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 ...
We are about the release a new version of a website for one of our clients.. His current website is on, the new domain with a complete different structure is located on So now we need to redirect traffic for the old one to the new one.. Is it best practise to redirect everything to the home page on the new domain or do we need to redirect each page to the correct page on the new domain?. ...
.cc domain names are short and easy to remember. Join the global community that markets their ideas and organizations with dotcc domain names.
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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
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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.. ...
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.. ...
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 ( ...
"Protein structure: Primary, secondary, tertiary & quatrenary (article)". Khan Academy. Retrieved 28 September 2022. Stratmann ... 2002), I.3. Proteins: The Shape and Structure of Proteins Alberts et al. (2002), I.3. Proteins: Protein Function Archived 25 ... without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly ... Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and ...
Disulfide groups stabilize the tertiary structures of proteins. Transferrins are iron binding proteins and acute phase ... Protein articles without symbol, Blood proteins, Storage proteins, Avian proteins). ... This process is determined by the structure of the protein backbone and the carbohydrate attachment site. In addition, ... Consequently, structurally this protein differs from its serum counterpart because of its glycosylation pattern. These proteins ...
Ponder JW, Richards FM (1987). "Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed ... PSVS Protein Structure Validation Server at the NESG based on information retrieval statistics PROSESS PROSESS (Protein ... Protein Structure Evaluation Suite & Server ResProx - protein model resolution-by-proxy Cyro-EM EM Data Bank, for EM map ... protein model resolution-by-proxy VADAR - Volume, Area, Dihedral Angle Reporter NMR PSVS (Protein Structure Validation Server ...
The Protein Folding Problem and Tertiary Structure Prediction K. M. Merz, Jr.; S. M. LeGrand Eds.; Birkhaüser: Boston, MA, 1994 ... 1994). The Protein Folding Problem and Tertiary Structure Prediction. Birkhäuser Basel. ISBN 978-1-4684-6833-5. Merz, Jr, ... Structure, Function and Dynamics of Lipid Bilayers K. M. Merz, Jr.; B. Roux Eds.; Birkhaüser: Boston, MA, 1996. Structure-Based ... A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules; W. D. Cornell; P. Cieplak ...
This secondary structure then folds to produce the tertiary structure of the protein. The tertiary structure is the proteins ... In the tertiary structure, key protein features e.g. the active site, are folded and formed enabling the protein to function. ... The primary structure of a protein (the polypeptide chain) can then fold or coil to form the secondary structure of the protein ... "Protein structure: Primary, secondary, tertiary & quaternary (article)". Khan Academy. Retrieved 11 March 2020. "proteolysis , ...
The spherical structure is induced by the protein's tertiary structure. The molecule's apolar (hydrophobic) amino acids are ... Even in the protein's denatured state, it can be folded into the correct structure. Globular proteins seem to have two ... In biochemistry, globular proteins or spheroproteins are spherical ("globe-like") proteins and are one of the common protein ... Regulatory roles are also performed by globular proteins rather than fibrous proteins. Structural proteins, e.g., actin and ...
Aloy, P.; Russell, R. B. (2003). "InterPreTS: protein Interaction Prediction through Tertiary Structure". Bioinformatics. 19 (1 ... Interactome Protein-protein interaction Protein function prediction Protein structure prediction Protein structure prediction ... "Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces". ... The field of protein-protein interaction prediction is closely related to the field of protein-protein docking, which attempts ...
The latter is known as the tertiary structure of a protein. So, whenever a receptor interacts with an undigested antigen, the ... Antigens are usually proteins that are too large to bind as a whole to any receptor so only specific segments, that form the ... Proteins are composed of repeating nitrogen-containing subunits called amino acids that in nature do not exist as straight ... Antigen Linear epitope Epitope mapping, finding (on an antigen protein) the epitope(s) for a specific antibody Goldsby, Richard ...
This protein is also predicted as a DNA binding protein. The protein may assume a tertiary structure of a coiled coil. ... The amino acid structure is highly conserved through mammals, and the secondary and tertiary structure is highly conserved in ... protein name). The mRNA is composed of 6 exons, and encodes a 15007.84 kD protein known as HT021. This protein has a pre- ... Its protein is expected to localize to the nucleus and bind DNA. Orthologs have been identified in all of the major animal ...
I-TASSER was used to predict the tertiary structure. The top model predicted eight alpha helices, including one between amino ... "I-TASSER server for protein structure and function prediction". Retrieved 2020-05-03. "Phobius". ... Uncharacterized Protein C15orf32 is a protein which in humans is encoded by the C15orf32 gene and is located on chromosome 15, ... Possible secondary structures of the 5' and 3' untranslated region in C15orf32 mRNA is given to the left and was predicted by ...
1285-1288; Protein electron transfer rates set by the bridging secondary and tertiary structure; doi:10.1126/science.1656523 ( ... In proteins, ET rates are governed by the bond structures: the electrons, in effect, tunnel through the bonds comprising the ... Especially in proteins, electron transfer often involves hopping of an electron from one redox-active center to another. The ... chain structure of the proteins. Electron equivalent Electrochemical reaction mechanism Solvated electron "Metals". Bitesize. ...
The secondary and tertiary structure of this protein is not well known. Vexin is considered rich in arginine, and poor in ... The isoelectric point of the protein is 10.42 which indicates the pH of the protein is basic. Vexin does contain a domain of ... Vexin is a protein encoded by VXN gene. VXN is found to be highly expressed in regions of the brain and spinal cord. VXN is ... The orthologs of vexin all show conservation of the SH3 protein domain family as well as a domain of unknown function (DUF4648 ...
