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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence. The secondary structure of proteins is determined by the pattern of hydrogen bonding. A large number of servers and tools are used to predict the secondary structure analysis.. Protein secondary structure refers to the local conformation proteins polypeptide backbone. There are two regular secondary structure states, α-helix (H) and β-strand (E), and one irregular secondary structure type, the coil region (C). Sander developed a secondary structure assignment method Dictionary of Secondary Structure of Proteins (DSSP)3, which automatically assigns secondary structure into eight states (H, E, B, T, S, L, G, and I) according to hydrogen-bonding patterns. These eight states are often further simplified into three states of helix, sheet and coil. The most widely used convention is that helix is designated as G, ...
Earlier chapters introduced alpha-helices and beta-sheets ( Secondary Structure), and some common motifs composed of 2 or 3 of these elements (Supersecondary Structure). Tertiary structure describes the folding of the polypeptide chain to orientate the different secondary structure elements in a particular arrangement. The previous chapter offered a description of certain types of domains, such as globular, membrane-spanning, and fibrous. As helices and sheets are units of secondary structure, so the domain is the unit of tertiary structure. In multi-domain proteins, tertiary structure includes the arrangement of domains relative to each other as well as that of the chain within each domain. There is a blurred distinction between supersecondary structure and tertiary structure. The introduction of the term supersecondary structure was necessary when it became clear that certain arrangements of two or three secondary structures are present in many different protein structures, even with ...
This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure types are considered, including
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
A powerful tool used to monitor secondary structure is circular dichroism (CD), which is the differential absorbance of left and right circularly polarized light. Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the proteins secondary structure. This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software.. Protein secondary structure can also be used to monitor protein folding and unfolding. An equilibrium study consists of collection of CD spectra as a function of increasing temperature or chemical denaturant. As the protein unfolds, the CD spectrum reflects this. Fitting data at a single wavelength or the full spectral scans during this denaturation process provides thermodynamic information such as the melting temperature ...
Activation helix orientation of estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations
Quanta will calculate hydrogen bonds and then analyze the secondary structure in its Protein Design Module, but it seems like a rather large investment if all you want to do is determine the secondary structure......... ........Tom Branham ...
Diatoms and sponges use proteins, long chain polyamines, and other biomolecules to assemble silica structures of controlled morphology. Investigated here are biosilicification peptides. Under mild conditions, these peptides produce silica nanoparticles from solutions of silicic acid, whereas harsh methods are currently employed to produce these nanoparticles commercially. Biomimetic precipitation studies have shown that LKα14 (Ac-LKKLLKLLKKLLKL- C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, co-precipitates with silica to form nanospheres. Previous work con- firmed the α-helical secondary structure in both the neat and silica-complexed states of the peptide and suggested that the tetrameric bundles of peptide that are known to form in solution persisted in the silica-complexed form. To further investigate the peptide aggregation, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how the ...
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Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between alpha-helix length and alpha-helix stability, which would be impossible to probe with alpha-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel beta-sheet stability. alpha-Helices become more stable as they grow longer. Our data show that a two-stranded beta-sheet (beta-hairpin) becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further beta-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be
The following is a list of how-to and tutorial content that matched your search term. ProgrammableWebs how-to content comes from two sources; full-blown tutorials that we publish ourselves and other highly relevant tutorials that we find elsewhere on the Web. This list represents on combination of both tutorial types and if you go to ProgrammableWebs API University, youll not only be able to find more, they are organized based on your role (API providers or developers who consumes APIs). If you know of a tutorial that would be of interest to the ProgrammableWeb community, wed like to know about it. Be sure to check our guidelines for making contributions to ProgrammableWeb ...
article{1e7da19b-137f-4fcf-9f74-7f6d6b4d2ece, abstract = {The loop region of chymotrypsin inhibitor 2 from barley has been employed as a scaffold for testing the intrinsic propensity of a peptide fragment to form a secondary structure. The helix formation of the nine amino acid residue segment Lys-Gln- Ala-Val- Asp- Asn- Ala-Tyr-Ala of helix E from subtilisin Carlsberg has been studied by the construction of a hybrid consisting of chymotrypsin inhibitor 2 (CI2) where part of the active loop has been replaced by the nonapeptide. An expression system for a truncated form of C12 where the 19 structureless residues of the N-terminus have been removed and Leu20 replaced,br/,,br, by methionyl was constructed from the entire 83-residue wild-type C12 gene by polymerase chain reaction,br/,,br, methodology. The gene encoding the hybrid was constructed from the truncated inhibitor gene. The stability of the truncated inhibitor and of the hybrid toward guanidinium chloride denaturation was examined. From ...
jay ananth wrote: , I need one help from u... , , search for best tools for the following : , 1.Secondary Structure prediction in RNA , 2.Protein Secondary Structure Prediction. , 3.Prediction of disordered regions in proteins.. , 4.Case Std on Structure-function relationships in proteins , 5.Prediction of transmembrane regions in proteins , 6.Characterization of antigenecity in polypeptides- epitope mapping , , , , Are you looking for computational tools to do the above ? Can you be more specific ? Autodock, Gromacs are some of the tools that you can use for protein structure prediction. -- Deepan ...
In recent years, the nuclear receptors (NR) dynamics have been studied extensively by various approaches. However, the transition path of helix 12 (H12) to an agonist or an antagonist conformation and the exchange pathway between these states is not clear yet. A number of accelerated molecular dynamics (aMD)
Motivation: Transmembrane beta-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few beta-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful. Results: Here, we present tobmodel; a method for generating 3D models of beta-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the beta-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average ...
The DSSP program works by calculating the most likely secondary structure assignment given the 3D structure of a protein. It does this by reading the position of the atoms in a protein (the ATOM records in a PDB file) followed by calculation of the H-bond energy between all atoms. The best two H-bonds for each atom are then used to determine the most likely class of secondary structure for each residue in the protein.. This means you do need to have a full and valid 3D structure for a protein to be able to calculate the secondary structure. Theres no magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you dont have the 3D structure ...
Many proteins are organized into several units. A structural domain is an element of the proteins overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the calcium-binding domain of calmodulin. Because they are self-stabilizing, domains can be swapped by genetic engineering between one protein and another to make chimeras. A motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). These elements are often called supersecondary structures. Fold refers to a global type of arrangement, like helix-bundle or beta-barrel. Structure motifs usually consist of just a few elements, e.g. the helix-turn-helix has just ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
This study demonstrates the feasibility of creating structurally complex and catalytically active enzymes by assembling randomized modules that are constructed from a limited set of building blocks and biased toward helical secondary structure by binary patterning. The binary distribution of hydrophilic/hydrophobic residues is inherent in the genetic code (NAN/NTN), and our results support suggestions (9, 26, 27) that modern enzymes could have evolved from primitive precursors constructed from a relatively small number of polar and nonpolar amino acids. There is, nevertheless, a low probability of finding catalysts, even when both position and identity of all critical active site residues are determined in advance. This finding contrasts with the ease of obtaining folded helical proteins through binary patterning (9), underscoring the exacting demands that catalysis places on protein design.. Extrapolating from our data and from modest sequence constraints on interhelical turns (23, 28-30), we ...
Beta sheets parallel, In parallel beta sheets, the adjacent polypeptide chains run in the same direction. Typically parallel beta sheets are large structures that usually consist of at least five strands. Parallel beta sheets usually have hydrophobic residues on both sides of the sheet.
C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Lecture 14 Secondary Structure Prediction. Bioinformatics Center IBIVU. Protein structure . Linus Pauling (1951). Slideshow 80412 by LeeJohn
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure ...
Lee, C., L. Kalmar, B. Xue, P. Tompa, G. W. Daughdrill, V. N. Uversky, and K-H. Han, Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins., Biochim Biophys Acta, vol. 1840, issue 3, pp. 993-1003, 2014 Mar. ...
Secondary structure of proteins refers to local and repetitive conformations, such as α‐helices and β‐strands, which occur in protein structures
Synonyms for alpha-helix, alpha-helix in Free Thesaurus. Antonyms for alpha-helix, alpha-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for alpha-helix, alpha-helix?
View Notes - Bio 1A Lect 2 Quiz from BIO 1A at Berkeley. Bio 1A Lect 2 Quiz 50% adenine aldose alpha alpha-helix amino Amino acids antiparallel beta beta-pleated sheets blood flow carbonyl cell
Its not true that the Ramachandran plot will determine the secondary structure of an amino acid. Ramachandran plots show the sterically allowed phi/psi angles of an amino acid. As such nearly all non-glycine amino acids are in alpha/beta spaces. Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense ...
As evidenced by a buried core of hydrophobic residues within globular proteins, hydrophobicity provides essential insights into the folding structure of pr
6. Helix Propensities of Amino Acid Residues via Thioester Exchange. Fisher, B. F.; Hong, S.H.; Gellman, S.H. J. Am. Chem. Soc. DOI: 10.1021/jacs.7b07930. 5. Detection and analysis of chimeric tertiary structures by backbone thioester exchange: Packing of an alpha helix against an alpha/beta-peptide helix, Price, J. L.;Hadley,E. B.;Steinkruger,J. D. and Gellman,S. H., Angew.Chem.Int.Ed Engl., 2010, 49, 368-371.. 4. Preferred Side-chain Constellations at Antiparallel Coiled-coil Interfaces, E. B. Hadley, O. D. Testa, D. N. Woolfson and S. H. Gellman Proc. Natl. Acad. Sci. USA 2008, 105, 530.. 3. An Antiparallel α-Helical Coiled-Coil Model System for Rapid Assessment of Side Chain Recognition at the Hydrophobic Interface, E. B. Hadley an d S. H. Gellman J. Am. Chem. Soc. 2006, 128, 16444.. 2. Thermodynamic Analysis of β-Sheet Secondary Structure Via Backbone Thioester Exchange, E. B. Hadley, A. M. Witek, F. Friere, A. J. Peoples and S. H. Gellman Angew. Chem. Int. Ed. 2007, 46, ...
