acid sequence". The Microbial World. University of Wisconsin-Madison ... Disulfide bonds play an important role in the folding and stability of some proteins, usually proteins secreted to the ...
Next Monod reviews the primary and tertiary structure of proteins. In reviewing the tertiary structure, what he calls the ... Allosteric interactions are mediated by discrete shifts in the proteins structure and this allows certain proteins to assume ... In regards to structure, all living beings are made up of proteins and nucleic acids and these are the same residues (twenty ... Finally, it is the primary structure of proteins that we shall consult for the "secret" to those cognitive properties thanks to ...
For example, proteins and larger RNA molecules cannot be crystallized if their tertiary structure has been unfolded; therefore ... When a new protein structure is solved by X-ray crystallography and deposited in the Protein Data Bank, its authors are ... Levy ED (November 2007). "PiQSi: protein quaternary structure investigation". Structure. 15 (11): 1364-7. doi:10.1016/j.str. ... or the Protein Data Bank (for protein and sometimes nucleic acids). Many structures obtained in private commercial ventures to ...
Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino ... The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply ... Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with ... Structures of some common lipids. At the top are cholesterol and oleic acid.[37] The middle structure is a triglyceride ...
A reduction in these linkages has the potential to change the tertiary structure, causing the protein to unfold. This ... after further studies this group concluded that the structure of the spore coat protein was different from keratin.[10] When ... Small acid-soluble proteins (SASPs) are found in endospores. These proteins tightly bind and condense the DNA, and are in part ... An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Firmicutes.[1][2] The ...
... s also play a part in forming the tertiary structure of protein through interaction of R-groups. (See also protein ... Proteins[edit]. In the secondary structure of proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. ... Intramolecular hydrogen bonding is partly responsible for the secondary and tertiary structures of proteins and nucleic acids. ... The role of hydrogen bonds in protein folding has also been linked to osmolyte-induced protein stabilization. Protective ...
Xia, Y.; Huang, E. S.; Levitt, M.; Samudrala, R. (2000). "Ab initio construction of protein tertiary structures using a ... Daggett, V.; Levitt, M. (1993). "Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations". Journal of ... "A refinement of the structure of lysozyme". Biochemical Journal. 125 (4): 92P. doi:10.1042/bj1250092Pa. PMC 1178298 . PMID ... "Evolutionarily consistent families in SCOP: Sequence, structure and function". BMC Structural Biology. 12: 27. doi:10.1186/ ...
The tertiary structure of proteins is also affected by the pH of the bathing solution. In addition, the pH of the ECF affects ... or tertiary) structure of the protein is altered.[21][22] The normal shape, and therefore function of very many of the ... The proteins that are particularly sensitive to changes in the ECF ionized calcium concentration are several of the clotting ... Calcium ions have a great propensity to bind to proteins.[20] This changes the distribution of electrical charges on the ...
... amino acid sequence predicted tertiary structure, carbohydrate recognition and analysis of the b-prims fold". Protein Science. ... Protein Expression and Purification. 21 (1): 134-140. doi:10.1006/prep.2000.1353. PMID 11162398.. ... where he is a full professor of cell and molecular biology and head of the Center for Protein Chemistry of Hemocentro de ... "Expression and the purification of a disulphide rich protein in a hydrophobic resin environment, bothropstoxin-I a Lys49- ...
... between thiol groups in two cysteine residues are an important component of the secondary and tertiary structure of proteins. ... Chemical structure. In biochemistry, a disulfide refers to a functional group with the structure R−S−S−R′. The linkage is also ... The in vivo oxidation and reduction of protein disulfide bonds by thiol-disulfide exchange is facilitated by a protein called ... The disulfide bond stabilizes the folded form of a protein in several ways: *It holds two portions of the protein together, ...
This database is the authoritative research tool for bioinformaticists using protein primary, secondary and tertiary structures ... Rutgers is also home to the RCSB Protein Data bank,[117] 'an information portal to Biological Macromolecular Structures' ... "RCSB Protein Data Bank". Archived from the original on April 18, 2015. Retrieved March 11, 2013.. ... H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. ...
... thus overcoming some forms of tertiary protein folding, and breaking up quaternary protein structure (oligomeric subunits). ... By binding to the proteins the detergent destroys their secondary, tertiary and/or quaternary structure denaturing them and ... For proteins, sodium dodecyl sulfate (SDS) is an anionic detergent applied to protein samples to coat proteins in order to ... It is an anionic dye, which non-specifically binds to proteins. The structure of CBB is predominantly non-polar, and it is ...
A reduction in these linkages has the potential to change the tertiary structure, causing the protein to unfold. This ... Small acid-soluble proteins (SASPs) are found in endospores. These proteins tightly bind and condense the DNA, and are in part ... StructureEdit. Variations in endospore morphology: (1, 4) central endospore; (2, 3, 5) terminal endospore; (6) lateral ... An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Firmicutes.[1][2] The ...
... and tertiary structure. To maintain this defined three-dimensional structure, proteins rely on various types of interactions ... Alan Fersht, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman, 1998. ... "Comparison of protein active site structures for functional annotation of proteins and drug design". Proteins. 65: 124-135. doi ... while other amino acids within the protein are required to maintain the tertiary structure of the enzyme.[2] ...
... secondary and tertiary structure as an original (boDMARD) and possess similar efficacy and safety as the original protein ... a raised C-reactive protein level.[citation needed] More recently, the term has been used to indicate a drug that reduces the ... tsDMARDs are drugs that were developed to target a particular molecular structure ...
... such as methods to predict the secondary and tertiary structure of proteins, to predict their molecular functions or cellular ... proteins similar to the query protein. If such a template protein is found, the structure of the protein of interest can be ... HMMs for the protein data bank of protein structures, for the Pfam database of protein family alignments, the SCOP database of ... But for a large fraction of the approximately 20 000 human proteins the structures and functions remain unknown. Many proteins ...
... portal Primary structure Secondary structure Tertiary structure Quaternary structure Structural domain Structural motif Protein ... "tertiary structure" of molecules, depends in a complicated way on the molecules' basic composition, or "primary structures." ... 3D encyclopedia of proteins and other molecules. Protein structure prediction Banaszak, Leonard J. (2000). Foundations of ... See protein structure prediction. In the past few years it has become possible for highly accurate physical molecular models to ...
... finding a surface and a method of attachment that allows the proteins to maintain their secondary or tertiary structure and ... Protein functional analysis is the identification of protein-protein interactions (e.g. identification of members of a protein ... protein-DNA, protein-RNA, protein-phospholipid, and protein-small-molecule interactions, to assay enzymatic activity and to ... A protein microarray (or protein chip) is a high-throughput method used to track the interactions and activities of proteins, ...