... ß propeller tertiary structure of the protein. Leucine Zipper: A motif found in regulatory proteins, as predicted by PSORT II ... One of the key attributes of MEGF8's tertiary structure is its 7-bladed beta propeller which is formed by the kelch motif found ... The high levels of cysteine residues contributes to the numerous disulfide bonds found in the mature protein's folded structure ... Retrieved 24 April 2014.[permanent dead link] Kelley LA, Sternberg MJ (26 February 2009). "Protein structure prediction on the ...
Shown to the right is a predicted tertiary structure of the protein. It is marked by long alpha-helices localized to the end of ... via sugar-binding proteins. The graph illustrates predicted N-glyc sites across the protein chain (x-axis represents protein ... PRR32 is a protein that in humans is encoded by the CXorf64 (Chromosome X Open Reading Frame 64) gene. It was also found that ... A list was generated of orthologs using the NCBI (protein) blast for PRR32, as well as UCSC's BLAT (BLAST-Like Alignment Tool. ...
Beratan, DN (1991). "Protein electron transfer rates set by the bridging secondary and tertiary structure". Science. 252 (5010 ... time that electron-transfer rates in proteins are determined by the electron orbital interactions in the protein structure. In ...
Shown to the right is a predicted tertiary structure of the protein. It is composed mostly of long alpha-helices with several ... The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015. Uhlén M et al, 2015. Tissue-based ... 2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs ... The protein is initially cleaved to remove the 26 amino acids from the N-terminus. This represents a signal peptide after it is ...
... is a 12-kD oxidoreductase protein. Thioredoxin proteins also have a characteristic tertiary structure termed the ... "Structural basis for target protein recognition by the protein disulfide reductase thioredoxin". Structure. 14 (11): 1701-10. ... "Identification of thioredoxin-binding protein-2/vitamin D(3) up-regulated protein 1 as a negative regulator of thioredoxin ... Thioredoxin proteins move from cell to cell, representing a novel form of cellular communication in plants. Thioredoxin has ...
Shown to the right is a predicted tertiary structure of the protein. It is marked by long alpha-helices with several coil ... "uncharacterized protein C10orf67, mitochondrial [Homo sapiens] - Protein - NCBI". Retrieved 2017-05-05. " ... The protein is initially cleaved to remove the 36 amino acid N-terminal signal peptide after it is localized to the ... "PHYRE2 Protein Fold Recognition Server". Retrieved 2017-05-05. "GDS4794 / 1553845_x_at". www.ncbi.nlm.nih ...
In this way proteins serve to organise and stabilise the rRNA tertiary structure. The function of the S4 domain is to be an RNA ... Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW (1998). "The crystal structure of ribosomal protein S4 reveals a two ... In molecular biology, S4 domain refers to a small RNA-binding protein domain found in a ribosomal protein named uS4 (called S9 ... this protein domain delivers nucleotide-modifying enzymes to RNA and to regulates translation through structure specific RNA ...
Protein folding prediction programs used to predict protein tertiary structure have also been expanding to better predict ... classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are ... protein-protein interaction when discussing quaternary structure of proteins and consider all assemblies of proteins as protein ... not all proteins will have a quaternary structure since some proteins function as single units. Protein quaternary structure ...
... was a volunteer computing project that used BOINC software to predict protein structure from protein sequence in ... Whereas the latter aims to study the dynamics of protein folding, [email protected] aimed to specify what the final tertiary ... However, for a time, [email protected] competed with other BOINC protein structure prediction projects, such as [email protected] Each ... List of volunteer computing projects [email protected] SIMAP Grid computing Protein structure prediction "BOINC: [email protected] Team ...
In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and ... Ribosomal L28e protein family is a family of evolutionarily related proteins. Members include 60S ribosomal protein L28. ... Human genes encoding protein containing this domain include RPL28. Ramakrishnan V, Moore PB (April 2001). "Atomic structures at ... Wool IG, Chan YL, Paz V, Olvera J (August 1990). "The primary structure of rat ribosomal proteins: the amino acid sequences of ...
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). Akamptisomerism - due to ... Dunbrack, R. L.; Cohen, F. E. (1997). "Bayesian statistical analysis of protein side-chain rotamer preferences". Protein ... Protein folding also generates stable conformational isomers which can be observed. The Karplus equation relates the dihedral ... Protein side chains exhibit rotamers, whose distribution is determined by their steric interaction with different conformations ...
It is vital that the protein crystal maintains its tertiary structure in each solvent. This process is repeated for multiple ... Gene prediction Protein-protein interaction prediction Protein structure prediction Structural genomics Functional genomics ... protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein ... doi:10.1093/protein/11.9.739. PMID 9796821. Wang S, Ma J, Peng J, Xu J (March 2013). "Protein structure alignment beyond ...
... protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share ... Small proteins typically have a tertiary structure that is maintained by disulphide bridges (cysteine-rich proteins), metal ... They are one of the common types of protein along with soluble globular proteins, fibrous proteins, and disordered proteins. ... or by making calculated variations on a known protein structure and its sequence (known as protein redesign). Rational protein ...
Fidler AL, Boudko SP, Rokas A, Hudson BG (April 2018). "The triple helix of collagens - an ancient protein structure that ... Theimer CA, Blois CA, Feigon J (March 2005). "Structure of the human telomerase RNA pseudoknot reveals conserved tertiary ... Brodsky B, Persikov AV (2005-01-01). "Molecular structure of the collagen triple helix". Advances in Protein Chemistry. 70: 301 ... For example: the beginning of a helical protein is its N terminus, and the beginning of a single strand of DNA is its 5' end. ...
Further interactions between residues of the individual amino acids form the protein's tertiary structure. For this reason, the ... The sequence of the amino acids in the polypeptide backbone is known as the primary structure of the protein. Like almost all ... primary structure of the amino acids in the polypeptide backbone is the map of the final structure of a protein, and it ... "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural ...