Two hypotheses have been proposed for the role of turns in protein folding. In one view, turns play a critical role in folding by bringing together and fostering interactions between regular secondary structure elements. This view is supported by mutagenesis studies indicating a critical role for particular residues in the turns of some proteins. Also, nonnative isomers of X-Pro peptide bonds in turns can completely block the conformational folding of some proteins. In the opposing view, turns play a passive role in folding. This view is supported by the poor amino-acid conservation observed in most turns. Also, non-native isomers of many X-Pro peptide bonds in turns have little or no effect on folding. ...
Lyu, P C; Wemmer, D E; Zhou, H X et al. (1993) Capping interactions in isolated alpha helices: position-dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry 32:421-5 ...
On Sun, 13 May 2007, Rolf Kalbermatter wrote: , Changelog , include/winsvc.h , Fix names of structure elements to match PSDK [...] , diff --git a/include/winsvc.h b/include/winsvc.h , index 7a29e8f..af56d29 100644 , --- a/include/winsvc.h , +++ b/include/winsvc.h , @@ -196,13 +196,13 @@ DECL_WINELIB_TYPE_AW(LPENUM_SERVICE_STATUS) , typedef struct _ENUM_SERVICE_STATUS_PROCESSA { , LPSTR lpServiceName; , LPSTR lpDisplayName; , - SERVICE_STATUS_PROCESS ServiceStatusProcess; , + SERVICE_STATUS_PROCESS ServiceStatus; , } ENUM_SERVICE_STATUS_PROCESSA, *LPENUM_SERVICE_STATUS_PROCESSA; [..] This patch is wrong. This field is really called ServiceStatusProcess in the PSDK. -- Francois Gouget ,fgouget at, You can have my guns when you pry them from my kids cold, dead hands ...
Scientists have identified where a four-stranded version of DNA exists within the genome of human cells, and suggest that it may hold a key to developing new, targeted therapies for cancer.
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for alpha-helix). {{ pdb }} {{ chain }} ...
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for alpha-helix). {{ pdb }} {{ chain }} ...
The amino-terminal extremity of the human immunodeficiency virus type 1 transmembrane protein (gp41) is thought to play a pivotal role in the fusion of virus membranes with the plasma membrane of the target cell and in syncytium formation. Peptides with sequences taken from the human immunodeficiency virus type 1 gp41 fusogenic (synthetic peptides SPwt and SP-2) and nonfusogenic (SP-3 and SP-4) glycoproteins adopt mainly a beta-sheet conformation in the absence of lipid, as determined by attenuated total reflection Fourier transform infrared spectroscopy, and after interaction with large unilamellar liposomes, the beta-sheet is partly converted into an alpha-helical conformation. Peptides SPwt and SP-2 but not SP-3 or SP-4 were able to promote lipid mixing as assessed by fluorescence energy transfer assay and dye leakage in a vesicle leakage assay. By using polarized attenuated total reflection Fourier transform infrared spectroscopy, SPwt and SP-2 were found to adopt an oblique orientation in ...
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome. We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3
in Journal of Protein Chemistry (1994), 13(1), 77-88. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 ... [more ▼]. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 peptide-lipid complexes was evaluated by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Those peptides belonging to the hydrophobic core domain of apo B-100 when associated with phospholipids were rich in beta sheet structure; a predominant alpha helical conformation was shown to be associated with one peptide located in a surface region of apo B-100. IR dichroic spectra revealed, in the case of the core peptides, that the beta sheet component is the only oriented structure with respect to the ...
In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible.. ...
In this study, hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used to classify blends produced from diesel S500 and different kinds of biodiesel produced by the TDSP methodology. The different kinds of biodiesel studied in this work were produced from three raw materials: soybean oil, waste cooking oil and hydrogenated vegetable oil. Methylic and ethylic routes were employed for the production of biodiesel. HCA and PCA were performed on the data from attenuated total reflectance Fourier transform infrared spectroscopy, showing the separation of the blends into groups according to biodiesel content present in the blends and to the kind of biodiesel used to form the mixtures ...
LmrP is an electrogenic H(+)/drug antiporter that extrudes a broad spectrum of antibiotics. Five carboxylic residues are implicated in drug binding (Asp142 and Glu327) and proton motive force-mediated restructuring (Asp68, Asp128 and Asp235). ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) and tryptophan quenching experiments revealed that phosphatidylethanolamine (PE) is required to generate the structural intermediates induced by ionization of carboxylic residues. Surprisingly, no ionization-induced conformational changes were detectable in the absence of PE, suggesting either that carboxylic acid residues do not ionize or that ionization does not lead to any conformational change. The mean pKa of carboxylic residues evaluated by ATR-FTIR spectroscopy was 6.5 for LmrP reconstituted in PE liposomes, whereas the pKa calculated in the absence of PE was 4.6. Considering that 16 of the 19 carboxylic residues are located in the extramembrane loops, the pKa values obtained in the ...
TY - JOUR. T1 - Proton nuclear magnetic resonance assignments and secondary structure determination of the Co1E1 rop (rom) protein. AU - Eberle, W.. AU - Klaus, W.. AU - Cesareni, G.. AU - Sander, C.. AU - Rosch, P.. PY - 1990. Y1 - 1990. N2 - The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy (1H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and 3J(HNα) coupling constants. One 7.2-kDa monomer of the homodimer consists of two antiparallel helices connected by a hairpin loop at residue 31. The C-terminal peptide consisting of amino acids 59-63 shows no stable conformation. The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the X-ray structure.. AB - ...
TY - JOUR. T1 - Salivary molecular spectroscopy. T2 - a sustainable, rapid and non-invasive monitoring tool for diabetes mellitus during insulin treatment. AU - Caixeta, Douglas C.. AU - Aguiar, Emília M. G.. AU - Cardoso-Sousa, Léia. AU - Coelho, Líris M. D.. AU - Oliveira, Stephanie W.. AU - Espindola, Foued S.. AU - Raniero, Leandro. AU - Crosara, Karla T. B.. AU - Baker, Matthew J.. AU - Siqueira, Walter L.. AU - Sabino-Silva, Robinson. PY - 2020/3/17. Y1 - 2020/3/17. N2 - Monitoring of blood glucose is an invasive, painful and costly practice in diabetes. Consequently, the search for a more cost-effective (reagent-free), non-invasive and specific diabetes monitoring method is of great interest. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used in diagnosis of several diseases, however, applications in the monitoring of diabetic treatment are just beginning to emerge. Here, we used ATR-FTIR spectroscopy to evaluate saliva of non-diabetic (ND), ...
Abstract This paper proposes a direct and efficient method to discriminate between counterfeit and authentic Cialis and Viagra samples by combining attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy with multivariate techniques. The chemical profile of 53 commercial samples (Viagra®, Cialis®) and 104 counterfeit samples (Viagra and Cialis) from distinct seizures were obtained from ATR-FTIR…. [...] ...
Looking for online definition of alpha helix conformation in the Medical Dictionary? alpha helix conformation explanation free. What is alpha helix conformation? Meaning of alpha helix conformation medical term. What does alpha helix conformation mean?
Research Corridor has published a new research study titled Circular Dichroism Spectroscopy Market - Growth, Share, Opportunities, Competitive Analysis and Forecast, 2017 - 2025. The Circular Dichroism Spectroscopy Market report studies current as well as future aspects of the Circular Dichroism Spectroscopy Market based upon factors such as market dynamics, key ongoing trends and segmentation analysis. Apart from the above elements, the Circular Dichroism Spectroscopy Market research report provides a 360-degree view of the Lipstick Packing industry with geographic segmentation, statistical forecast and the competitive landscape.. Browse the complete report at Geographically, the Circular Dichroism Spectroscopy Market report comprises dedicated sections centering on the regional market revenue and trends. The Circular Dichroism Spectroscopy Market has been segmented on the basis of geographic regions into North America, ...
Transmembrane helix-helix interactions may have at least two major functions: 1) intramolecular helix-helix interactions would serve to stabilize the tertiary structure of the protein in the membrane bilayer, and 2) helix-helix interactions between two or more integral membrane proteins appear to regulate ligand-initiated response systems. X-Ray crystallography of the α1-subunit of Na/K-ATPase (Figure 6) indicates that 5 of the 10 helices (M4, M5, M6, M7 and M8) lie largely within the core of the α1-subunit, whereas the remaining 5 helices (M1, M2, M3 M9 and M10)) are on the periphery. Computer-generated projections of each helix (Figure 7) indicate that helices within the core are disordered whereas peripheral helices are largely ordered. This suggests that the disordered helices contribute to and/or maintain the tertiary structure of the α1-subunit, whereas the peripheral ordered helices are available for interaction with ordered helices of neighboring integral membrane proteins.. In our ...
The model six-residue linear peptide AAGDYY-NH2 from TEM-1 beta -lactamase inhibitor protein and BLIP was predicted to adopt a beta -turn conformation and synthesized in order to elucidate the mechanism of beta -turn formation and stability. Its structural preferences in solution were comprehensively characterized using CD (circular dichroism), FT-IR and H-1-NMR spectroscopy. The set of observed short- and medium-range NOEs, the restrained molecular dynamics simulation, CD and FT-IR spectroscopy were consistent with the formation of beta -turn in solution by the model peptide. The results implicate beta -turn playing an important role in the process of protein folding. ...
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus sigma NS. Here, we compared the abilities of NSP2 and sigma NS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while sigma NS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Prediction of trans-membrane helices continues to be a difficult task with a few prediction methods clearly taking the lead; none of these is clearly best on all accounts. Recently, we have carefully set up protocols for benchmarking the most relevant aspects of prediction accuracy and have applied it to|30 prediction methods. Here, we present the extension of that analysis to the level of an automatic web server evaluating new methods
The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design. PubMed: 26987712. Doi: 10.1038/srep23397.. ...