... proteins are characterized by a beta sheet (the secondary structure), folded into the LSm fold (the tertiary structure), ... Other proteins with very similar structures were subsequently discovered and named LSm proteins. New members of the LSm protein ... Proteins with similar structures are grouped into a hierarchy of protein families, superfamilies, and folds. The LSm protein ... Based on structure, the known LSm proteins divide into a group consisting of the bacterial LSm proteins (Hfq, YlxS and MscS) ...
... binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure ... Human protein. Pfam family with Human protein. 2. 40S ribosomal protein S2. RS2_HUMAN. PF03719 Ribosomal protein S5, C-terminal ... A ribosomal protein (r-protein or rProtein[1][2][3]) is any of the proteins that, in conjunction with rRNA, make up the ... 40S ribosomal protein S9. RS9_HUMAN. PF01479 S4 domain. 9. 40S ribosomal protein S9. RS9_HUMAN. PF00163 Ribosomal protein S4/S9 ...
Protein tertiary structure predictions. server Selvita Protein Modeling Platform Package of tools for protein modeling. Free ... On-line server for peptide structure prediction. Server Secondary structure prediction[edit]. Main article: Protein structure ... This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, ... Commercial protein structure prediction application. Home page I-TASSER Threading fragment structure reassembly. On-line server ...
Their tertiary structures are different; apolactoferrin is characterized by "open" conformation of the N-lobe and the "closed" ... The fraction of protein extracted from milk, contains 3.3% RNA, but, the protein preferably binds to double-stranded DNA rather ... Occurrence of iron-containing red protein in bovine milk was reported as early as in 1939; however, the protein could not be ... Lactoferrin: structure, function, and applications: proceedings of the 4th International Conference on Lactoferrin: Structure, ...
When a protein is denatured, secondary and tertiary structures are altered but the peptide bonds of the primary structure ... Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary ... See also: Protein structure. *In quaternary structure denaturation, protein sub-units are dissociated and/or the spatial ... 3) Tertiary Structure : three-dimensional structure of alpha helixes and beta helixes folded 4) Quaternary Structure : three- ...
These classes group structures with similar secondary structure composition, but different overall tertiary structures and ... The source of protein structures is the Protein Data Bank. The unit of classification of structure in SCOP is the protein ... Designed proteins [58788] (44): Experimental structures of proteins with essentially non-natural sequences. Not a true class ... coiled-coil proteins [57942] (7): Not a true class. *Low resolution protein structures [58117] (26): Peptides and fragments. ...
how community structure, function and stability is determined.[36][37]. Ecological pyramids[edit]. See also: Ecological pyramid ... Abbreviations: P=Producers, C1=Primary consumers, C2=Secondary consumers, C3=Tertiary consumers, S=Saprotrophs.[4] ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... Pyramid structure can vary across ecosystems and across time. In some instances biomass pyramids can be inverted. This pattern ...
The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars than, ... In turn, smaller veins branch from the secondary veins, known as tertiary or third order (or higher order) veins, forming a ... and flattened leaf stems called phyllodes which differ from leaves both in their structure and origin.[4][7] Some structures of ... Rudall, Paula J. (2007). Anatomy of flowering plants: an introduction to structure and development (3rd ed.). Cambridge: ...
... protein itself is not lost).[16] Lentils have the second-highest ratio of protein per calorie of any legume, after soybeans. ... "Food Structure. 5: 241-246 - via *^ Bora, Pushkar Singh (2002). "Functional properties of native and ... Tertiary gene pool: L. lamottei and L. tomentosus. Crosses generally fail between members of different gene pools. However, ... Raw lentils are 8% water, 63% carbohydrates including 11% dietary fiber, 25% protein, and 1% fat (table). Lentils are a rich ...
Structure of the octahedral n-butyllithium hexamer, (C4H9Li)6.[138] The aggregates are held together by delocalised covalent ... The balance between potassium and sodium is maintained by ion transporter proteins in the cell membrane.[231] The cell membrane ... and aryl ketones to tertiary carbinols (Ar'2C(Ar)OH). Finally, they may be used to synthesise other organometallic compounds ... Structure and Bonding. 21: 89-144. doi:10.1007/BFb0116498. ISBN 978-3-540-07109-9. . Retrieved 4 October 2013.. ...
Available protein structures:. Pfam structures / ECOD PDB. RCSB PDB; PDBe; PDBj. PDBsum. structure summary. ... tertiary branching involved in mammary gland duct morphogenesis. Sources:Amigo / QuickGO. Orthologs. ... protein binding. • enzyme binding. • receptor binding. • lipid binding. • RNA polymerase II transcription factor activity, ... The progesterone receptor (PR), also known as NR3C3 or nuclear receptor subfamily 3, group C, member 3, is a protein found ...
This is because they lack a specialized structure called a loop of Henle, which is present in the nephrons of birds and mammals ... The albumin (9) further protects the embryo and serves as a reservoir for water and protein. The allantois (8) is a sac that ... mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary ... Geckos, skinks, and other lizards that are captured by the tail will shed part of the tail structure through a process called ...
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack ... forming two nearly symmetrical halves by tertiary structure (C2 symmetry; one macromolecule is the mirror image of the other).[ ... The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins ... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ...
It was quickly realized that spectra of the low-field imino protons were providing clues to the tertiary structure of tRNA in ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... Structure determinationEdit. The exchangeable and non-exchangeable protons are usually assigned to their specific peaks as two ... Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics ...
This section relies too much on references to primary sources. Please improve this section by adding secondary or tertiary ... James Watson, co-discoverer of structure of DNA, Nobel Laureate.. *Scott Lowe (currently at MSKCC), research on p53, Member of ... A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ... RNA interference (RNAi) and small-RNA biology; DNA replication; RNA splicing; signal transduction; genome structure; non-coding ...
... results in small changes in tertiary structure at the subunit interface leading to large changes in quaternary structure.[8] ... Structure[edit]. The glycogen phosphorylase monomer is a large protein, composed of 842 amino acids with a mass of 97.434 kDa ... Residues 397-437 form this structure, which allows the protein to covalently bind to the glycogen chain a full 30 Å from the ... I. Isolation and characterization of the protein-glycogen complex". Journal of Biological Chemistry. 245 (24): 6642-6648. PMID ...
For chiral tertiary amines, NRR′R″ can only be resolved when the R, R′, and R″ groups are constrained in cyclic structures such ... which is one of the primary influences on the three-dimensional structures of proteins.[18] ... Tertiary (3°) amines-In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a ... StructureEdit. Alkyl aminesEdit. Alkyl amines characteristically feature tetrahedral nitrogen centers. C-N-C and C-N-H angles ...
Tertiary dentin is only formed by an odontoblast directly affected by a stimulus; therefore, the architecture and structure ... which includes dentine-specific proteins), and 10% water (which is adsorbed on the surface of the minerals or between the ... Tertiary dentin (including reparative dentin or sclerotic dentin) - pathologicEdit. Tertiary dentin is dentin formed as a ... The structure of the dentinal tubules contributes to both its porosity and its elasticity. Elephant tusks are formed with a ...