Thus, arginine's positive charge (at physiological pH) is removed, altering the protein's tertiary structure. The reaction uses ... This increases the hydrophobicity of the protein, which can lead to changes in protein folding, affecting the structure and ... autoantibodies often attack citrullinated proteins. The presence of anti-citrullinated protein antibody is a standard test for ... Citrullinated proteins are also found in the cellular debris accompanying the destruction of cells in alzheimer disease, and ...
Finally, multiple tertiary structures can combine to form the quaternary structure of a protein. Nucleic acids are polymers ... Proteins have four distinct levels of organization (primary, secondary, tertiary, and quartenary). The primary structure ... The folding of alpha helices and beta sheets gives a protein its three-dimensional or tertiary structure. ... giving rise to the secondary structure of a protein. The two common types of secondary structures are alpha helices and beta ...
On the tertiary structure of the protein layers of chloroplasts *Hosemann, R. ...
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. ...
The tertiary structure of a protein is stabilized by hydrophobic interactions, electrostatic forces (salt bridges), and ... Tertiary structure specifies the spatial layout of amino acids that are far apart in the linear structure as well as those ... The arrangement of amino acids specifies the ultimate 3 -D structure of any specific protein. The polypeptide chain folds ... Find out a qualitative test for proteins, fats and oils, and starch amino acids and test any fruit juice, saliva, sweat, and ...
What is the secondary structure of a protein? What is tertiary for that matter? This article answers these questions and more. ... Tertiary Structure. The structure of a protein in 3D space is what defines its function:. *A hormone must fit its receptor ... Levels of Protein Structure. We have already discovered that the primary structure of a protein is the sequence of amino acids ... The secondary structures have now folded to occupy a specific 3D space - this is tertiary structure and is vital to the ...
A possible configuration (tertiary structure) of a protein molecule. With respect to prion proteins, the molecules with large ... Prions are considered to consist of protein only, and the abnormal isoform of this protein is thought to be the agent that ... A structure engineered to receive accumulated heat from ventilation systems and equipment and transfer this heat to water, ... Viruses whose particle diameter is ,50 nm and whose outer surface is the protein of the particle itself and not that of host ...
Protein Structure, Tertiary * Shikimic Acid / chemistry * Shikimic Acid / metabolism * Structure-Activity Relationship ... The crystal structure of the DAH7PS-inhibitor complex was solved to 2.35 Å. Both the position of the inhibitor and the ... This structure also identifies a water molecule that is located in the appropriate position to attack the re face of P- ... conformational changes of active site residues observed in this structure correspond closely to the predictions from the ...
Development and analysis of the parallel ant colony optimization algorithm for solving the protein tertiary structure ... Parallel ant colony optimization algorithm for solving protein tertiary structure prediction problem given its amino acid ... Ключові слова: combinatorial optimization, protein tertiary structure prediction, ant colony optimization, parallel algorithms ...
Both the predicted tertiary structure of the protein and the phylogenetic trees based on this region were influenced by the ... Low complexity regions (LCRs) provide plasticity in surface proteins of Plasmodium species, but its implication in vaccine ... Plasmodium vivax merozoite surface protein 3α (PvMSP3α) is a promising vaccine candidate which has shown strong association ... Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to ...
Protein Structure, Tertiary. Sowell J, Frei B, Stevens JF. 2004. Vitamin C conjugates of genotoxic lipid peroxidation products ... Proto-Oncogene Proteins c-akt. Zhang W-J, Wei H, Hagen T, Frei B. 2007. Alpha-lipoic acid attenuates LPS-induced inflammatory ... Protein Phosphatase 2. Smith AR, Visioli F, Frei B, Hagen TM. 2006. Age-related changes in endothelial nitric oxide synthase ... Protein Conformation. Sowell J, Frei B, Stevens JF. 2004. Vitamin C conjugates of genotoxic lipid peroxidation products: ...
Two proteins, CifA and CifB, underlie the genetic basis of CI and rescue, but how amino acid sites across these proteins ... The results of this study reveal a phenotypic complexity underlying the expression of these proteins and provide relevance to ... I-TASSER generated protein tertiary structure predictions for Cif proteins and their mutants using the on-line server with ... Protein structure prediction Is the Subject Area "Protein structure prediction" applicable to this article? Yes. No. ...
Protein Structure, Tertiary. 2. 2011. 4055. 0.070. Why? Genetic Loci. 1. 2014. 2579. 0.070. Why? ... Receptor-Like Protein Tyrosine Phosphatases, Class 3. 1. 2015. 31. 0.140. Why? ...
A protein with tertiary structure. *. B. A lipid made of three fatty acids and glycerol ... Molecular Structure Of Chemistry Molecular Structure Of Chemistry Chapter 2 Molecules of life - water, minerals and ... At which level of protein structure are interactions between R groups most important? ... A change in a proteins three-dimensional shape or conformation due to disruption of hydrogen bonds, disulfide bridges, and ...
The peroxidase activity increase preceded the loss of protein tertiary structure. Monounsaturated tetraoleoyl-CL (TOCL) induced ... while hydrophobic interactions are involved when cyt cs tertiary structure is lost. In the presence of CL, cyt c peroxidase ...
... tertiary and quaternary structure of proteins. Interactions that stabilise protein structure, denaturation and renaturation of ... Atomic structure and periodicity. Molecular structure and chemical bonding using the VSEOR model. Nomenclature of iorganic ions ... Proteins. Lipids. Water. Chemical and nutritional aspects of food processing: implications of different processing techniques ... Practical: Molecular structure (model building), synthesis and properties of simple organic compounds. ...
... and unfolded proteins. A large class of proteins has no defined tertiary structure. These proteins have structured parts (or ... Structured proteins can be unfolded (e.g. by temperature, pressure or chemically) to examine stable unfolded intermediates, ... As an extreme case a complete unstructured protein should behave as a stiff random polymer chain [1-3]. Structure and dynamics ... Knowledge on dynamics is important to understand the structuring process prior to function, the dynamics of folding or the ...