The cpssp package ------------------------------------------------------------------------------ This package is released under the LaTeX Project Public License v1.3c or later (see The cpssp package allows you to draw a two-dimensional representation of a proteins secondary structure in LaTeX. Besides, it is possible to graphically compare protein secondary structure predictions. One can both compare predictions from a single program for several protein sequences (which have been aligned using any appropriate algorithm) and predictions from several programs for a single protein sequence. Installation: Run cpssp.ins through LaTeX and follow the instructions. -- Wolfgang Skala June 6th, 2009 ...
For the current problem we define a neural network with one input layer, one hidden layer and one output layer. The input layer encodes a sliding window in each input amino acid sequence, and a prediction is made on the structural state of the central residue in the window. We choose a window of size 17 based on the statistical correlation found between the secondary structure of a given residue position and the eight residues on either side of the prediction point [2]. Each window position is encoded using a binary array of size 20, having one element for each amino acid type. In each group of 20 inputs, the element corresponding to the amino acid type in the given position is set to 1, while all other inputs are set to 0. Thus, the input layer consists of R = 17x20 input units, i.e. 17 groups of 20 inputs each.. In the following code, we first determine for each protein sequence all the possible subsequences corresponding to a sliding window of size W by creating a Hankel matrix, where the ith ...
An alpha helix (α-helix) is a twisted part of a protein. It is one of the two most common parts of the secondary structure, or shape, of a protein. The other is the beta sheet. An alpha helix is created by alternating groups of atoms. There is a carbonyl group, created by a carbon atom double bonded to an oxygen atom, and an amine group, created by a nitrogen atom bonded to a hydrogen atom. Each section containing one of each of these groups is called a residue, a general term for a small part of a molecule. Each amine group forms a hydrogen bond with the carbonyl group four residues earlier. A prion is a protein that causes disease by changing the shape of another protein. It does this by changing some of the alpha helices, which are more common in normal cells, to beta sheets, which are more common in prions. The alpha helix consists of 3.6 residues per turn. All hydrogen bonds face in the same direction. If two or more alpha helices come together, they become a tertiary structure. (Ex. Five ...
Synonyms for a-helix in Free Thesaurus. Antonyms for a-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for a-helix?
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
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). ...
Secondary structure formation of FRA16B DNA following denaturation and re-annealing (reduplexing) reaction. (A) Gel electrophoresis analysis of re-annealed FRA1
This presentation is designed as an aid in teaching material on the secondary structures of proteins. Buttons are intended for the instructors use and are labeled with key words only. Movies are timed so as to allow for explanations between the movements and views of the molecule. To obtain the greatest benefit from the presentation, it is helpful to become fully familiar with the buttons ...
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins.
Circular Dichroism (CD) analysis from SGS - meet regulatory requirements with class-leading CD spectroscopic analysis, alpha helix beta sheet analysis, and secondary and tertiary structure analysis. Learn more.
The mechanism of beta-sheet formation remains a fundamental issue in our understanding of the protein folding process, but is hampered by the often encountered kinetic competition between folding and aggregation. The role of local versus nonlocal interactions has been probed traditionally by mutagenesis of both turn and strand residues. Recently, rigid organic molecules that impose a correct chain reversal have been introduced in several small peptides to isolate the importance of the long-range interactions. Here, we present the incorporation of a well-studied beta-turn mimic, designated as the dibenzofuran-based (DBF) amino acid, in the B1 domain of streptococcal protein G (B1G), and compare our results with those obtained upon insertion of the same mimic into the N-terminal beta-hairpin of B1G (O Melnyk et al., 1998, Lett Pept Sci 5:147-150). The DBF-B1G domain conserves the structure and the functional and thermodynamical properties of the native protein, whereas the modified peptide does ...
A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Torque force may be applied by the ribosome co-translationally, and when accompanied by simultaneous restriction of the rotational mobility of the distal part of the growing chain, the resulting tension in the protein backbone would facilitate the formation of local secondary structure and direct the folding process. Our model of the early stages of protein folding in vivo postulates that the free motion of both terminal regions of the protein during its synthesis and maturation is restricted. The long-known but
Major Professor: Dr. Tim Cross. Structure determination of M. Tuberculosis small helical membrane proteins in lipid by solid state nuclear magnetic resonance. ...
A regular stress test helps to assess coronary blockages by monitoring EKG changes during treadmill exercise protocols. Although helpful in making a diagnosis, a regular stress test lacks the sensitivity and specificity of nuclear stress tests.. For more information on regular stress tests, please visit our Heart Center.. ...
Many different proteins aggregate into amyloid fibrils characterized by cross-beta structure. beta-strands contributed by distinct protein molecules are generally found in a parallel in-register alignment. Here, we describe the web server for a novel algorithm, prediction of amyloid structure aggreg …
The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding.s profile, publications, research topics, and co-authors
These three amino acids perform a proton relay reaction to transfer electrons between substrate and cofactor. 3α-HSD is capable of running the reaction both ways, either oxidizing or reducing the substrate and cofactor depending on the state of the testosterone. Tyr55 acts as acid, and donates a proton to the steroid--,Tyr55 forms a hydrogen bond to Lys84 for stabilization--,Lys84 forms a salt link to Asp50 for further stability. In Dr. Bantas protein, this reaction must only be run so that the sugar will be oxidized and the cofactor, reduced. The transfer of electrons from cofactor to circuit is already fairly efficient, but the key to an efficient reaction is in transferring the electron from substrate to cofactor. This is where the catalytic triad is extremely important. Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). ...
Online resource for oligonucleotide and primer design, calculting melting temperature, secondary structure determination, PCR resource and primer databases
The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Secondary structure was predicted by using the programs PSIPRED and ALB. The residues predicted as helical are marked by H by PSIPRED and by H and & by ALB, and those predicted as -structural are marked by E by PSIPRED and by S and B by ALB ...
1qkx: Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II region of the Ramachandran plot.
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The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. 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. . ...
Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a parallel structure. I learned that these beta strands are a zigzag sequence of amino acids, but what traits of beta strands differentiate it from the primary structure? Or are the beta strands just primary structures that link together to make beta sheets?. ...
The publication AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 10000 of the best publications in CiteWeb. Also in the category Chemistry it is included to the Top 1000. Additionally, the publicaiton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 1000 among other scientific works published in 1996 ...
1EM7: Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.
GCE CIE Biology - In this article we will explain the primary structure, secondary structure, tertiary structure and quaternary structure of proteins, and also describe the four ma
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The pG1 pseudoGTPase domain adopts a small GTPase fold, with a central 6-stranded beta-sheet surrounded by four alpha-helices. The conserved GTPase motifs from the pG1 pseudoGTPase domain, which is not a nucleotide- binding domain ...
1JTN: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Vilayanur Ramachandran tells us what brain damage can reveal about the connection between celebral tissue and the mind, using three startling delusions as examples.
The behavior of nested sequences as it relates to the Show Dialogs option has always been poorly documented and confusing to many users. The Helix Reference, prior to this amendment mentions only one combination of nested options.. In addition, sequence related bugs in earlier versions of Helix resulted in other areas of the code that did not function according to documentation. Changes were made (in Helix 4.5.3) that resulted in problems for users who had built nested sequences and were accustomed to the previous behavior. Furthermore, in an attempt to address another longstanding bug, the Helix 5.0 team went too far, not only fixing the bug, but also breaking an intended (but never documented) function of conditional sequences.. Changes in Helix 5.3 correct incorrect behaviors and implements the originally intended behavior, while providing a mechanism for avoiding problems for collections that rely on one of the prior behaviors.. We have also attempted to document the correct behavior of ...
Dr. A. Ramachandran, M.D.,Ph.D.,D.Sc.,FRCP.(Lond).(Edin)., an internationally acknowledged pivotal figure in the field of contemporary Diabetes Health Care and Researc..
In protein structure, STRIDE (Structural identification) is an algorithm for the assignment of protein secondary structure ... Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23(4):566-79. doi:10.1002/prot. ... 2005). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol 5 ... from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the Protein ...
"PHYRE2 Protein Fold Recognition Server". Retrieved 2019-04-22. "CFSSP: Chou & Fasman Secondary Structure ... "SOPMA secondary prediction". "GOR protein prediction". "I-TASSER results". Retrieved 2019-05-05. " ... The protein has an isoelectric point (pI) of 11. The predicted molecular weight (mW) is 160kDa for the human protein, but ... Protein Domain Structure Visualization". Retrieved 2019-05-02. " ...
"Advanced Protein Secondary Structure Prediction Server". Retrieved 2018-05-05. "Phobius". ... This protein is included in the neuroblastoma breakpoint family of proteins. The NBPF19 gene is a protein-encoding gene in ... There are 14 predicted repeats within the protein sequence likely to be sites of sumoylation. The tertiary structure of NBPF19 ... The protein product of the NBPF19 transcript is composed of 3,843 amino acids and weights 440.5 kD. It contains 45 DUF1220 ...
Kyngas J, Valjakka J (1998). "Unreliability of the Chou-Fasman parameters in predicting protein secondary structure". Protein ... Chou PY, Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence". Advances in ... Kabsch W, Sander C (1983). "How good are predictions of protein secondary structure?". FEBS Lett. 155 (2): 179-82. doi:10.1016/ ... Chen H, Gu F, Huang Z (2006). "Improved Chou-Fasman method for protein secondary structure prediction". BMC Bioinformatics. 7 ( ...
"JPred: A Protein Secondary Structure Prediction Server". Retrieved 2018-04-24. Kelley, Lawrence. " ... Several other proteins have been predicted to interact with C3orf67: CLK1 Phosphorylates serine/arginine-rich proteins involved ... "NCBI Protein". National Center for Biotechnology Information. "Protein Molecular Weight Calculator". ... The protein has been identified as one of seventeen (17) genes that may play a novel role in the intersection of tumor ...
PSIPRED List of protein structure prediction software "JPred4: A Protein Secondary Structure Prediction Server". Retrieved 16 ... "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins. 40 (3): 502- ... In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The ... Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the ...