Protein-energy malnutrition (PEM), also known as protein-calorie malnutrition Iron deficiency: nutritional anaemia which can ... In planning health care structure for the future, it is desirable to move from a 'fee-for-service' mechanism, to address the ... secondary and tertiary care. In twelfth plan period entire Below Poverty Line(BPL) population will be covered through RSBY ... while also ensuring that there is no compromise in terms of standards of delivery and that the incentive structure does not ...
tertiary granule membrane. • cytosol. • plasma membrane. Biological process. • cellular defense response. • myeloid cell ... GO:0001948 protein binding. Cellular component. • integral component of membrane. • integral component of plasma membrane. • ... Available structures. PDB. Ortholog search: PDBe RCSB List of PDB id codes. ... Structurally MDL-1 is a type II transmembrane protein with a short cytoplasmic tail and without signaling motifs, therefore it ...
Kisspeptin is a protein that regulates the release of GnRH from the hypothalamus, which in turn regulates the release of LH and ... The structure of GNRH1. (from PDB: 1YY1​). The underlying cause of Kallmann syndrome or other forms of hypogonadotropic ...
... it is this structure that recognizes polyubiquitinated proteins and transfers them to the catalytic core.[15] An alternative ... but substantial tertiary structure, and in particular nonlocal interactions such as disulfide bonds, are sufficient to inhibit ... The protein degradation processEdit. Ribbon diagram of ubiquitin, the highly conserved protein that serves as a molecular tag ... Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks ...
Proteins are held in their tertiary structure by a distributed, internal network of cooperative interactions (hydrophobic, ... Similarly, at the protein level, proteins that function as dimers may form a heterodimer composed of one protein from each ... In enzymes, the protein structure orients a few, key amino acids into precise geometries to form an active site to perform ... Horovitz A (1996). "Double-mutant cycles: a powerful tool for analyzing protein structure and function". Folding & Design. 1 (6 ...
A process in which proteins or nucleic acids lose the quaternary, tertiary, and secondary structure which is present in their ... especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures ... A cylindrical cell structure found in most eukaryotic cells, composed mainly of a protein called tubulin.. centrosome. An ... G protein. A family of proteins that act as molecular switches inside cells, and are implicated in transmitting signals from a ...
For example, the discovery by Luis Alvarez and Walter Alvarez of an iridium-rich layer at the Cretaceous-Tertiary boundary made ... by comparing sequences of DNA or proteins. The result of a successful analysis is a hierarchy of clades - groups that share a ... cells with complex internal structures, may have been present earlier, their evolution speeded up when they acquired the ... Although this early study compared proteins from apes and humans, most molecular phylogenetics research is now based on ...
Chapman, M. S.; Suh, S. W.; Curmi, P. M.; Cascio, D.; Smith, W. W.; Eisenberg, D. S. (1988). "Tertiary structure of plant ... Proteins[2]. Amyloid[3]. Structural biology[4][5][6]. Institutions. Howard Hughes Medical Institute. University of Oxford. ... His research group hosts the Database of Interacting Proteins.[16] Career[edit]. *Postdoctoral research, Princeton University ( ... Eisenberg, David J. (1965). Some problems in the electronic structure of molecules (PhD thesis). University of Oxford.. ...
OPM protein. 2k6o. Available protein structures:. Pfam. structures. PDB. RCSB PDB; PDBe; PDBj. ... tertiary granule lumen. Biological process. • positive regulation of interleukin-8 secretion. • defense response. • negative ... protein binding. Cellular component. • extracellular region. • specific granule. • intracellular. • extracellular exosome. • ... Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures.[8] Most cathelicidins are ...
These mutations cause the cell to make prion proteins with an abnormal structure. The abnormal protein PrPSc accumulates in the ... The abnormal PrPSc isoform has a different secondary and tertiary structure from PrPC, but identical primary sequence. Circular ... ATP-dependent protein binding. • metal ion binding. • tubulin binding. • protein binding. • identical protein binding. • copper ... PRNP (prion protein) is the human gene encoding for the major prion protein PrP (proetase-resistant-protein, Pr for prion, and ...
... within 432-591 residues of CASS4 and 449-610 residues of p130Cas/BCAR1 at the level of secondary and tertiary structures. Also ... "Entrez Gene: Cas scaffolding protein family member 4".. *^ a b Tikhmyanova N, Little JL, Golemis EA (April 2010). "CAS proteins ... Structure[edit]. Figure 1. Interaction network and domain structure scheme of Cass4. SH3 domain (SH3) preceded by a short ... Cas scaffolding protein family member 4 is a protein that in humans is encoded by the CASS4 gene.[5] ...
Proteins have unique properties that allow them to become allergens, such as stabilizing forces in their tertiary and ... A histamine, the structure shown, causes a person to feel itchy during an allergic reaction. A common medication to stop this ... The harmful proteins are those that do not break down due to the strong bonds of the protein. IgE antibodies bind to a receptor ... Are the transferred proteins resistant to digestion - a trait shared by many allergenic proteins?[115] Genes approved for ...
Structure[edit]. Gene[edit]. The AKR1B1 gene lies on the chromosome location of 7q33 and consists of 10 exons. There are a few ... "Tonicity-responsive enhancer binding protein regulates the expression of aldose reductase and protein kinase C δ in a mouse ... Protein[edit]. AKR1B1 consists of 316 amino acid residues and weighs 35853Da. It does not possess the traditional dinucleotide ... stress-activated protein kinase signaling cascade. • cellular response to peptide. • daunorubicin metabolic process. • ...
J. Elks (14 November 2014). The Dictionary of Drugs: Chemical Data: Chemical Data, Structures and Bibliographies. Springer. pp ... "Audit of domperidone use as a galactogogue at an Australian tertiary teaching hospital". Journal of Human Lactation. 29 (1): 32 ... Protein binding. ~92%[1]. Metabolism. Hepatic (CYP3A4/5) and intestinal (first-pass)[1][4]. ...
In whole milk, 14% of the flavins are bound noncovalently to specific proteins.[15] Egg white and egg yolk contain specialized ... July 2004). "High-dose riboflavin treatment is efficacious in migraine prophylaxis: an open study in a tertiary care centre". ... forms part of its structure) and "flavin", the ring-moiety which imparts the yellow color to the oxidized molecule (from Latin ... Free riboflavin is naturally present in foods along with protein-bound FMN and FAD. Bovine milk contains mainly free riboflavin ...