... secondary and tertiary protein structure prediction; quantitative structure activity relationships; bioinformatics. *BTEC 5P22 ... Focus on protein and lipid dynamics, protein and lipid interactions, protein conformational changes associated with enzymatic ... Structure and dynamics of macromolecules Physical and theoretical approaches to understanding structure and function of ... enzyme/protein structure and function, in addition to cellular and molecular biology. Research areas in the Chemical ...
Highly similar tertiary structures have been previously reported for the related proteins neocarzinostatin, macromomycin, and ... Chemistry and Structure Elucidation of the Kedarcidin Chromophore. Leet, J.E., Schroeder, D.R., Langley, D.R.,& ... a preliminary model of apokedarcidin built using the program CONGEN starting from the X-ray structure of the homologous protein ... A qualitative analysis of the secondary structure is presented on the basis of 3J alpha NH coupling constants, deviations of ...
... the protein could both keep a stable structure and a good orientation, allowing active sites to be available to other proteins ... orthogonal-bundle proteins, same analysis is performed for proteins from other structure motifs. Besides the study in these ... The results showed that protein stabilities and structures are dependent on the types of surfaces and their different ... The result showed that by tethering a protein on a surface, the melting temperature of a part of the protein changed, which ...
Here we report the crystal structure of the antagonist Noggin bound to BMP-7, which shows that Noggin inhibits BMP signalling ... So far, the three-dimensional structures of BMP antagonists and the structural basis for inactivation have remained unknown. ... The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as ... Russell, R. B. & Barton, G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and ...
mechanisms of protein synthesis;. *primary, secondary, tertiary and quaternary structure of proteins; ... You will study protein structure, enzyme kinetics and basic metabolism; understanding how each of these processes function and ... This module aims to teach you core concepts in biochemistry including topics on structure of proteins, enzyme kinetics and ... 2. Recall the range and structures of biological molecules. *3. Summarise the relationship between chemical structure and ...
Those are sequence identity but several tertiary structures. The domains are Single domain protein with poorly integrated ... Looks like it is fair to cancel these two proteins for server prediction.. Another paper about these two proteins has been ...
... is the physical process by which a polypeptide folds into its characteristic three-dimensional structure.[1] ... Computational prediction of protein tertiary structure De novo or ab initio techniques for computational protein structure ... Proteins. Protein biosynthesis - Posttranslational modification - Protein folding - Protein structure - Protein structural ... Protein methods - Proteasome List of types of proteins - List of proteins - Membrane protein - Globular protein - Fibrous ...
All these processes involve the participation of cellular proteins, mitochondrial proteins, and virus specific proteins. This ... Others modulate the permeability transition pore and either prevent or induce the release of the apoptotic proteins from the ... hijack the host mitochondrial proteins to function fully inside the host cell. ... Some viruses encode the Bcl2 homologues to counter the proapoptotic functions of the cellular and mitochondrial proteins. ...
Protein Structure, Tertiary Substances * Actins * Adenosine Triphosphatases * Myosins Grant support * R01 GM032443/GM/NIGMS NIH ...
"Protein Structure, Tertiary" "Histidine" Françoise Vilaine Journal articles1 document. * Julie Beneteau, Denis Renard, Laurent ... Affinity Binding Sites Molecular Sequence Data Arabidopsis Proteins Polysaccharides Animals Plant Lectins Protein Binding ... Oligopeptides Acetylglucosamine Protein Biosynthesis Aphids Arabidopsis Histidine Plant Exudates Amino Acid Sequence ...
Is there anyone else who doesnt believe sodium chloride can alter the tertiary structure of a protein in a aqueous medium? ... MJD: "Is there anyone else who doesnt believe sodium chloride can alter the tertiary structure of a protein in a aqueous ... All food protein contaminated vaccines AND all vaccines that contain bacterial proteins that can cross react with food proteins ... vinu @79: " all vaccines that contain bacterial proteins that can cross react with food proteins". If bacterial proteins can ...
... modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res., 2014, 42(W1), W252-8. [ ... I. Structure of Davicratinic Acid A and Effects of Davidia Tannins on Drug-Resistant Bacteria and Human Oral Squamous Cell ... Santiago, C.; Pang, E.L.; Lim, K.H.; Loh, H.S.; Ting, K.N. Inhibition of penicillin-binding protein 2a (PBP2a) in methicillin ... Yuan, B.; Cheng, A.; Wang, M. Polysaccharide export outer membrane proteins in Gram-negative bacteria. Future Microbiol., 2013 ...
Computational modeling suggests that A578S should considerably affect the tertiary structure of the K13 protein, thereby ... Results were aligned to reference PF3D7 kelch protein, putative (PF13_0238) mRNA, complete coding sequence (National Center for ... Slow-clearing parasites also exhibited decreased expression of proteins involved in DNA replication and decelerated development ... Various single amino acid substitutions in the K13 protein are associated with a mean increase of 116% in the parasite ...