Advanced Protein Secondary Structure Prediction Server". T, Ashok Kumar (2013-04-01). "CFSSP: Chou and Fasman Secondary ... CFSSP has predicted that C20orf196 secondary structure is 57.1% alpha helices, 48.8% beta strands, and 16.6% beta turns. ... Zhang Y (January 2008). "I-TASSER server for protein 3D structure prediction". BMC Bioinformatics. 9: 40. doi:10.1186/1471-2105 ... Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation ...
Newlove T, Konieczka JH, Cordes MH (April 2004). "Secondary structure switching in Cro protein evolution". Structure. 12 (4): ... The crystal structure of the lambda Cro repressor reveals a HTH DNA-binding protein with an alpha/beta fold that differs from ... Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought ... Ohlendorf DH, Tronrud DE, Matthews BW (July 1998). "Refined structure of Cro repressor protein from bacteriophage lambda ...
Many proteins may adopt a beta sheet as part of their secondary structure. In beta sheets, sections of a single polypeptide may ... "Secondary structure of Proteins". Retrieved 2017-04-01.. ... G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures ... Beta sheets can also be either a parallel or anti-parallel secondary structure. However, an anti-parallel beta sheet is ...
Andersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". Structure. 10 (2 ... The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic- ... STRIDE (protein) an alternative algorithm Chris Sander (scientist) Kabsch W, Sander C (1983). "Dictionary of protein secondary ... where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins. DSSP begins by ...
Sen TZ, Jernigan RL, Garnier J, Kloczkowski A (June 2005). "GOR V server for protein secondary structure prediction". ... This may still provide valuable information, though, on a possible partial structure for this protein. FAM83A is expressed in ... Protein FAM83A (family member with sequence similarity 83) also known as tumor antigen BJ-TSA-9 is a protein that in humans is ... This protein is predicted to contain one domain of unknown function 1669 (DUF1669), which places this protein into the PLDc_ ...
... is an information theory-based method for the prediction of secondary structures in proteins. It was developed in the late ... List of protein structure prediction software Garnier, J.; Gibrat, J. F.; Robson, B. (1996). "GOR method for predicting protein ... "Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins". J Mol ... The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position ...
"[email protected] : GOR4 secondary structure prediction". Retrieved 2019-05-05. "JPred: A Protein Secondary Structure ... Predictions of C16orf78's secondary structure consist primarily of alpha helices and coiled coils. Phyre2 also predicted ... "CFSSP: Chou & Fasman Secondary Structure Prediction Server". Retrieved 2019-05-05. " ... Uncharacterized protein C16orf78(NP_653203.1) is a protein that in humans is encoded by the chromosome 16 open reading frame 78 ...
... (also known as alpha pleated sheet or polar pleated sheet) is an atypical secondary structure in proteins, first ... A missing in action secondary structure. Proteins 79:937-946. doi:10.1002/prot.22935 Armen RS, DeMarco ML, Alonso DO, Daggett V ... These proteins undergo a conformational change from largely random coil or alpha helix structures to the highly ordered beta ... Although the alpha sheet is only rarely observed in natural protein structures, it has been speculated to play a role in ...
... use of this normalized CD is important in studies of protein structure. Methods for estimating secondary structure in polymers ... It may be of interest to note that the protein CD spectra used in secondary structure estimation are related to the π to π* ... That is, for instance, a protein molecule with a helical secondary structure can have a CD that changes with changes in the ... Most notably, UV CD is used to investigate the secondary structure of proteins. UV/Vis CD is used to investigate charge- ...
... and the quartenary structure. Protein secondary structure prediction is a main focus of this subfield as the further protein ... are determined based on the secondary structure. Solving the true structure of a protein is an incredibly expensive and time- ... Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo (December 1, 2015). "Protein secondary structure prediction using deep ... Annotations of proteins in protein databases often do not reflect the complete known set of knowledge of each protein, so ...
"Protein Secondary Structure Prediction using logic-based machine learning". Protein Engineering. 5 (7): 647-657. doi:10.1093/ ... Applications included the discovery of rules for protein folding (with Ross King) and drug design as well as systems such as ... Tatjana Zrimec used the system to investigate how playing robots could develop structured knowledge about their world while ... Structured Induction in Expert Systems. Turing Institute Press. ASIN 0201178133. Muggleton, Stephen (1990). Inductive ...
... and predictions of secondary structure". Protein Science. 3 (4): 600-7. doi:10.1002/pro.5560030408. PMC 2142870. PMID 8003978. ... From crystal structures and kinetic assays, it is believed that FPPS catalyzes the condensation reaction in three concerted ... A notable example of the former is the farnesylation of small G-proteins including Ras, CDC42, Rho, and Rac. The attachment of ... The structure and mechanism of farnesyl pyrophosphate synthase (FPPS), a type of geranyltranstransferase, is well characterized ...
"Exploiting the past and the future in protein secondary structure prediction." Bioinformatics 15.11 (1999): 937-946. Pollastri ... "Porter: a new, accurate server for protein secondary structure prediction." Bioinformatics 21.8 (2005): 1719-1720. Kiperwasser ... Translation Handwritten Recognition Protein Structure Prediction Part-of-speech tagging Dependency Parsing Entity Extraction ... The general structure of RNN and BRNN can be depicted in the right diagram. By using two time directions, input information ...
A machine learning approach to the problem of predicting a protein's secondary structure from its primary structure (PROMIS) ( ... "Machine learning approach for the prediction of protein secondary structure". Journal of Molecular Biology. 216 (2): 441-457. ... "Identification and application of the concepts important for accurate and reliable protein secondary structure prediction". ... King has also developed an algorithm for converting protein coding DNA sequences into music with Colin Angus of The Shamen. The ...
Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular ... Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and ... database and the DSSP algorithm for assigning secondary structure to the amino acids of a protein, given the atomic-resolution ... "A database of protein structure families with common folding motifs". Protein Science. 1 (12): 1691-1698. doi:10.1002/pro. ...
ISBN 978-1-4398-1071-2. Rao ST, Rossmann MG (May 1973). "Comparison of super-secondary structures in proteins". Journal of ... Rossmann and Rossmannoid fold proteins are extremely common. They make up 20% of proteins with known structures in the Protein ... Kessel A (2010). Introduction to Proteins: Structure, Function, and Motion. Florida: CRC Press. p. 143. ... "A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit". Journal of Molecular ...
Rao ST, Rossmann MG (May 1973). "Comparison of super-secondary structures in proteins". Journal of Molecular Biology. 76 (2): ... Here is a list of examples in which unrelated proteins have similar tertiary structures but different functions. Whole protein ... tyrosinase and insect storage proteins, respectively. They have different molecular weight and structure. However, the proteins ... The structure of immunoglobulin G-binding bacterial proteins A and H do not contain any sequences homologous to the constant ...
Protein Science. doi:10.1002/pro.3671. Rao ST, Rossmann MG (May 1973). "Comparison of super-secondary structures in proteins". ... In 1970 his laboratory found the structure of dogfish lactate dehydrogenase, one of the largest early proteins to be solved. In ... publishing on the structure of an Iresin Diester and a terpenoid, and writing computer programs for analysing structures. ... Calculating electron density structure from X-ray crystallography results by Rossmann's team had long been one of the larger ...
Rao ST, Rossmann MG (1973). "Comparison of super-secondary structures in proteins". J Mol Biol. 76 (2): 241-56. doi:10.1016/ ... NAD bound to proteins in the Protein Data Bank NAD Animation (Flash Required) β-Nicotinamide adenine dinucleotide (NAD+, ... have found that NAD+ directly regulates protein-protein interactions. They also show that one of the causes of age-related ... "A conserved NAD binding pocket that regulates protein-protein interactions during aging". Science. 355 (6331): 1312-1317. ...
Methods for predicting both secondary structure and tertiary structure - including homology modeling, protein threading, and ... 2001). EVA: large-scale analysis of secondary structure prediction. Proteins Suppl 5:192-9. PMID 11835497 Eyrich VA, Marti- ... running benchmark project for assessing the quality and value of protein structure prediction and secondary structure ... were compared to results from each week's newly solved protein structures deposited in the Protein Data Bank. The project aimed ...
... protein threading, de novo protein structure prediction, and secondary structure prediction is available in the list of protein ... tertiary structure), or interchain, i.e., when occurring between different structures (quaternary structure). Protein structure ... such as protein-protein interactions (PPI), protein-peptide interactions, protein-ligand interactions (PLI), and protein-DNA ... ProtCID: The Protein Common Interface Database Database of similar protein-protein interfaces in crystal structures of ...
VADAR identifies and assigns protein secondary structure using 3 different algorithms. These three methods are then combined to ... VADAR's method of secondary structure identification generally identifies a higher fraction of secondary structure elements ... Secondary structure assignments for each residue are listed under the column labeled SCND STRUC. The first secondary structure ... VADAR's secondary structure assignments appear to agree more closely with secondary structures identified by visual inspection ...
The predicted secondary structure of the protein includes 8 short alpha-helices (15.6% of the protein), 14 short extended ... Garnier, J.; Gibrat, J. F.; Robson, B. (1996). "GOR method for predicting protein secondary structure from amino acid sequence ... LOC100287387 is a protein that in humans is encoded by the gene LOC100287387. The function of the protein is not yet understood ... The protein contains a nuclear localization signal, and most likely acts in the nucleus. There are no confirmed protein ...
ISBN 978-0-262-63110-5. Qian, N.; Sejnowski, T.J. (1988). "Predicting the secondary structure of globular proteins using neural ... Rost, B.; Sander, C. (1993). "Prediction of protein secondary structure at better than 70% accuracy" (PDF). Journal of ... However, neural networks transformed domains such as the prediction of protein structures. In 1992, max-pooling was introduced ... the ISBI 2012 Segmentation of neuronal structures in EM stacks challenge, the ImageNet Competition and others. Deep, highly ...
how community structure, function and stability is determined.[36][37]. Ecological pyramids[edit]. See also: Ecological pyramid ... Aquatic producers, such as planktonic algae or aquatic plants, lack the large accumulation of secondary growth as exists in the ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... Pyramid structure can vary across ecosystems and across time. In some instances biomass pyramids can be inverted. This pattern ...