Protein tertiary structure. *Sullivan reaction. *Cystinosis. ReferencesEdit. *^ Nelson, D. L.; Cox, M. M. (2000) Lehninger, ... a site of redox reactions and a mechanical linkage that allows proteins to retain their three-dimensional structure.[1] ... It was not recognized as being derived of proteins until it was isolated from the horn of a cow in 1899.[2] Human hair and skin ... In cell biology, cystine residues (found in proteins) only exist in non-reductive (oxidative) organelles, such as the secretory ...
A number of tertiary structures may fold into a quaternary structure. The science of the tertiary structure of proteins has ... Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide ... The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary ... Contemporary methods are able to determine, without prediction, tertiary structures to within 5 Å (0.5 nm) for small proteins ( ...
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.. Biasini M1, Bienert S1, ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental ...
... Shambhu Malleshappa Gowder,1 Jhinuk ... The analysis of protein structures provides plenty of information about the factors governing the folding and stability of ... It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using ... the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so ...
... a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. This approach ... Given some similarity in sequence between two proteins, ... Modelling Protein Structure from Remote Sequence Similarity: An ... Taylor W.R. (1994) Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction. ... Taylor, W. R. and Orengo, C. A. (1989b). Protein structure alignment. J. Molec. Biol., 208:1-22.CrossRefGoogle Scholar ...
RNA-Binding Domain Proteins in Kinetoplastids: a Comparative Analysis Javier De Gaudenzi, Alberto C. Frasch, Christine Clayton ...
Gene triplication deduced from the tertiary structure of a muscle calcium binding protein.. Kretsinger RH. ...
structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. Posted: Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. Posted: Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. by AlexanderSimmons on Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. by Proteinglow on Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is ... possible for many protein sequence segments to exhibit multiple 3D... ... Multi-structural segments protein structure protein structure comparison protein structure conservation URMSD ... Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments. ...
Assessment of template based protein structure predictions in CASP9, Proteins: Structure, Function, and Bioinformatics, 2011, ... Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method†. Authors. *. ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ...
... more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures ... Several novel techniques are employed for protein tertiary structure prediction, but the ... in Protein Tertiary Structure Prediction Several novel techniques are employed for protein tertiary structure prediction, but ... Critical assessment of methods of protein structure prediction (CASP) - round IX. Proteins, Structure, Function & ...
Protein Structure: Tertiary; Scattering: Radiation; Molecular Sequence Data; Spectrophotometry: Ultraviolet; Structure-Activity ... De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure ... De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure. Journal of ... De novo Backbone and Sequence Design of an Idealized α/β-barrel Protein: Evidence of Stable Tertiary Structure, Journal of ...
... and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane Protein Complex through 1H Spin ... Helical Transmembrane Protein Complex 1 H Spin Diffusion magic angle Quaternary Structure helical transmembrane model protein ... Probing secondary, tertiary, and quaternary structure along with protein−cofactor interactions through ,sup,1,/sup,H spin ... Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane ...
Protein tertiary structure. The tertiary structure of a polypeptide (or protein containing only one polypeptide) refers to its ... inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide ... the polypeptides tertiary structure follows uniquely from its primary structure (i.e., the order of amino acids). As a result ... The tertiary structure of a polypeptide will determine its chemical properties on a larger scale; however, ...
Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with ... Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is ... Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing ... Success of structure based drug discovery severely hinges on the availability of structures. ...
We developed TCP, a tool for designing chimera proteins based on the tertiary structure information. TCP is robust and ... Although the designing the chimera proteins based on the tertiary structure information is required in such situations, there ... In light of the problem, we developed a tool named TCP (standing for a Tool for designing Chimera Proteins), which extracts ... The test results of our method indicate that the TCP is robust and applicable to various shapes of proteins. ...
Does secondary structure determine tertiary structure in proteins? Proteins: Structure, Function and Genetics. 2005 Nov 1;61(2 ... Gong, Haipeng ; Rose, George D. / Does secondary structure determine tertiary structure in proteins?. In: Proteins: Structure, ... Gong, H., & Rose, G. D. (2005). Does secondary structure determine tertiary structure in proteins? Proteins: Structure, ... Gong, H & Rose, GD 2005, Does secondary structure determine tertiary structure in proteins?, Proteins: Structure, Function ...
Crystal structure of theLeishmania majorMIX protein: A scaffold protein that mediates protein-protein interactions Academic ... BH3-only proteins: a 20-year stock-take Academic Article * Bax Crystal Structures Reveal How BH3 Domains Activate Bax and ... Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1 Academic Article ... Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body ...
GP4Rate is a C++ program which combines Gaussian processes and phylogenetics to infer conserved sites in protein tertiary ... Protein Protein Sequence Protein Structure RNA RNA-Seq Secondary Structure Sequence Sequencing Simulation SNP Structure Tool ... Posted by admin at 4:30 pm Tagged with: GP4Rate, Important Region, Protein Tertiary Structures 71 views. Sorry, the comment ... GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures. 3D molecular model ...
Specific recognition in the tertiary structure of beta-sheets of proteins. by Shneior Lifson et al. ... Specific recognition in the tertiary structure of beta-sheets of proteins.. @article{Lifson1980SpecificRI, title={Specific ... StrandPairsViewer: A Toolkit for Visualization and Analysis of Amino Acids Pairs in Protein Sheet Structures. Ning Zhang, Shan ... recognition in the tertiary structure of beta-sheets of proteins.}, author={Shneior Lifson and Christian Sander}, journal={ ...
The tertiary structure is determined by four interactions: hydrogen bonding,... ... The three-dimensional conformation of a polypeptide chain of a globular protein in its native folded state. ... What is protein tertiary structure?. 4 years ago by Pozzter Q&A 0 replies, read ~321197 times ... polypeptide chain of a globular protein in its. native folded state. The tertiary structure is. determined by four interactions ...
"Protein Structure, Tertiary" by people in this website by year, and whether "Protein Structure, Tertiary" was a major or minor ... The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions ... "Protein Structure, Tertiary" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ( ... Protein Structure, Tertiary*Protein Structure, Tertiary. *Tertiary Protein Structure. *Protein Structures, Tertiary ...
Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we ... Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase  Polydorides, ... Neuralized Encodes a Peripheral Membrane Protein Involved in Delta Signaling and Endocytosis  Pavlopoulos, Elias; Pitsouli, ... Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular ...
PROTEIN TERTIARY STRUCTURE Sites are offered for calculating and displaying the 3-D structure of oligosaccharides and proteins ... Structures derived from NMR coordinates:. GeNMR (GEnerate NMR structure) - generates 3D protein structures using NOE-derived ... 3D-Match - Comparing 3D structures of two proteins (Softberry). iPBA - is a tool for comparison of protein structures based on ... With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology ...
Newly described small molecules that inhibit BET proteins BRD2, BRD3, and BRD4 reduce proliferation of NUT (nuclear protein in ... Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in ... Epigenetic proteins have recently emerged as novel anticancer targets. Among these, bromodomain and extra terminal domain (BET ... Hsp70, best known as a protein chaperone with well-defined peptide-refolding properties, is known to interact with ARE-like RNA ...