  • 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). (
  • The quaternary structure of the insulin hormone. (
  • When more than one polypeptide chain join forces for a common cause, quaternary structure is born. (
  • The classic examples of proteins with quaternary structure are haemoglobin, collagen and insulin. (
  • The haem groups in the quaternary structure of the haemoglobin molecule combine with oxygen to form oxyhaemoglobin. (
  • Formation of quaternary structure usually involves the "assembly" or "coassembly" of subunits that have already folded. (
  • Protein synthesis, folding, and tertiary and quaternary structure ultimately determine much of the body's structure and function. (
  • Secondary, tertiary and quaternary structure is often collectively termed as the higher order structure (HOS) of a protein. (
  • Arrangement of the multiple polypeptides in space results the quaternary structure of a protein. (
  • By analyzing 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. (
  • structure and bonding in organic molecules. (
  • The most important of them are the porins, which freely allow the transport (export and import) of the molecules (proteins, ions, nutrients, and ATP) less than 10 kDa across the membranes. (
  • Most folded proteins have a hydrophobic core in which side chain packing stabilizes the folded state, and charged or polar side chains on the solvent-exposed surface where they interact with surrounding water molecules. (
  • For the most part, scientists have been able to study many identical molecules folding together en masse . (
  • The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. (
  • Several amino acids are linked together to form a peptide by peptide bonds, while several peptides are linked together to form protein molecules. (
  • Class I and class II molecules allow antigen presentation to the specific T-cell receptor via a specific structural groove in its tertiary structure. (
  • Class III MHC molecules include several proteins with other immune functions, such as cytokines, heat shock proteins, and parts of complement system. (
  • Parallel ant colony optimization algorithm for solving protein tertiary structure prediction problem given its amino acid sequence is introduced. (
  • To test the expandability of the protein stability prediction pattern derived for mainly-alpha, orthogonal-bundle proteins, same analysis is performed for proteins from other structure motifs. (
  • Looks like it is fair to cancel these two proteins for server prediction. (
  • Using established prediction algorithms, we localized the IDRs in Ca V 3.2 protein and identified several Ca V 3.2iPA candidates that significantly reduced Ca V 3.2 current in HEK293 cells stably expressing human wide-type Ca V 3.2. (
  • I am running structure prediction of a protein whose tertiary structure is unknown. (
  • Some viruses encode the Bcl2 homologues to counter the proapoptotic functions of the cellular and mitochondrial proteins. (
  • Viruses like Herpes simplex virus 1 deplete the host mitochondrial DNA and some, like human immunodeficiency virus, hijack the host mitochondrial proteins to function fully inside the host cell. (
  • All these processes involve the participation of cellular proteins, mitochondrial proteins, and virus specific proteins. (
  • Although the majority of the mitochondrial proteins are encoded by nuclear DNA and imported into the mitochondria (reviewed by [ 21 , 28 - 31 ]), mitochondria synthesize few proteins that are essential for their respiratory function [ 1 , 27 ]. (
  • Genetic variations in multiple parts of the mitochondrial genome may contribute to structural and functional differences in mitochondrial proteins, leading to oxidative stress in cells that then predisposes them to further damage. (
  • Draw the structure of the amino acid alanine. (
  • Two proteins, CifA and CifB, underlie the genetic basis of CI and rescue, but how amino acid sites across these proteins contribute to CI and/or rescue remain unknown. (
  • Structure and dynamics within the unfolding process and for the unfolded protein are influenced by geometrical restrictions as remaining disulfide bonds (see animation of unfolded Ribonuclease A with 4 disulfide bonds), by charges on the amino acid strand or by stiffer regions with e.g. a preserved secondary structure. (
  • Proteins destined to mitochondria have either internally localized [ 28 ] or amino terminal localized [ 21 ] presequences known as mitochondria/matrix localization signals (MLS), which can be 10-80 amino acid long with predominantly positively charged amino acids. (
  • The amino-acid sequence (or primary structure ) of a protein predisposes it towards its native conformation or conformations. (
  • Various single amino acid substitutions in the K13 protein are associated with a mean increase of 116% in the parasite clearance half-life (t 1/2 ) ( 4 ). (
  • Read Online Amino Acid Metabolism Mcqs And Answers Multiple Choice Questions- Amino acid and protein chemistry 1-A mutation has changed an isoleucine residue of a protein to Glutamic acid, which statement best describes its location in a endobj Biology MCQs for Class 12 Chapter Wise with Answers PDF Download was Prepared Based on Latest Exam Pattern. (
  • During the development of proteins for use as biologics, the primary structure (amino acid sequence) is important in defining protein activity. (
  • Particular gene sequence is used to determine the amino acid sequence in both peptides and proteins. (
  • The sequence of amino acid determines the major characteristics of a protein, while this amino acid sequence is defined by the particular gene sequence. (
  • The primary structure is the amino acid sequence of a protein. (
  • Although they have 20 to 70% amino acid sequence identity, these proteins share a conserved tertiary structure comprised of ten beta sheets and two alpha helixes. (
  • Although the tertiary structures of Protein A and Protein G are very similar, their amino acid compositions differ significantly, resulting in different binding characteristics. (
  • Small peptides, especially those derived from natural proteins as inhibitory peptide aptamers (iPAs), can produce highly effective and selective blockade of specific nociceptive molecular pathways to reduce pain with minimal off-target effects. (
  • By contrast, peptides contain a low degree of tertiary structure. (
  • For this reason, peptides tolerate a much wider range of conditions than proteins. (
  • This basic difference in native structures is also reflected in that proteins are not easily renatured, while peptides often renature spontaneously. (
  • Amino acids, peptides, and proteins are often referred to as related terms, yet they are different in their characteristics. (
  • Amino acids are the building blocks of both peptides and proteins. (
  • Peptides are short linear chains of amino acids, whereas proteins are very long chains of amino acids. (
  • In contrast, peptides are not organized in a stable three-dimensional structure. (
  • Unlike peptides, proteins are considered as macromolecules. (
  • All the peptides exist as linear chains while proteins can exist as primary, secondary, tertiary, and quaternary. (