As a result, structural proteins, resulting from polypeptide products of gag and gag-pol genes, that are necessary for the HIV ... published a paper that showed the three-dimensional structure of HIV's protease enzyme.[5] Other researchers claim that this ... Secondary alcohols. *Tert-butyl compounds. Hidden categories: *Articles with changed EBI identifier ... "Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant ...
... of patients with myelodysplastic syndromes with the highest expression in refractory anemia with excess of blasts and secondary ...
The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars than, ... The veins branching from these are secondary or second order veins. These primary and secondary veins are considered major ... and flattened leaf stems called phyllodes which differ from leaves both in their structure and origin.[4][7] Some structures of ... and connected by intermediate tertiary veins rather than loops between secondaries, as in Cornus.. Cladodromous. Secondaries ...
"Fractal Structure of a White Cauliflower" (PDF). Journal of Korean physical society. 46 (2): 474-477. arXiv:cond-mat/0409763 . ... 100 grams of raw white cauliflower provides 25 calories, is low in fat, carbohydrates, dietary fiber and protein (table).[20] ... Secondary producers, having 0.4-1.3 million tonnes annually, were the United States, Spain, Mexico and Italy.[19] ... "Secondary Edible Parts of Vegetables". Vegetarian. 5.. *^ "Vegan Cauliflower-Based Pizza Crust, Now in 3D". Veg news ...
Clark, JD, Variability in primary and secondary technologies of the Later Acheulian in Africa in Milliken, S and Cook, J (eds ... In some instances (at least the Tlingit), they developed social stratification, slavery, and complex social structures such as ... Large game animals such as deer were an important source of protein in Middle and Upper Paleolithic diets. ... though Lower Paleolithic hominins such as Homo habilis and Homo erectus are likely to have had more complex social structures ...
Some transferred chloroplast DNA protein products get directed to the secretory pathway[27] (though many secondary plastids are ... Linear structureEdit. Chloroplast DNA has long been thought to have a circular structure, but some evidence suggests that ... Protein targeting and importEdit. See also: Protein targeting. The movement of so many chloroplast genes to the nucleus means ... A protein kinase drifting around on the outer chloroplast membrane can use ATP to add a phosphate group to the Toc34 protein, ...
Candidiasis secondary to the use of inhaled steroids may be treated by rinsing out the mouth with water after taking the ... Hyphae penetrate to the depth of the stratum spinosum, and appear as weakly basophilic structures. Polymorphonuclear cells also ... This adhesion involves adhesins (e.g., hyphal wall protein 1), and extracellular polymeric materials (e.g., mannoprotein). ... If candidiasis is secondary to corticosteroid or antibiotic use, then use may be stopped, although this is not always a ...
Sparkling wine like French Champagne, Catalan Cava or Italian Prosecco can be made by means of a secondary fermentation. ... Wine tannins adds balance, complexity, structure and makes a wine last longer, so they play an important role in the aging of ... "Ethanol Causes Acute Inhibition of Carbohydrate, Fat, and Protein Oxidation and Insulin Resistance". J. Clin. Invest. 81 (4): ...
Mann, T. (2012). Spermatophores: Development, Structure, Biochemical Attributes and Role in the Transfer of Spermatozoa. ... Editing is concentrated in the nervous system and affects proteins involved in neural excitability and neuronal morphology. ... "Locomotion by Abdopus aculeatus (Cephalopoda: Octopodidae): walking the line between primary and secondary defenses". Journal ... Both the structures and editing sites are conserved in the coleoid genome and the mutation rates for the sites are severely ...
... vitamins and proteins. Since higher concentration of fat and protein in the sake would lead to off-flavors and contribute rough ... The reason for polishing is a result of the composition and structure of the rice grain itself. The core of the rice grain is ... with a secondary transport in autumn, once the weather had cooled, known as hiyaoroshi 冷卸し ("cold wholesale distribution") - ... and contains less protein and lipid than the ordinary rice eaten by the Japanese. Sake rice is used only for making sake, ...
"Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and ... There are no recorded instances of vestigial nuclei in any other secondary plastid-containing organisms, yet they have been ... The B. natans genome contains 293 genes that code for proteins as compared to the 465 genes in G. theta. B. natans also only ... Most of the genes that moved to the host cell involved protein synthesis, leaving behind a compact genome with mostly single- ...
... protein itself is not lost).[16] Lentils have the second-highest ratio of protein per calorie of any legume, after soybeans. ... "Food Structure. 5: 241-246 - via *^ Bora, Pushkar Singh (2002). "Functional properties of native and ... A major part of the world's red lentil production undergoes a secondary processing step. These lentils are dehulled, split and ... Raw lentils are 8% water, 63% carbohydrates including 11% dietary fiber, 25% protein, and 1% fat (table). Lentils are a rich ...
Masculine secondary sexual characteristics include androgenic hair, voice deepening, emergence of the Adam's apple, broadening ... Numerous reports have shown androgens alone are capable of altering the structure of the brain,[11] but identification of which ... "G protein-coupled receptors: extranuclear mediators for the non-genomic actions of steroids". Int J Mol Sci. 15 (9): 15412-25 ... Indeed, androgens are capable of altering the structure of the brain in several species, including mice, rats, and primates, ...
Structure of the octahedral n-butyllithium hexamer, (C4H9Li)6.[138] The aggregates are held together by delocalised covalent ... This secondary hydrogen gas explosion produces the visible flame above the bowl of water, lake or other body of water, not the ... The balance between potassium and sodium is maintained by ion transporter proteins in the cell membrane.[231] The cell membrane ... Structure and Bonding. 21: 89-144. doi:10.1007/BFb0116498. ISBN 978-3-540-07109-9. . Retrieved 4 October 2013.. ...
AR NTD antagonists bind covalently to the NTD of the AR and prevent protein-protein interactions subsequent to activation that ... Singh SM, Gauthier S, Labrie F (2000). "Androgen receptor antagonists (antiandrogens): structure-activity relationships". Curr ... the development of masculine secondary sexual characteristics like male-pattern facial and body hair growth (or hirsutism), ... Blood proteinsEdit. In addition to their antigonadotropic effects, estrogens are also functional antiandrogens by decreasing ...
Like all serine protease inhibitors, A1AT has a characteristic secondary structure of beta sheets and alpha helices. Mutations ... The term alpha-1 refers to the protein's behavior on protein electrophoresis. On electrophoresis, the protein component of the ... which could confer this protein particular protein-cell recognition properties. The single cysteine residue of A1AT in position ... As protein electrophoresis is imprecise, the A1AT phenotype is analysed by isoelectric focusing (IEF) in the pH range 4.5-5.5, ...
This is because they lack a specialized structure called a loop of Henle, which is present in the nephrons of birds and mammals ... The albumin (9) further protects the embryo and serves as a reservoir for water and protein. The allantois (8) is a sac that ... Most reptiles lack a secondary palate, meaning that they must hold their breath while swallowing. Crocodilians have evolved a ... Geckos, skinks, and other lizards that are captured by the tail will shed part of the tail structure through a process called ...
The following structures are the most common sites of joint dislocations:. *Dislocated shoulder *Shoulder dislocations account ... of hip dislocations occur secondary to traffic accidents, the remaining percentage is due based on falls, industrial accidents ... syndrome is genetically inherited disorder that is thought to affect the encoding of the connective tissue protein's collagen ... Special attention should be focused on the neurovascular exam both before and after reduction, as injury to these structures ...
Structure[edit]. Muscle spindles are found within the belly of muscles, between extrafusal muscle fibers.[b] The specialised ... Secondary type II sensory fibers (medium diameter) end adjacent to the central regions of the static bag and chain fibres.[2] ... Innervated muscle structure involved in reflex actions and proprioception. For the class of neurons characterized by a large ... Likewise, secondary type II sensory fibers respond to muscle length changes (but with a smaller velocity-sensitive component) ...
Ferrer-Orta C, Arias A, Agudo R, Pérez-Luque R, Escarmís C, Domingo E, Verdaguer N (February 2006). "The structure of a protein ... Additionally,5' end NCR that contain secondary structural elements is required for RNA replication and poliovirus translation ... NMR solution structures of poliovirus VPg and VPgpU show that uridylylation stabilizes the structure of the VPg, which is ... The rest of the genome encodes structural proteins at the 5' end and non-structural proteins at the 3' end in a single ...
In 1977, the structure of VFDF was determined as a secondary, bicyclic amine alkaloid, and it was renamed anatoxin-a.[35][36] ... They have the same chemical structure as proteins, except they are shorter. In a cyclic peptide, the ends link to form a stable ... Chemical structure of cyanotoxins[25] Structure Cyanotoxin Primary target organ in mammals Cyanobacteria genera ... Chemical structure[edit]. Cyanotoxins usually target the nervous system (neurotoxins), the liver (hepatotoxins) or the skin ( ...
"Crystal structure of a human TATA box-binding protein/TATA element complex". Proceedings of the National Academy of Sciences of ... These secondary interactions induce bending of the DNA and helical unwinding.[20] The degree of DNA bending is species and ... Structure[edit]. Sequence and prevalence[edit]. Figure 2. Mechanism for transcription initiation at the TATA box. Transcription ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ...
Salman D, Okuda LH, Ueno A, Dautu G, et al «Evaluation of novel oocyst wall protein candidates of Toxoplasma gondii» (en anglès ... Afonso C, Paixão VB, Costa RM «Chronic Toxoplasma infection modifies the structure and the risk of host behavior» (en anglès). ... Shojaee S, Teimouri A, Keshavarz H, Azami SJ, Nouri S «The relation of secondary sex ratio and miscarriage history with ... Dubey JP, Lindsay DS, Speer CA «Structures of Toxoplasma gondii tachyzoites, bradyzoites, and sporozoites and biology and ...
This section relies too much on references to primary sources. Please improve this section by adding secondary or tertiary ... James Watson, co-discoverer of structure of DNA, Nobel Laureate.. *Scott Lowe (currently at MSKCC), research on p53, Member of ... A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ... RNA interference (RNAi) and small-RNA biology; DNA replication; RNA splicing; signal transduction; genome structure; non-coding ...