Tertiary Structure[edit]. The tertiary structure of a protein is the three-dimensional structure of the protein. This three- ... Determination of Tertiary Structure[edit]. The tertiary structure of a protein is determined through X-Ray Crystallography and ... Tertiary structure is also the most important protein structure that is used in determining the enzymatic activity of proteins ... In order for a protein to be functional (except in food), it must have an intact tertiary structure. If a tertiary structure of ...
... natively unstructured proteins) and exist in random conformations. The function of proteins depends on their structure,… ... and they show the greatest variety of structures. Many have intricate three-dimensional folding patterns that result in a ... Proteins are the largest and most varied class of biological molecules, ... Protein Folding. How and why do proteins naturally form secondary, tertiary, and quaternary structures? This question is a very ...
Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
This chapter explains the basics of tertiary organization of Proteins, It includes myoglobin ... Protein Structure-Proteins are organized in tertiary Structure- ... Protein Structure: How the Proteins are organized in tertiary ... Basic points on Tertiary Structure of Proteins:. The folding of a protein is connects to the Genomic function ... The best example of Tertiary Structure of Proteins are Myoglobin (Muscle Respiratory Pigment) and Ribunuclease. (RNA digestive ...
Clustering in the protein tertiary structure:. To determine whether a group of k amino acid replacements in a protein with ... To analyze protein tertiary structures, I first obtained a list of all human genes associated with a PDB structure file from ... Clustering of amino acid changes in protein tertiary structure. (a) The horizontal axis shows -log10(P3D), calculated only for ... They occur in well-defined domains of a proteins tertiary structure and show a large excess of amino acid replacement over ...
  • Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. (
  • Wrinch demonstrated this with the Cyclol model, the first prediction of the structure of a globular protein. (
  • Taylor, W.R. (1991) Towards protein tertiary fold prediction using distance and motif constraints. (
  • In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. (
  • At the same time, the remaining 2% of the sequences may pose problems for the sequence alignment based structure prediction methods. (
  • Several novel techniques are employed for protein tertiary structure prediction, but the more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures. (
  • It is quite apparent that efforts in tertiary structure prediction have saturated to a level where there is an immediate need for methodological innovations - beyond templates of folds to avoid falling into a trap of Lamarckism in protein folding. (
  • 2013) as incoporated in the continually evolving freely accessible Bhageerath-H webserver for protein tertiary structure prediction ( (Jayaram et al. (
  • 2012). We show that it is possible to push the accuracies in protein structure prediction beyond 60% even for tough targets. (
  • Bhageerath - Targeting the Near Impossible: Pushing the Frontiers of Atomic Models for Protein Tertiary Structure Prediction. (
  • Critical assessment of methods of protein structure prediction (CASP) - round IX. (
  • PHYRE 2 - P rotein H omology/analog Y R ecognition E ngine - this is my favourite site for the prediction of the 3D structure of proteins. (
  • ORION - is a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. (
  • I-TASSER was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. (
  • Robetta - is a protein structure prediction service that is continually evaluated through CAMEO. (
  • Motivation: Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). (
  • It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols. (
  • An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. (
  • As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. (
  • In this research, we attempted to determine if certain protein structure features, known as tertiary contacts, can improve the prediction of protein three-dimensional structure. (
  • From our calculations we were able to create a prediction filter based on our known literature-derived tertiary contacts of whether amino acid residues are buried or on the surface of a protein. (
  • From our tertiary contact prediction filter, it was shown that approximately 80% of the amino acid residues in our protein learning set were correctly filtered to be on the surface of a protein. (
  • From the tertiary contact prediction filter, we hope that tertiary contacts can be utilized in conjunction with other prediction approaches to more accurately predict where amino acids may be located in a protein. (
  • This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction , including homology modeling , protein threading , ab initio methods, secondary structure prediction , and transmembrane helix and signal peptide prediction. (
  • Below is a list which separates programs according to the method used for structure prediction. (
  • The present invention relates to drug design, and more particularly to drug design achieved rationally through the simulation and prediction of conformational features of selected oligopeptides or polypeptides for the purpose of predicting and making bioactive peptidomimetic compound structures. (
  • Antigenicity of the protein was also evaluated by Chou & Fasman beta-turn prediction method. (
  • Explain why ab initio protein folding, or the prediction of tertiary structure from a sequence, is considered one of the most challenging problems in computational biology. (
  • Efforts to predict tertiary structure from the primary structure are known generally as protein structure prediction. (
  • However, the environment in which a protein is synthesized and allowed to fold are significant determinants of its final shape and are usually not directly taken into account by current prediction methods. (
  • Automated protein tertiary structure prediction from sequence information alone remains an elusive goal to computational prescriptions. (
  • secondary structure prediction, generation of plausible main chain loop dihedrals and side chain dihedral optimization, considerable progress has been achieved in our laboratory ( ) and elsewhere for proteins with less than 100 amino acids. (
  • Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence-that is, the prediction of its secondary and tertiary structure from primary structure. (
  • Structure prediction is different from the inverse problem of protein design. (
  • the performance of current methods is assessed in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). (
  • A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. (
  • The key biological molecules are carbohydrates, lipids, proteins and nucleic acids. (
  • Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . (
  • DNA sequences comprising nucleic acids encoding fusion proteins comprising an Fc portion of an antibody attached at the N-terminus of an OB protein moiety, vectors comprising such DNA sequences, host cells comprising such vectors or DNA sequences, and processes for preparing such fusion proteins, and. (
  • The interactions and bonds of side chains within a particular protein determine its tertiary structure. (
  • In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions. (
  • Finally, ^1H NMR spectra of the folded and unfolded proteins provided evidence for specific interactions in the folded protein. (
  • Exploring beta-sheet structure and interactions with chemical model systems. (
  • The tertiary structure is determined by four interactions: hydrogen bonding, electrostatic interactions (ionic), hydrophobic interactions and covalent cross-linkages. (
  • 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. (
  • Protein structures are governed primarily by hydrophobic effects and by interactions between polar residues and other types of bonds. (
  • This will eliminate many of the ionic interactions that were necessary for maintenance of the folded shape of the protein. (
  • There is also the ionic interactions , the hydrophobic interaction (stronger in the center of the protein), the hydrogen bonds stabilizing folding, the forces Van der Waals , the disulfide bridges . (
  • The interactions between the side-chains of amino acids are responsible for the formation of the tertiary structure. (
  • The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. (
  • Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. (
  • By calculating and analyzing sequence homology and related values, it was shown that tertiary contacts, which typically are long-range amino acid interactions separated by at least 10 amino acids in sequence length, generally have lower pair averaged sequence homology-based values. (