  • One reason for falling hair, brittle hair or unmanageable hair is poor protein metabolism. (
  • Problems of protein metabolism often result in weak or brittle nails. (
  • This thesis focuses primarily on mitochondrial uncoupling protein 2 (UCP2) for which we proposed a tertiary structure, and whose main role is control of the oxidative stress in the body. (
  • Physiologically, any bleaching therapy has the ability to increase free radical levels in the pulp-dentin complex, which may induce oxidative stress in odontoblasts and tertiary dentin formation. (
  • Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure . (
  • [1] Each protein begins as a polypeptide , translated from a sequence of mRNA as a linear chain of amino acids. (
  • This polypeptide lacks any developed three-dimensional structure (the left hand side of the neighboring figure). (
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein). (
  • The polypeptide chains are folded into complicated three-dimensional (3D) structures. (
  • A deficiency of this enzyme causes inadequate synthesis of essential proteins in the body, which can detrimentally affect hair and nails. (
  • [7] A well studied example is the bacterial GroEL system, which assists in the folding of globular proteins . (
  • structural proteins must be shaped to maximise mechanical strength. (
  • So far, the three-dimensional structures of BMP antagonists and the structural basis for inactivation have remained unknown. (
  • Over 70,000 X-ray and NMR structures are now available in protein structural repositories and no physico-chemical solution is in sight. (
  • Recent reports of the crystal structure of the glycoprotein hormone human chorionic gonadotrophin show that cystine knots are proving to be versatile structural motifs that enable the construction of a variety of proteins with different functional properties. (
  • This extra level of organization increases the variety of structures built around this simple structural motif. (
  • Because the surfaces used for dimer formation are mostly hydrophobic, the uniqueness of each dimer accounts for the lack of sequence homology and raises questions about the effectiveness of reverse sequence fitting in this kind of structure as a predictor of structural homology. (
  • Both spectral and thermotropic data indicate that, in terms of structural hierarchy, these proteins can be divided into two distinct groups, gamma II and gamma IIIB belonging to one and gamma IIIA and gamma IVA to the other. (
  • The regular alpha helix and beta sheet structures fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling . (
  • Proteins generally contain a high degree of tertiary structure, kept together by van der Waals' forces, ionic and hydrophobic interactions, and hydrogen bonding. (
  • Their native state is dominated by secondary structures, stabilized mainly by hydrogen bonding. (
  • The most common types of secondary structures are the α helix and the β pleated sheet, held in place by hydrogen bonds. (
  • The secondary structure is produced by forming hydrogen bonds between two nearby amino acids, thus resulting structures called β-plated sheets, and coils called α-helices. (
  • It likely that one of the causes of these adverse effects are the free oxygen radicals released during the reaction, which do not act in a specific way and may act on the organic matrix of dental structures 13 , breaking up the lipids and proteins of dental tissues 14 . (
  • They knew their physical chemistry, and knew that a protein wasn't going to be important because you couldn't get enough of it into solution to lower the colligative freezing point. (
  • Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes. (
  • Length of a peptide is less than approximately 100 amino acids, while that of a protein is more than 100 amino acids. (
  • Proteins are the most diverse group of biological macromolecules. (
  • In the end, whole results indicated the biological function of the target protein to be an acetyltransfarase. (
  • Fatty acid-binding proteins (FABPs) are a family of fatty acid-binding small proteins essential for lipid trafficking, energy storage and gene regulation. (
  • Here we show tertiary structures of SPH1118 with six different conformations as determined by X-ray crystallography. (
  • Bacteriorhodopsin is an example, the detailed structure of which has been determined by crystallography . (
  • Basidiocarps of A. hygrometricus are rich in proteins, carbohydrates, minerals, crude fibre and essential amino acids with lower concentration of fat. (
  • 4 Edible mushrooms are low calorie-low fat food supplement with generous amount of proteins, carbohydrates, vitamins, minerals amino acids 5 and dietary fibre. (
  • In eukaryotic organisms chaperones are known as heat shock proteins . (
  • The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as diverse as establishment of the embryonic dorsal-ventral axis, induction of neural tissue, formation of joints in the skeletal system and neurogenesis in the adult brain. (
  • Hogan, B. L. Bone morphogenetic proteins: multifunctional regulators of vertebrate development. (
  • So we're going to go through its inflammatory modulating effects of what's called BMPs, which I'm going to refer to pretty frequently throughout the presentation, that's called bone morphogenetic proteins. (
  • So the complex itself is composed of what's called bone morphogenetic proteins. (
  • A protein is composed of one or more long unbranched chains called polypeptides and yet the building blocks of proteins are amino acids. (
  • Availability of the complete genomes of 34 invertebrates, together with transcriptomes and ESTs, allowed us to systematically investigate the gene structure and alternative splicing of FABP genes over a wide range of phyla. (
  • The genomic loci for FABP genes were diverse and their genomic structure varied. (
  • Although, providing the massive amount of data by recent genome sequencing projects but many of these genomes are still not fully annotated as well as consist of genes/proteins with unknown function and structure. (
  • This group of genes code for proteins found on the surfaces of cells that help the immune system recognize foreign substances. (
  • Here we report the crystal structure of the antagonist Noggin bound to BMP-7, which shows that Noggin inhibits BMP signalling by blocking the molecular interfaces of the binding epitopes for both type I and type II receptors. (
  • Protein folding, considered to be the holy grail of molecular biology, remains intractable even after six decades since the report of the first crystal structure. (
  • Molecular simulation methodologies have evolved to a stage to provide a computational solution to the tertiary structures of small proteins. (
  • The 2.57-Å structure reveals fine details for each molecular component within the Csy complex as well as the direct and water-mediated interactions between proteins and CRISPR RNA (crRNA). (
  • We have already discovered that the primary structure of a protein is the sequence of amino acids, determined by information encoded in DNA. (