原生質絲有分兩種:初生原生質絲(primary plasmodesmata)及次生原生質絲(secondary plasmodesmata)。初生原生質絲在細胞分裂期間出現,而次生原生質絲是真正溝通成熟植物細胞的通道。[6] ... FT protein movement contributes to long distance signalling in floral induction of Arabidopsis. Science. 2007, 316 (5827): 1030 ... Plasmodesmata: structure, function and biogenesis. Current Opinion in Plant Biology. December 2008, 11 (6): 680-686
Andersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". Structure. 10 (2 ... The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic- ... Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical ... where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins. ...
Structure[edit]. The glycogen phosphorylase monomer is a large protein, composed of 842 amino acids with a mass of 97.434 kDa ... resulting in the formation of a glucose molecule with a secondary carbocation at the 1 position. Finally, the deprotonated ... Residues 397-437 form this structure, which allows the protein to covalently bind to the glycogen chain a full 30 Å from the ... results in small changes in tertiary structure at the subunit interface leading to large changes in quaternary structure.[8] ...
... structured intermittent therapy (SIT) - structured treatment interruption (STI) - study endpoint - subarachnoid space - ... safe sex - safer sex - salmonella - salvage therapy - SAMHSA - sarcoma - seborrheic dermatitis - secondary prophylaxis - sepsis ... proteins - protocol - protozoa - provirus - pruritus - pseudo-Cushing's syndrome - pseudovirion - PUBMED - pulmonary - purified ... core protein - correlates of immunity/correlates of protection - creatinine - cross-resistance - cryotherapy - cryptococcal ...
... which is one of the primary influences on the three-dimensional structures of proteins.[18] ... Reduction of these imines gives secondary amines: R′2C=NR + H2 → R′2CH-NHR. Similarly, secondary amines react with ketones and ... Secondary (2°) amines-Secondary amines have two organic substituents (alkyl, aryl or both) bound to the nitrogen together with ... 3) , secondary ammonium (R. 2NH+. 2) , tertiary ammonium (R3NH+). Small aliphatic amines display significant solubility in many ...
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with ... Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary ... Distant relationships between proteins whose primary structures are unalignable can sometimes be found by secondary structure. ... Secondary-structure prediction methods were evaluated by the Critical Assessment of protein Structure Prediction (CASP) ...
... This example shows a secondary structure prediction method that ... 1] Rost, B., and Sander, C., "Prediction of protein secondary structure at better than 70% accuracy", Journal of Molecular ... 2] Holley, L.H. and Karplus, M., "Protein secondary structure prediction with a neural network", PNAS, 86(1):152-6, 1989. ... 3] Kabsch, W., and Sander, C., "How good are predictions of protein secondary structure?", FEBS Letters, 155(2):179-82, 1983. ...
A physical basis for protein secondary structure. Rajgopal Srinivasan and George D. Rose ... Residue boundaries in each element of secondary structure element and percentage of the ensemble found in helix (H), strand (S ... The statistical bias toward native secondary structure in helix (red), strand (green), turn (blue), and generalized turn (black ... Percentage of ensemble found in each element of native secondary structure, averaged over 10 independent simulations, together ...
Does anyone know where I can find a database of protein secondary ,structure on-line? Ideally, for each protein in the database ... Database of Protein Secondary Structure Needed. Catherine Letondal letondal at Tue Sep 19 07:14:20 EST ... I would ,find its amino-acid sequence and *known* (not predicted) secondary ,structure. , , Thanks in advance for any replies, ... More information about the Proteins mailing list. ... Database of Protein Secondary Structure Needed *Next message: ...
Availability: The executable program for predicting protein secondary structure is available from the authors free of charge. ... is an important step towards elucidating its three dimensional structure, as well as its function. Presently, the best ... Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) ... dimensional structure protein secondary structure variable long-ranged information correct prediction evolutionary information ...
Prediction of protein secondary structure at better than 70% accuracy.. Rost B1, Sander C. ... neural network on a non-redundant data base of 130 protein chains to predict the secondary structure of water-soluble proteins ... The accuracy in predicting the content of three secondary structure types is comparable to that of circular dichroism ... The inclusion of protein family information in this form increases the prediction accuracy by six to eight percentage points. A ...
Protein Data Bank (PDB) STING Schneider, R.; de Daruvar, A. & Sander, C. (1997). "The HSSP database of protein structure- ... HSSP is also a database of homology-based implied protein structures. ... This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of ... HSSP is a database that combines structural and sequence information about proteins. ...
The prediction of protein secondary structures is not only of great importance for many biological applications but also ... Machine Learning Techniques for Protein Secondary Structure Prediction:An Overview and Evaluation ... Recent research on secondary structure prediction is mainly based on widely known machine learning techniques, such as ... Keywords: Amino acids encoding; evolutionary information; long-range dependencies; machine learning; protein secondary ...
It is well known that protein secondary-structure information can help the process of performing multiple alignment, in ...
The service predicts secondary protein structures by analyzing amino acid sequences submitted and detecting hydrogen-bonded ... The API returns indicators of hydrogen-bonded residues detected within the input data for use in secondary structure prediction ... Potential for hydrogen bonds is associated with resulting secondary structures, providing a partial indicator that may be used ...
... ... API methods support submission of a protein sequence from experimental data. The API returns predictions of secondary sequences ... This collection of three services -- GORI, GORIII, and GORIV -- provide predictions of secondary protein sequences using ... The highest score is taken to indicate the protein conformation. ...
Primary and secondary structure of bovine retinal S antigen (48-kDa protein). T Shinohara, B Dietzschold, C M Craft, G Wistow, ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ... Primary and secondary structure of bovine retinal S antigen (48-kDa protein) ...
This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure ...
The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from ... The first one contains 114 protein samples, and the second one contains 1845 protein samples. ... Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many ... Singh, M. (2006) Predicting Protein Secondary and Super Secondary Structure. [7] Schmidt, W.F., Kraaijveld, M.A. and Duin, R.P ...
... corelation between codon and protein secondary structures *Next message: correlation between codon and protein secondary ... corelation between codon and protein secondary structures *Next message: correlation between codon and protein secondary ... corelation between codon and protein secondary structures. CCoburn CCoburn at Wed Jan 7 18:58:10 EST 1998 ... Argos P. Title Protein secondary structural types are differentially coded on messenger RNA. Source Protein Science. Vol 5(10 ...
... beta-turn and random-coil regions were predicted for protein protease inhibitors. It appears that in all the inhib ... 11334619 - Amino acid distributions in integral membrane protein structures.. 9466929 - Shear numbers of protein beta-barrels: ... 22544739 - Crystal structure of dnak protein complexed with nucleotide exchange factor grpe in dna.... 19290549 - Reducing ... Next Document: Homology of the predicted secondary structures of the N-terminal fragments of preproteins.. ...
A decision graph explanation of protein secondary structure prediction ... Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level ... Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level ... directly from protein sequence. Therefore, analyzing protein secondary structure is indispensable. In the previous work, ...
Figure 1: Secondary structure distribution around aspartic acid residues binding Mn+2 ions in all the proteins (a); in proteins ... Figure 3: Secondary structure distribution around glutamic acid residues binding Mn+2 ions in all the proteins (a); in proteins ... Figure 2: Secondary structure distribution around histidine residues binding Mn+2 ions in all the proteins (a); in proteins ... for proteins from GC-poor bacteria; % for proteins from bacteria with average genomic G + C; and just % for proteins from GC- ...
1.1 - Protein Surface Accessibility and Secondary Structure Predictions. Version 1.1: Caching system has been implemented. View ... The Z-score is related to the surface prediction, and not the secondary structure.. Instructions Output format Article abstract ... NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method ...
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.. Kabsch W, Sander C ...
... secondary structures of amino acid residues in proteins can be predicted from the primary sequence with more than 75% per- ... Combining prediction of secondary structure and solvent accessibility in proteins Proteins. 2005 May 15;59(3):467-75. doi: ... when using the actual RSA values derived from known protein structures), the accuracy of secondary structure prediction ... secondary structures of amino acid residues in proteins can be predicted from the primary sequence with more than 75% per- ...
Molecular Biology (Protein Secondary Structure) Data Set Download: Data Folder, Data Set Description ... Ning Qian and Terrnece J. Sejnowski (1988), "Predicting the Secondary Structure of Globular Proteins Using Neural Network ... Abstract: From CMU connectionist bench repository; Classifies secondary structure of certain globular proteins ... what secondary structure it is a part of within the protein. There are three choices: alpha-helix, beta-sheet, and random-coil ...
Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Δδ) ... The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. ... Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Δδ) ... Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861 ...
The Secondary Structure of Proteins Biochemistry Lecture Aid by Frieda Reichsman This presentation is designed as an aid in ... teaching material on the secondary structures of proteins. Buttons are intended for the instructors use and are labeled with ...
An encoding scheme for protein folding on lattice models, inspired by parametric L-systems, was proposed. The encoding ... Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. ... Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. In: Talbi EG., Liardet P., ... Secondary Structure Evolutionary Algorithm Encode Scheme Memetic Algorithm Inference Procedure These keywords were added by ...
Protein Secondary Structure Prediction Website Is Open. by wanglj on Tue Mar 30, 2010 10:38 pm ... Based on the described research achievements, now we open the protein secondary structure prediction website, for the aim of ... we have got the leading position in predicting protein secondary structure, and apply the KDTICM and its software ICCKDSS in ... research communication and international technology service in Internet which concludes providing protein secondary structure ...
... trimeric membrane protein, YadA-M. The protein YadA (Yersinia adhesin A) is an important virulence factor of enteropathogenic ... Assignment and secondary structure of the YadA membrane protein by solid-state MAS NMR Sci Rep. 2012;2:803. doi: 10.1038/ ... secondary structure elements were predicted, which, combined with several long-range interstrand restraints, yielded the ... We report the complete solid-state MAS NMR resonance assignment of a medium-sized, trimeric membrane protein, YadA-M. The ...