  • It is the different interactions between the side chains of the amino acids that stabilize the tertiary structure. (
  • The third level of protein structure where side chain interactions dictate the direction of the folding. (
  • In protein science , Protein Interaction Domains (Protein-Protein Interaction Domains) are recognition modules in proteins that mediate interactions between specific proteins involved in signal transduction pathways, which fold to form recognition pockets complementary to the short interaction sequence motifs on their ligands. (
  • Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. (
  • its structure resulting from interactions between amino acid side chains. (
  • How side chain interactions can impact the tertiary structure of proteins. (
  • The completion of the human genome project has opened a new area for studying nucleic acid and protein interactions using nucleic acid cross-linking reagents, and advances have also been made in the area of biosensors and microarray biochips for the detection and analysis of genes, proteins, and carbohydrates. (
  • Most isoforms share a common C-terminal domain, which contains two zinc finger motifs that are required for hetero- or homo-dimerization, and for interactions with other proteins. (
  • Making the bend: DNA tertiary structure and protein-DNA interactions. (
  • Given some similarity in sequence between two proteins, a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. (
  • Here we discuss our recent efforts, based on some newer sequence alignment protocols (Jayaram, 2008), quantum mechanical corrections to the molecular mechanics generated structures and structure/fold invariant metrics (Mittal et al. (
  • The function of proteins depends on their structure, and defining the structure of individual proteins is a large part of modern Biochemistry and Molecular Biology. (
  • Even such small proteins contain hundreds of atoms and have molecular weights of over 5000 Daltons (Da). (
  • Most proteins with a molecular weight greater than 50,000 consist of two or more noncovalently-linked monomers. (
  • In addition to general chemistry texts, information about protein structure can be found in texts for biochemistry, organic chemistry, general biology, genetics, and molecular biology. (
  • Organic compounds with the same molecular formula but different structures and, therefore, different properties. (
  • Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. (
  • In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. (
  • Here we suggest a molecular mechanism for electromechanical coupling and gating polarity in non-domain-swapped K v channels on the basis of the cryo-electron microscopy structure of KAT1, the hyperpolarization-activated K v channel from Arabidopsis thaliana . (
  • This structure provides a molecular description of the core of the Tat translocation system and a framework for understanding the unique Tat transport mechanism. (
  • In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. (
  • By analysing these properties, we can provide you with valuable information on secondary, tertiary and quaternary structures of protein molecules, such as monoclonal antibodies, and provide evidence that the molecule maintains conformational stability. (
  • The primary structure of a polypeptide of protein determines its secondary, tertiary, and quaternary structures. (
  • M2 - explain the tertiary and quaternary structures of proteins. (
  • A number of tertiary structures may fold into a quaternary structure. (
  • The robust nature of the approach derives from the stability of the fold of the protein under mutational pressures. (
  • This is so conservative that, for two proteins, sequence similarity can be almost undetectable yet the overall fold can remain the same. (
  • Taylor, W.R. (1993) Protein fold refinement: building models from idealised folds using motif constraints and multiple sequence data. (
  • 2000). This saturation may show completeness of protein fold space - an unlikely possibility. (
  • Alternatively, it either implies the need for development of higly sensitive newer experimental methods to unveil the unexplored regions of protein fold space, or, beckons the development of more accurate, time efficient, non-template based computational strategies for unravelling the uniqueness and diversity of protein structures. (
  • Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? (
  • PEP-FOLD 3 is a de novo approach aimed at predicting peptide structures from amino acid sequences. (
  • Disulfide bonding can form within and between polypeptide chains as proteins fold to its native conformation. (
  • Many have intricate three-dimensional folding patterns that result in a compact form, but others do not fold up at all ("natively unstructured proteins") and exist in random conformations. (
  • To understand how proteins fold, we will start with the basics of structure, and progress through to structures of increasing complexity. (
  • Many polypeptides fold into compact, globular structures in which amino acid residues that are distant from each other in primary structure come into close proximity in the folded structure. (
  • The second level of protein structure where the linear sequence of proteins begins to fold into regular repeating patterns. (
  • The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. (
  • The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. (
  • Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. (
  • These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm. (
  • Primary structure is simply the sequence of residues making up the protein. (
  • Thus primary structure involves only the covalent bonds linking residues together. (
  • So the primary structure of a small protein would consist of a sequence of 50 or so residues. (
  • There is no theoretical maximum size, but the largest protein so far discovered has about 30,000 residues. (
  • Deletions of 5 to 8 residues within predicted α- helices resulted in the failure of export of the mutant protein from the cell. (
  • Proteins are large biomolecules , or macromolecules , consisting of one or more long chains of amino acid residues . (
  • Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides , or sometimes oligopeptides . (
  • The sequence of amino acid residues in a protein is defined by the sequence of a gene , which is encoded in the genetic code . (
  • Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (
  • Review of Protein Chemistry and Structure. (
  • Since the publication of the first edition of Chemistry of Protein Conjugation and Cross-Linking in 1991, new cross-linking reagents, notably multifunctional cross-linkers, have been developed and synthesized. (
  • It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. (
  • In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. (
  • Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power to discover within Protein Explorer and its connections to complementary structural bioinformatics resources! (
  • The emphasis of the course is structural bioinformatics with focus on various computational methods to simulate, analyze and model protein structure, dynamics and function. (
  • The tertiary structure of a polypeptide (or protein containing only one polypeptide) refers to its shape, or more precisely the complete description its molecules' positions in three-dimensional space. (
  • To obtain PDB coordinates for a protein of your interest, go to the Protein Data Bank or Molecules to Go or NCBI . (
  • The aggregation of nonpolar side chains in the interior of a protein is favored by the increase in Entropy of the water molecules that would otherwise form cages around the hydrophobic groups. (
  • Proteins are the largest and most varied class of biological molecules, and they show the greatest variety of structures. (
  • This spatial configuration must meet those of other structures of other molecules, dimensional structure, biological role and stereo-specificity therefore are necessarily linked. (
  • Macromolecular Crystals: The Growth of Crystals Is Now the Key to Deducing the Structure of Large Molecules. (
  • Proteins perform a vast array of functions within organisms , including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. (
  • Pyrx with Autodock vina was used to screen the compounds from Drug bank and Protein Data Bank to find the molecules that can bind to the active site between 1 to 142 amino acids. (
  • This quiz is based on the various aspects of the structure of protein molecules and amino acids. (
  • Any mixture of secondary, tertiary, or quaternary protein molecules which appear as clumps in or outside the cell. (
  • But in nowadays The evolutions in motif identification and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. (
  • Liam J. McGuffin , Jennifer D. Atkins , Bajuna R. Salehe , Ahmad N. Shuid , Daniel B. Roche , IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1. (
  • Decoding the design principles of amino acids and the chemical logic of protein sequences. (