  • When the chain pleats, the structure is called a beta-pleated sheet .The amount of coiling or pleating depends on the primary structure (sequence of amino acids. (
  • primary structure, in turn determined by DNA sequences) is vital to its function - but this shape can be distorted. (
  • The primary sequence of a protein defines its structure and function. (
  • HOS characterization is a critical component of biologics development and should be performed alongside functional analysis and primary structure characterization to allow a full understanding of the overall protein structure. (
  • The tertiary protein structure is generally conserved over longer time periods than the primary one. (
  • Sequence similarity was brought in through Protein Data Bank and non-redundant database using BLASTp program of NCBI and a search for templates revealed that yjaB shares 97% homology to a protein of Escherichia coli, indicating this protein is evolutionary conserved and was found with acetyltransfarase. (
  • Mitochondria contain a single 16 kb circular DNA genome, which codes for 13 proteins (mostly subunits of respiratory chains I, II, IV, and V), 22 mitochondrial tRNAs and 2 rRNAs [ 25 , 26 ]. (
  • The tertiary structure of a protein is stabilized by hydrophobic interactions, electrostatic forces (salt bridges), and disulfide links. (
  • Hydrophobic and Hydrophilic interactions - in the water based environment of the cell, the protein will fold so that water is excluded from hydrophobic regions (e.g. in the centre of the structure), with hydrophilic regions facing outwards in contact with water. (
  • At which level of protein structure are interactions between R groups most important? (
  • These findings suggest that electrostatic CL/cyt c interactions are central to the initiation of the peroxidase activity, while hydrophobic interactions are involved when cyt c's tertiary structure is lost. (
  • Understanding protein-surface interactions is key to improving the performance of protein microarrays, but current understanding of the behavior of proteins on surfaces is lacking. (
  • For a next-level understanding of protein-surface interactions, a novel coarse-grain surface model was developed, parameterized, and validated according to experimental results from different groups. (
  • Our findings support the convergent consequence of inhibiting degradation of invading DNA by these Acr proteins, albeit with different modes of interactions with the type I-F CRISPR-Cas system. (
  • The intracellular domain communicates via protein-protein interactions against effector proteins , which in turn pass a signal to the destination. (
  • The secondary structures have now folded to occupy a specific 3D space - this is tertiary structure and is vital to the function of the protein. (
  • Three-dimensional structures and the secondary structures were predicted. (
  • Both the position of the inhibitor and the conformational changes of active site residues observed in this structure correspond closely to the predictions from the intermediate modeling. (
  • Here, we use evolution-guided, substitution mutagenesis of conserved amino acids across the Cif proteins, coupled with transgenic expression in uninfected Drosophila melanogaster , to determine the functional impacts of conserved residues evolving mostly under purifying selection. (
  • Protein folding may involve covalent bonding in the form of disulfide bridges formed between two cysteine residues or the formation of metal clusters. (
  • A hypothetical protein yjaB of these bacteria, consisting of 147 residues was picked out for in silico analysis. (
  • As the start point of the research, part of this research showed that the stability of five mainly-alpha, orthogonal-bundle proteins tethered to surfaces can be correlated to the shape of the loop region where the tether is placed and the free rotation ability of the part of proteins near surfaces. (
  • The immobilization of myoglobin in sodium alginate films was investigated with the aim of evaluating the protein stability in an ionic polymeric matrix. (
  • Due to the complex nature of protein drugs, it is important to characterize the protein's higher-order structure (HOS) to understand its stability, folding, structure, and functional activity. (
  • Kinases can cause posttranslational modifications of the progesterone receptor (PR) to influence cellular localization and protein stability. (
  • These interact with each other and their surroundings in the cell to produce a well-defined, three dimensional shape, the folded protein (the right hand side of the figure), known as the native state . (
  • The resulting three-dimensional structure is determined by the sequence of the amino acids. (
  • Experimentally determining the three dimensional structure of a protein is often very difficult and expensive. (
  • For many proteins the correct three dimensional structure is essential to function. (
  • Protein higher order structure (HOS) include the three-dimensional structures that are necessary for structure and function. (
  • The three-dimensional shape of a protein. (
  • Usually proteins have stable three dimensional structures. (
  • The regions of secondary structure are then folded further in space to form the final three dimensional structures of the protein. (
  • But, if the three-dimensional structure is yet undiscovered, then they can be classified based on experimentally verifiable membrane topology . (
  • Often folding involves first the establishment of regular secondary and supersecondary structures, particularly alpha helices and beta sheets , and afterwards tertiary structure . (
  • In the majority of receptors with known structures, transmembrane alpha helices constitute most of the transmembrane component. (
  • This structure is extremely important - in the case of enzymes, any change to the shape of the molecule will deactivate the enzyme. (
  • Heating a protein increases the kinetic energy in the molecule (scientific term for movement energy). (
  • This structure also identifies a water molecule that is located in the appropriate position to attack the re face of P-enolpyruvate during the course of the reaction, allowing the catalytic mechanism for this enzyme to be clearly defined. (
  • One of the following is optically found in protein molecule? (
  • These subjects are dealt with in general terms in the Strategies for Protein Purification Handbook and more specifically according to target molecule in the handbooks Affinity Chromatography, Vol. 1: Antibodies, 18103746 and Vol. 2: Tagged Proteins, 18114275 available from Cytiva. (
  • This protein circulates in the bloodstream in an inactive form, bound to another molecule called von Willebrand factor, until an injury that damages blood vessels occurs. (
  • The Protein G molecule contains two binding domains. (
  • SGS combines biophysical techniques with more sensitive orthogonal approaches to provide you with a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation. (
  • 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. (
  • Therefore scientists have tried to use different biophysical techniques to manually fold a protein. (