Loops in globular proteins: a novel category of secondary structure Message Subject. (Your Name) has forwarded a page to you ... The protein loop, a novel category of nonregular secondary structure, is a segment of contiguous polypeptide chain that traces ... A systematic study was made of 67 proteins of known structure revealing 270 omega loops. Although such loops are typically ... Loops are almost invariably situated at the protein surface where they are poised to assume important roles in molecular ...
Suppression of conformational heterogeneity at a protein-protein interface.  Daniels, Kyle G; Deis, LN; Oas, Terrence Gilbert ... intermediates in the folding of all globular proteins, regardless of their native structure. However, experimental refolding ... Short-lived alpha-helical intermediates in the folding of beta-sheet proteins.  Chen, E; Everett, ML; Holzknecht, ZE; ... The structure of irisin reveals a novel intersubunit β-sheet fibronectin type III (FNIII) dimer: implications for receptor ...
Creation and visualization of secondary structure consensus for protein families. Authors. MIDLIK Adam HUTAŘOVÁ VAŘEKOVÁ Ivana ... Every protein family has a set of characteristic secondary structure elements (SSEs, namely helices and ß-strands). Their ... currently more than 150 000 structures). Furthermore, most protein structures can be classified into protein families based on ... we introduce computational methods for extracting and visualizing the secondary structure consensus for a given protein family ...
  • A combination of three levels of networks results in an overall three-state accuracy of 70.8% for globular proteins (sustained performance). (
  • This is a data set used by Ning Qian and Terry Sejnowski in their study using a neural net to predict the secondary structure of certain globular proteins [1]. (
  • Ning Qian and Terrnece J. Sejnowski (1988), "Predicting the Secondary Structure of Globular Proteins Using Neural Network Models" in Journal of Molecular Biology 202, 865-884. (
  • Ken, A.: Dill, Theory for the folding and stability of globular proteins. (
  • Several lines of evidence point strongly toward the importance of highly alpha-helical intermediates in the folding of all globular proteins, regardless of their native structure. (
  • Automatic identification of secondary structure in globular proteins. (
  • Qian, N., Sejnowski, T.J.: Predicting the secondary structure of globular proteins using neural network models. (
  • Many globular proteins have multiple alpha-helical portions separated by long stretches of non-helical regions. (
  • They make up the core of many globular proteins. (
  • contains a subset of this data set, where the structural assignment of every residue is reported for each protein sequence. (
  • In the following code, we first determine for each protein sequence all the possible subsequences corresponding to a sliding window of size W by creating a Hankel matrix, where the ith column represents the subsequence starting at the ith position in the original sequence. (
  • API methods support submission of a protein sequence from experimental data. (
  • The complete amino acid sequence of bovine S antigen (48-kDa protein) has been determined by cDNA and partial amino acid sequencing. (
  • Searching of the National Biomedical Research Foundation data bank revealed no extensive sequence homology between S antigen and other proteins. (
  • However, these preferences are not strong enough to produce a reliable method of predicting secondary structure from sequence alone. (
  • The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). (
  • The Primary structure contains a sequence of 20 different types of amino acids. (
  • Protein folding, or the prediction of the tertiary structure from linear sequence, is an unsolved and ubiquitous problem that invites research from many fields of study, including computer science, molecular biology, biochemistry and other. (
  • NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. (
  • Owing to the use of evolutionary information and advanced machine learning protocols, secondary structures of amino acid residues in proteins can be predicted from the primary sequence with more than 75% per-residue accuracy for the 3-state (i.e., helix, beta-strand, and coil) classification problem. (
  • The idea is to take a linear sequence of amino acids and to predict, for each of these amino acids, what secondary structure it is a part of within the protein. (
  • HSSP is a database that combines structural and sequence information about proteins. (
  • However, there will always be some differences between the members of the family and a single structure is not enough to represent the whole family of structures, just as a single amino acid sequence is not enough to represent the whole family of sequences. (
  • 1] Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence. (
  • The influence of amino‐acid sequence on protein structure. (
  • Structural protein descriptors in 1‐dimension and their sequence‐based predictions. (
  • The newly developed method utilizes the knowledge of the GOR-V information theory and the power of the neural networks to classify a novel protein sequence in one of its three secondary structure classes (helices, strands, and coils). (
  • They can be used either as sequence-to-structure classifier, structure-to-structure classifier, or both. (
  • This paper addresses the problem of post-processing the outputs of multi-class support vector machines used as sequence-to-structure classifiers with a structure-to-structure classifier estimating the class posterior probabilities. (
  • Analysis of the secondary structure of the wild-type, mutant, and pseudorevertant LamB signal sequences suggests that the secondary mutations restore export by allowing the formation of a stable α-helical conformation in the central, hydrophobic region of the signal sequence. (
  • DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. (
  • Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relationship. (
  • The new method models the PSI-BLAST profile of a protein sequence using a multivariate Gaussian distribution, and simultaneously takes into account the dependency between the profile and secondary structure and the dependency between profiles of neighboring residues. (
  • However, with using a neural network for the sequence-to-structure prediction while building the HMM only at the secondary structure level [ 19 , 20 ], SAM-T04 should not be regarded as a pure HMM-type method. (
  • Instead of fully recovering the whole three dimensional structure from amino acid sequence, protein secondary structure prediction only aimed at predicting the local structures such as alpha helices, beta strands and turns for each small segment of a protein. (
  • Predicted protein secondary structure can be used for improving fold recognition, ab initial protein prediction, protein motifs prediction and sequence alignment. (
  • Sequence analysis of the polymerase 1 gene and the secondary structure prediction of polymerase 1 protein of human influenza virus A/WSN/33. (
  • The deduced sequence of P1 protein is enriched in basic amino acids, particularly arginine. (
  • If your sequence has homology to a known structure you should reconsider the utility of making a prediction: a prediction is unlikely to be better than using the structure of a known homologue. (
  • Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. (
  • Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. (
  • For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. (
  • Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview . (
  • Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. (
  • Once all conforniational structures are accurately assigned, their natural diversity of sequence and environment in proteins can be explored to understand how they are formed. (
  • a-Helix formation in various mixtures of 2,2,2- trifluoroethanol (TFE), a known helix-inducing solvent, can be used to predict whether a sequence will form a helix at the protein core vs. the solvent-exposed protein surface. (
  • Nuclear magnetic resonance spectroscopy of a TFE solvated peptide composed of two helix-favoring pentapeptides flanking a helix-indifferent pentapeptide shows that the structure adopts N-terminal and C-terminal helices separated by two non-helical residues in the indifferent sequence. (
  • A number of sequence-based methods exist for protein secondary structure prediction. (
  • Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. (
  • Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained. (
  • Modern sequence-based prediction methods can provide information on the secondary structure content of these proteins without the need for producing any protein. (
  • Recent years have seen large improvements in the per-residue secondary structure prediction from sequence [ 1 , 2 ], although they are still limited in their accuracies, especially when applied to certain classes of protein, most notably those with high β-sheet content. (
  • The pioneering work of Chou in predicting secondary structure from sequence was through an elaborate and elegant covariance matrix approach [ 12 ]. (
  • In this study we have examined the performance of sequence based prediction methods using a neural network methodology, versus the experimentally-determined methods of CD and FTIR for assessing secondary structure content. (
  • The secondary structure content prediction for sequence prediction methods is generally not reported after publication of the crystal structure. (
  • The current highest reported secondary structure content prediction by sequence in the literature is r = 0.92 for α-helix and r = 0.81 for β-sheet [ 13 ]. (
  • It first uses PSIPRED to predict the secondary structure for each protein sequence. (
  • Conclusion: The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the predicted secondary structure sequences, which is capable of characterizing the sequence order information, local interactions of the secondary structural elements, and spacial arrangements of a helices and b strands. (
  • The secondary structure of a protein can be altered by either a mutation in the primary sequence of amino acids that make up the protein or by extreme conditions that force the proteins to denature or lose their shape. (
  • If even one amino acid is changed in the primary sequence, the secondary structure of a protein can be drastically affected. (
  • Explore the linkage between protein sequence and structure. (
  • The easy way to understand the difference is the primary structure is the amino acid sequence and the secondary is the first stage in how the protein folds (the other being the tertiary). (
  • Using this coarse-grained mapping, protein conformation can be approximated by a linear sequence of mesostates. (
  • You can submit the sequence in a free, case independent format, just don't forget to remove any extra information (like protein name, code etc). (
  • Membrane protein sequence is the minimal input required by the prediction program. (
  • The exponential growth of newly discovered protein sequences by different scientific communities has made a large gap between the number of sequence-known and the number of structure-known proteins. (
  • Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. (
  • Three years before Pauling's guess was verified by the publications of the first X-ray structures (16, 17), one group had already ventured to predict secondary structure from sequence (18). (
  • Basically any imaginable theoretical algorithm had been applied to the problem of predicting secondary structure from sequence. (
  • Sequence comparison of homologous proteins has provided a way to pinpoint the residues that contribute constructively to stability and to guide the engineering of protein stability. (
  • Primary structure is simply the sequence of residues making up the protein. (
  • So the primary structure of a small protein would consist of a sequence of 50 or so residues. (
  • The primary structure comprises the amino acid sequence. (
  • Primary structure of a protein is the amino acid sequence of the protein, which is linear. (
  • The codon sequence of the protein-coding gene determines the order of amino acids in the polypeptide chain. (
  • These results suggest that the extent of sequence variation, recombination events and selective pressures in the PvMSP-7E locus seem to be differentially affected by protein secondary structure. (
  • The original method was published by Garnier, Osguthorpe and Robson in 1978, and was one of the first successful methods to predict protein secondary structure from amino acid sequence. (
  • In addition, it appears that sites undergoing positive selection are more likely than expected to occur close to one another in the protein sequence. (
  • Expansion contains an N-terminal domain similar in sequence to the MH2 domain characteristic of Smad proteins, which are the central mediators of the effects of the TGF- β signalling pathway. (