  • However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. (
  • They are linked by peptide sequences usually short and without secondary structure. (
  • can calculate comparative models for a large number of protein sequences, using many different template structures and sequence-structure alignments. (
  • Protein primary structures can be directly sequenced , or inferred from DNA sequences . (
  • Large sequence databases now exist that collate known protein sequences. (
  • In protein science , Protein Interaction Motifs (Protein Interaction Binding Motifs) are short amino acid sequences which are the binding sites on the ligands of protein interaction domains. (
  • Two of the main sources for generating the new families added to release 27.0 were Protein Data Bank (PDB) structures =-=(8)-=- and human sequences. (
  • We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. (
  • Most such methods do rely on comparisons between the sequence to be predicted and sequences of known structure in the Protein Data Bank and thus account for environment indirectly, assuming the target and template sequences share similar cellular contexts. (
  • Ankyrin Repeat (ANK Repeat) is a protein interaction motif that contains a 33-amino acid long sequence that often occurs in tandem arrays (as amino acid repetitive sequences ). (
  • The secondary structure of proteins where the polypeptide chains are almost completely extended during the process of folding. (
  • Using this coarse-grained mapping, protein conformation can be approximated by a linear sequence of mesostates. (
  • The three-dimensional conformation of a polypeptide chain of a globular protein in its native folded state. (
  • In order to maintain potency and activity, some of the most critical parameters to maintain are protein conformation (tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). (
  • However, analytical monitoring of the protein conformation has been frequently omitted due to time constraints, the complexity of techniques commonly employed and the inherent lack of sensitivity to subtle changes shown by some biophysical methods. (
  • The biologically active form of Globular Proteins are in Tertiary structure, which is in three-dimensional conformation. (
  • Secondary structure is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule. (
  • Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO-NH amide moiety into a fixed conformation. (
  • A method of rational drug design includes simulating polypeptides in a way that predicts the most probable secondary and/or tertiary structures of a polypeptide, e.g., an oligopeptide, without any presumptions as to the conformation of the underlying primary or secondary structure. (
  • Structure determination of membrane proteins with magic angle spinning NMR is rapidly developing. (
  • Bezanilla, F. How membrane proteins sense voltage. (
  • Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. (
  • The protein of interest has four domains due to gene duplication. (
  • A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. (
  • Its identification may point to functionally important regions of a gene and is thus of potential interest to protein engineers who alter proteins to produce new functions. (
  • The codon sequence of the protein-coding gene determines the order of amino acids in the polypeptide chain. (
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (
  • section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (
  • This gene encodes a transcription factor that belongs to the family of zinc-finger DNA-binding proteins associated with chromatin remodeling. (
  • What does this gene/protein do? (
  • This gene encodes a member of the four-and-a-half-LIM-only protein family. (
  • Also, this gene is down-regulated during transformation of normal myoblasts to rhabdomyosarcoma cells and the encoded protein may function as a link between presenilin-2 and an intracellular signaling pathway. (
  • What pathways are this gene/protein implicaed in? (
  • Tumorigenesis is frequently associated with activating mutations in β-catenin gene inducing nuclear expression of β-catenin protein. (
  • The molcular biology lectures include topics like DNA structure and replication, RNA and transcription, protein synthesis, gene expression and basic recombinant DNA techniques. (
  • In some proteins, the linear polypeptide chain is cross-linked: Disulfide bonds. (
  • Hydrogen bonds formed between amino acids are responsible for the formation of the secondary structure of a protein while disulfide and salt bridges form the tertiary structure. (
  • However, proteins can become cross-linked, most commonly by disulfide bonds , and the primary structure also requires specifying the cross-linking atoms, e.g., specifying the cysteines involved in the protein's disulfide bonds. (
  • The primary structure of polypeptides and proteins is the sequence of amino acids in the polypeptide chain with reference to the locations of any disulfide bonds. (
  • Tertiary structure is largely maintained by disulfide bonds. (
  • Hydrogen bonds fine tune the tertiary structure by selecting the unique structure of a protein from among a relatively small number of hydrophobically stabilized conformations. (
  • Thermal unfolding monitored by near-UV CD revealed a cooperative transition with an apparent T_m of 65 °C. Moreover, the artificial protein did not exhibit any affinity for the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid (ANS), providing additional evidence that the artificial barrel is not in the molten globule state, contrary to previously designed artificial a/ b-barrels. (
  • The hydrophobic effect is the major determination of original protein structure. (
  • This is due to the exposure of hydrophilic, acidic ad basic amino acids to the outside and hiding of the hydrophobic amino acids such as aromatic amino acids and the amino acids with alkyl groups in the core of the protein structure. (
  • A major force stabilizing the tertiary structure is the hydrophobic interaction among nonpolar side chains in the core of the protein. (
  • Instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes . (
  • Hydrophobic interaction is the main stabilizing force for subunits in quaternary structure. (
  • The property of protein of being non-polar and hydrophobic, as well as having an increase in intensity from 200 to 219, indicates the protein folding. (
  • The shift from 342 to 337 nm along with blue shift indicates hydrophobic properties and the removal of protein from the water environment. (
  • The secondary structures are tightly packed in the protein core in a hydrophobic environment. (
  • Other α helices buried in the protein core or in cellular membranes have a higher and more regular distribution of hydrophobic amino acids, and are highly predictive of such structures. (
  • In the natural course of making a protein, polypeptides are elongated by the addition of amino acids to the C-terminal end of the growing chain. (
  • Long chains of amino acids, called polypeptides, make up the multicomponent, large complexes of protein. (
  • In general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. (
  • There are four levels of structure found in polypeptides and proteins . (
  • Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism . (
  • Digestion breaks the proteins down for use in the metabolism. (
  • Part of an enzyme needed for energy, and protein metabolism. (
  • It is based on the nonredundant data set of 218 monomeric proteins. (
  • Hemoglobin's quaternary structure is the package of its monomeric subunits. (
  • 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. (
  • consist of a sufficient and balanced supply of both essential and nonessential amino acids in order to ensure high levels of protein production. (
  • The templates used for model building consist of representative multiple structure al. (
  • Most proteins consist of linear polymers built from series of up to 20 different L -α- amino acids . (
  • The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. (
  • Far-UV CD spectra with prominent bands at 222 nm and 208 nm revealed the presence of α-helix secondary structures (50%) in fairly good agreement with the model. (
  • Various types of secondary structures have been discovered, but by far the most common is the orderly repeating forms known as the a-helix and the b sheet. (
  • This is very compact three-dimensional structure, the wound has previously viewed and secondary structures of the segments without secondary structure . (
  • The two main secondary structures are the alpha helix and the anti-parallel beta-pleated sheet. (
  • A single polypeptide or protein may contain multiple secondary structures. (
  • Meets the grading criterias: P3 - describe the primary and secondary structures of proteins. (
  • In these secondary structures regular patterns of H bonds are formed between neighboring amino acids, and the amino acids have similar Φ and Ψ[clarification needed] angles. (