  • Mononuclear cells were analyzed by immunoprecipitation or by flow-cytometric analysis, following incubation with a conformation-specific p53 antibody, which discriminates unfolded p53 tertiary structure. (
  • The IL-6 conformation of these deletion-carrying proteins has been studied by immunoprecipitation with two kinds of monoclonal antibodies (mAb's): mAb's that show preference towards denatured hIL-6, or conformation-specific mAb's. (
  • Proteins delta 21-51 and delta 127-174 have kept a part of the IL-6 tertiary structure since they are still recognized by some conformation-specific mAb's. (
  • These proteins can only function when all subunits are present. (
  • Terms for developmental and adult lung structures, tissues, and cells were included, providing comprehensive ontologies for application at varying levels of resolution. (
  • As a result, approximately 300 terms for fetal and postnatal lung structures, tissues, and cells were identified for each species. (
  • This module aims to teach you core concepts in biochemistry including topics on structure of proteins, enzyme kinetics and metabolic pathways. (
  • To our knowledge, these are the first ontologies designed to include terminology specific for developmental structures in the lung, as well as to compare common anatomic features and variations between mouse and human lungs. (
  • Recombinant Protein G has been modified to eliminate its binding to albumin. (
  • In biology, identifying the tertiary structure of a protein helps determine its functions. (
  • Heliorhodopsin (HeR) is a seven-helical transmembrane protein with a retinal chromophore that corresponds to a new rhodopsin family. (
  • Majority of proton transfers are mediated by transmembrane protein ADP/ATP translocator (AAC) and via mitochondrial uncoupling proteins 1-5 (UCP1-5). (
  • Transmembrane receptors are typically classified based on their tertiary structure . (
  • [2] [3] Many membrane receptors include transmembrane proteins . (
  • Like any integral membrane protein, a transmembrane receptor may be divided into three domains. (
  • In certain receptors, such as the nicotinic acetylcholine receptor , the transmembrane domain forms a protein pore through the membrane, or around the ion channel . (
  • Prior to ligand binding, the extracellular protein loses flexibility while the intracellular portion gains it. (
  • POROS™ MabCapture™ G Select Resin is a high-throughput, lower-priced Protein G chromatography resin manufactured using our own Protein G ligand to enable high-throughput purification performance. (
  • Subcellular localization predictions shows it is a cytoplasmic protein. (
  • Furthermore, though less routine, the role of LC-MS in product characterization and structure elucidation of "unknowns" in both pharmaceutical and biopharmaceutical analysis is indispensable. (
  • While each protein is predicted to harbor three functional domains, there is no knowledge on how sites across these Cif domains, rather than in any one particular domain, contribute to CI and rescue. (
  • Whether sustained normocortisolism induced by medical therapy induces re-expression of functional sst 2 protein in corticotroph adenomas and whether this increases the ACTH-lowering potency of octreotide remains to be established. (
  • For these reason, otolaryngologists who undertake functional endoscopic sinus surgery almost routinely obtain a CT scan before undertaking surgery in order to evaluate the exact bony structures and the mucous membranes of patients. (
  • These proteins have very little sequence homology, but they all have an unusual arrangement of six cysteines linked to form a 'cystine-knot' conformation. (
  • We discuss how these findings advance an expanded view of Cif protein evolution and function, inform the mechanistic and biochemical bases of Cif-induced CI/rescue, and continue to substantiate the Two-by-One genetic model of CI. (
  • This class challenges the traditional structure-function paradigm. (
  • Knowledge on dynamics is important to understand the structuring process prior to function, the dynamics of folding or the function as an unstructured protein itself. (
  • An ensemble of 15 apokedarcidin solution structures has been generated by variable target function minimization (DIANA program) and refined by simulated annealing (X-PLOR program). (
  • The function of proteins depends on its native tertiary structure. (
  • In order to clarify their function mechanism and regulate their function, we perform the structure determination of proteins and thermodynamic analysis. (
  • The purpose of this exercise is to guide you through the process of finding information and making predictions about the structure and function of a protein given a gene for it. (
  • Antifreeze proteins are of such potential commercial interest because they function quite differently to the typical antifreeze currently used to protect car engines, for example. (
  • Structure and function of the factor VIII gene and protein. (
  • Many bioinformatic tools were used to predict the 3D structure and function of this protein. (
  • Bioinformatics approach is an alternative to laboratory-based methods that makes of algorithms and databases to predict protein function. (
  • Researchers are using this special light to study the structure and function of energy and quantum materials. (
  • Besides the study in these small two-state proteins, a further analysis of surface-induced change of folding mechanism is also studied with a multi-state lysozyme protein 7LZM. (
  • Besides the change of folding mechanism, by tethering the lysozyme protein to a certain site, the protein could both keep a stable structure and a good orientation, allowing active sites to be available to other proteins in bulk solution. (
  • [2] The mechanism of protein folding is not completely understood. (
  • Basidiocarp of this macrofungi contains considerable amount of carbohydrate, protein, fibre, minerals, vitamins, essential amino acids and very minute concentration of fat. (
  • Für AROS konnte gezeigt werden, dass der mittlere Bereich des Proteins für die Inhibition verantwortlich ist. (
  • Inhibition of AKT or MEK1/2 increased total and nuclear PR protein in OSIS. (
  • Find out a qualitative test for proteins, fats and oils, and starch amino acids and test any fruit juice, saliva, sweat, and urine for them. (
  • Breast milk is a complete food that contains vitamins, minerals, fats, sugars, and proteins, and it is recommended for the proper nutrition of newborns. (
  • All those deletion-carrying hIL-6 (delta hIL-6) proteins were then produced in Xenopus laevis oocytes and examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). (
  • Pyrrolidine dithiocarbamate is a potent antioxidant against hypochlorous acid-induced protein damage. (
  • One extensively studied species is an Alaskan beetle, Dendroides canadensis , which produces one of the most potent antifreeze proteins known. (
  • Information on sleep duration was obtained through a structured questionnaire interview. (
  • All of these delta hIL-6 proteins were inactive in the IL-6 hybridoma growth factor (HGF) assay and unable to inhibit the HGF activity of the recombinant human wild-type IL-6 (wt hIL-6). (