  • These areas are almost "independent" from the rest of the tertiary structure of the globular protein . (
  • Serving as the basic structural molecule of all the tissues in the body, protein makes up nearly 17 percent of the total body weight. (
  • Also, for a protein composed of a single polypeptide molecule, tertiary structure is the highest level of structure that is attained. (
  • Suppose that when drawing a Lewis structure for a molecule, you end up with a structure in which the central at. (
  • its structure resulting from the union of more than one protein molecule, called subunit proteins. (
  • Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin. (
  • The primary structure may be thought of as a complete description of all of the covalent bonding in a polypeptide chain or protein. (
  • This process of destroying the three-dimensional protein structure is called denaturation. (
  • We will conclude this section of the course with a consideration of denaturation and renaturation -- the forces involved in loss of a macromolecule's native structure (that is, its normal 3-dimensional structure), and how that structure, once lost, can be regained. (
  • what structure does denaturation destroy? (
  • Reversible and irreversible denaturation of proteins. (
  • The secondary structure of recombinant proteins can change through complex formation with other proteins. (
  • Proteins are chains of amino acids joined together by peptide bonds. (
  • Tertiary structure or the globular form of proteins is water-soluble under physiological conditions. (
  • Fingerprint Dive into the research topics of 'Does secondary structure determine tertiary structure in proteins? (
  • Fingerprint Dive into the research topics of 'Erythropoietin structure-function relationships. (
  • The tertiary structure of a polypeptide or protein is the three-dimensional arrangement of the atoms within a single polypeptide chain. (
  • It also incorporates a n ew ab initio folding simulation called Poing to model regions of your proteins with no detectable homology. (
  • H spin diffusion with MAS NMR is demonstrated for a helical transmembrane model protein complex. (
  • An example of a protein with many a-helical structures is the keratin that makes up human hair. (
  • tertiary structure The folding of the helical coil of a polypeptide chain. (
  • We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. (
  • The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. (
  • Do you want more information on amino acids and proteins? (
  • The side chains project outward and contact any solvent, producing a structure something like a bottle brush or a round hair brush. (
  • Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. (
  • 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. (
  • Also, ionic bonds called salt bridges form between positively- and negatively-charged side-chains of amino acids, further stabilizing the tertiary structure. (
  • The process whereby water-fearing protein side chains interact more favorably with themselves than with water to create a hydrophilic exterior. (
  • Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. (
  • Chemical methods typically synthesise peptides in the opposite order to biological protein synthesis (starting at the C-terminus). (
  • TatC captures substrate proteins by binding their signal peptides. (
  • Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures. (
  • 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. (
  • The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. (
  • As a part of our on-going efforts in this direction and to facilitate tertiary structure selection/rejection in containing the combinatorial explosion of trial structures for a specified amino acid sequence, we describe here a web-enabled tool ProRegIn (Protein Regularity Index) developed based on the regularity in the 𝛷, Ψ dihedral angles of the amino acids that constitute loop regions. (
  • We have analysed the dihedrals in loop regions in a non-redundant dataset of 7351 proteins drawn from the Protein Data Bank and categorized them as helix-like or sheet-like (regular) or irregular. (
  • This allows for the easy identification of regions and types of structural flexibility present in a protein of interest. (
  • The interacting regions may be adjacent, with a short loop in between, or far apart, with other structures in between. (
  • The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. (
  • In conclusion, compared with existing methods for in vivo testing of protein function, this complementation assay provides a rapid method for investigating protein structure/function relationships in plants. (
  • Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . (
  • Improved methods for building protein models in electron density maps and the location of errors in these models. (
  • In protein science , Protein Interaction Domains and Motifs are 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. (
  • M. Bradford, "A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding", Anal. (
  • Inhibition of apoptosis and NF-κB activation by vaccinia protein N1 occur via distinct binding surfaces and make different contributions to virulence. (
  • Protein biosynthesis is most commonly performed by ribosomes in cells. (
  • As a result, inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide range of biological applications, and one that is still far from fully understood. (
  • In biological systems, proteins are produced during translation by a cell's ribosomes . (
  • p>This section provides any useful information about the protein, mostly biological knowledge. (
  • Though it may not be immediately obvious, proteins do follow certain recognisable folding patterns. (
  • Examination of protein structures resolved by X-ray diffraction and NMR has revealed a variety of folding patterns common to many different proteins. (
  • The present study analysed the role of transforming growth factor-β1 (TGF-β1) and four-and-a-half LIM domain protein 2 (FHL2) in pilomatricoma in synopsis with their expression patterns in human anagen hair. (
  • Because there are two different subunits, hemoglobin exhibits heteroquaternary structure. (
  • The fourth level of protein structure that refers to the spatial arrangement of the subunits within the protein. (
  • This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups. (
  • In a b sheet, the polypeptide chain folds back on itself so that polypeptide strands like side by side, and are held together by hydrogen bonds, forming a very rigid structure. (
  • Again, the polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the a-helix, these bonds are formed between neighbouring polypeptide (b) strands. (
  • In addition, hydrogen bonds also help in stabilizing the 3D-structure. (
  • Explanations of structural biology terms and concepts , e.g. asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value, etc. all at About Macromolecular Structure . (
  • its structure resulting from hydrogen bonds between the C=O and N-H groups of different amino acids. (
  • A representation of the 3D structure of the protein myoglobin showing turquoise α-helices . (
  • They occur in well-defined domains of a protein's tertiary structure and show a large excess of amino acid replacement over silent substitutions. (
  • To understand protein's role and function in the human body, it is important to understand its basic structure and composition. (
  • Taken together, the results indicate that the de novo designed α/β-barrel protein adopts a stable three-dimensional structure in solution. (
  • Indeed, they have their own and are stable tertiary structure independently of the rest of the polypeptide chain. (
  • 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. (
  • Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . (
  • D2 - discuss the relationship between the structure and function of proteins. (
  • Observing the structures of proteins within the cell and tracking structural changes under different cellular conditions are the ultimate challenges for structural biology. (
  • serves as a blueprint for proteins and, through the actions of proteins, for all cellular structures and activities. (
  • The assay distinguished mutations that generate fully functional, nonfunctional, and partially functional proteins. (
  • To explore this question, backbone dihedral angles were extracted from the known three-dimensional structure of 2,439 proteins and mapped into 36 labeled, 60° × 60° bins, called mesostates. (
  • I am using Swiss-PdbViewer to determine the structure of a fluorescent protein with a sequence homology to know fluorescent proteins, such as GFP and DsRed. (
  • Mad Cow Disease is a great way to get the students to pay attention before you lunge into the difficult lecture on protein synthesis (you start with prions, then work backwards). (
  • Studies on the enzymatic synthesis of optically pure tertiary alcohols. (