  • These two proteins share 56% amino-acid similarity that is concentrated in the N-terminal part of the sequence. (
  • They are annotated in the NCBI database as modular proteins containing an N-terminal MH2 domain and a variable C-terminal region which does not present sequence similarity to other characterized domains. (
  • State-of the art protein secondary structure (PSS) prediction methods employ machine learning (ML) techniques, compared to early approaches based on statistical information and sequence homology. (
  • The primary structure of polypeptides and proteins is the sequence of amino acids in the polypeptide chain with reference to the locations of any disulfide bonds. (
  • The most common way to denote a primary structure is to write the amino acid sequence using the standard three-letter abbreviations for the amino acids. (
  • In this example, you will build a neural network to learn the structural state (helix, sheet or coil) of each residue in a given protein, based on the structural patterns observed during a training phase. (
  • in the BioNetbook ( ). (
  • The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. (
  • Argos P. Title Protein secondary structural types are differentially coded on messenger RNA. (
  • A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. (
  • However, the information on preferable 3D structural motifs is available mostly for Ca 2+ and Zn 2+ binding proteins. (
  • The aim of this study was to find out whether there is a secondary structural motif which is characteristic for relatively short parts of polypeptide chains around Mn 2+ binding amino acid residues. (
  • In fact, the same kind of secondary structural motif may be found in several 3D structural motifs. (
  • For example, four from eight 3D structural motifs for Zn 2+ binding include such a secondary structural motif as beta hairpin. (
  • That is why the knowledge on preferable secondary structural motifs around each of the amino acid residues may be even more helpful for prediction of ion binding sites than the knowledge on the 3D structural motifs for the complete coordination spheres. (
  • Protein structural data, deposited in the Protein Data Bank, are a valuable source of information and their amount is continuously growing (currently more than 150 000 structures). (
  • These collective findings indicate that phosphorylation induces unique secondary structural changes that may enhance the functional capacity of native phosphorylated amelogenins like LRAP to stabilize an ACP precursor phase during early stages of enamel mineral formation. (
  • SSpro/ACCpro 5: Almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. (
  • Deep-ultraviolet resonance Raman (DUVRR) spectra is sensitive to secondary structural motifs but, similar to circular dichroism (CD) and infrared spectroscopy , requires the application of multivariate and advanced statistical analysis methods to resolve the pure secondary structure Raman spectra (PSSRS) for determination of secondary structure composition. (
  • Solid-state NMR spectroscopy is routinely used to determine the structural and dynamic properties of both membrane proteins and peptides in phospholipid bilayers [1-26]. (
  • T. A. Cross and S. J. Opella, "Solid-State NMR Structural Studies of peptides and Proteins in Membranes," Current Opinion in Structural Biology, Vol. 4, No. 4, 1994, pp. 574-581. (
  • Classification of rhodopsin structures by modern methods of structural bioinformatics. (
  • Motivation: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. (
  • At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. (
  • Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. (
  • The DSM 17, DSM 20 , DSM 1000 , and the Multiscan support protein secondary structural studies. (
  • The considerable increase of the protein structural database allows to cross the line from the classical secondary structure description of proteins. (
  • While still confronted with numerous problems, defining structural alphabets is an emerging concept in the field of protein structure analysis. (
  • In Lhis chapter, we shall discuss the structural features of proteins, the forces that hold them together, and their hierarchical organization to form complex structures. (
  • However, before we begin our discussion of these hasic structural motifs, let us consider the geometrical properties of the peptide group because its understanding is prerequisite to that of any structure containing it. (
  • In the 1930s ancl 1940s, Linus Pauling and Rohert Corey determined the X-ray structures of several amino acids and dipeptides in an effort to elucidate the structural con- straints on the conformations of a polypeptide chain. (
  • Although there has been a growth in the number of crystal structures of proteins as the result of Structural Protemics programmes worldwide, their production has not kept pace with the sequencing effort. (
  • We used a very large dataset comprising 4,389 protein alignments with structural annotations to estimate new amino-acid substitution matrices for various structural configurations. (
  • Background: Prediction of protein structural classes (a, b, a + b and a/b) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. (
  • Results: We propose a new method to predict protein structural classes on the basis of features extracted from the predicted secondary structures of proteins rather than directly from their amino acid sequences. (
  • The resulting feature vectors are finally fed into a simple yet powerful Fisher's discriminant algorithm for the prediction of protein structural classes. (
  • Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences. (
  • Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions. (
  • Plasmonic nanoantennas offer new applications in mid-infrared (mid-IR) absorption spectroscopy with ultrasensitive detection of structural signatures of biomolecules, such as proteins, due to their strong resonant near-fields. (
  • This novel sensor is a highly promising and versatile tool for in vitro structural analysis of thin protein layers. (
  • Development of Novel Multi-Objective Based Model for Protein Structural Class Prediction. (
  • The knowledge of protein structural class provides useful information towards the determination of protein structure. (
  • Accurate determination of protein structural class using a suitable computational method has been a challenging problem in protein science. (
  • On the basis of such a statistical framework a low complexity functional link artificial neural network and a complex novel hybrid model using radial basis function neural network and multi-objective algorithm based classifier are introduced to predict protein structural class. (
  • is not generally possible to predict the energetic and structural response to mutation in proteins, although the statistics of isolated helices and parts of sheets are predictable to varying degrees (=-=Munoz et al. (
  • 1996). Some insight into protein stabilization has also been gained from the structural comparison of thermophilic proteins with their mesophilic counterparts (Russell & Taylor, 1995). (
  • This flexibility allows glycine to form turns between secondary structural elements. (
  • This work opens up the possibility to observe structural changes of proteins in solution in real time via a label-free method. (
  • Furthermore, the results reveal that 2D-IR spectroscopy is sensitive to changes in secondary structure at the few percent level, which means that it provides superior contrast to IR absorption when considering Ca 2+ induced structural change in human CaM. (
  • By revealing quantitative structural insight into Calmodulin, Minnes et al have proven that ultrafast 2D-IR -in combination with Principal Component Analysis - can act as an accurate, efficient reporter of protein secondary structure change. (
  • PSS transition sites represent structural information of protein backbones, and reduce the input space and learning parameters in the PSS prediction model. (
  • The prediction of protein secondary structures is not only of great importance for many biological applications but also regarded as an important stepping stone for solving the mystery of how amino acid sequences fold into tertiary structures. (
  • Hence this paper reviews the theoretical and experimental literature of these models with a focus on informational issues involving evolutionary and long-range information of protein sequences. (
  • The service predicts secondary protein structures by analyzing amino acid sequences submitted and detecting hydrogen-bonded residues within those structures. (
  • This collection of three services -- GORI, GORIII, and GORIV -- provide predictions of secondary protein sequences using methods based on the information theory of Garnier, Osguthorpe, and Robson. (
  • The API returns predictions of secondary sequences associated with the input data based on estimates of conformational states. (
  • 1974) and the known amino acid sequences, the alpha-helical, beta-sheet, beta-turn and random-coil regions were predicted for protein protease inhibitors. (
  • In this paper, a new method for predicting protein secondary structure from amino acid sequences has been proposed and implemented. (
  • The variable regions were located in the putative external loop structures, while the predicted β-strands were formed by conserved sequences. (
  • Notably, different bacterial porins are remarkably similar in their β-barrel structure, although their primary sequences have little homology ( 8 , 12 , 18 , 36 ). (
  • However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. (
  • With the growing availability of a large number of new genome sequences, there is an ongoing interest in the structures of the proteins represented by the open reading frames in those genomes. (
  • The primary sequences and secondary structures are known for over 1,000 different proteins. (
  • Correlation of these sequences and structures revealed that some amino acids are found more often in alpha helices, beta sheets, or neither. (
  • Using neural networks to predict the structure of proteins from amino acid sequences is a very common technique. (
  • The analysis of frequencies of occurrence of secondary structure for singlets and doublets of residues in a protein database enables prediction of secondary structure for new amino acid sequences. (
  • Additionally we discuss new highly interesting and important applications of the the GOR method to chameleon sequences in protein folding simulations, and for prediction of protein aggregation propensities. (
  • Many efforts have been made to extract useful information of protein secondary structure from sequences [ 3 - 10 ]. (
  • Rapid progress in genomics has led to the discovery of millions of protein sequences while less than 0.2% of the sequenced proteins' structures have been resolved by X-ray crystallography or NMR spectroscopy which are complex, time consuming, and expensive. (
  • A successful PSS prediction model can be utilized in homology detection tools for distant protein sequences and protein tertiary structure prediction methods to reduce the complexity of the protein structure prediction which has important applications in medicine, agriculture and the biological sciences. (
  • Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (
  • The highest score is taken to indicate the protein conformation. (
  • Secondary structure prediction and circular dichroic spectroscopy show that S antigen is composed predominantly of beta-sheet conformation. (
  • Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. (
  • H. Susi, S. N. Timasheff and L. Stevens, "Infrared Spectra and Protein Conformation in Aqueous Solutions: The Amide I Band in H2O and D2O Solutions," Jounral Biology Chemistry, Vol. 242, 1967, pp. 5460-5466. (
  • The UV-visible spectral range of the backbone-sidechain CT transitions is determined by the chemical nature of the donor, bridge and acceptor groups within each amino acid, amino acid conformation and the protein secondary structure where the amino acids are located. (
  • SECONDARY STRUCTURE A polymer's secondary structure (2 0 structure) is defined as the local conformation of its backbone. (
  • Proteins The ________ helix is a common motif in the secondary structure of proteins, a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone carbonyl group of the amino acid four residues earlier. (
  • This is the first folding level of protein conformation. (
  • Disulfide bonding can form within and between polypeptide chains as proteins fold to its native conformation. (
  • In order to maintain potency and activity, some of the most critical parameters to maintain are protein conformation (tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). (
  • However, analytical monitoring of the protein conformation has been frequently omitted due to time constraints, the complexity of techniques commonly employed and the inherent lack of sensitivity to subtle changes shown by some biophysical methods. (
  • Secondary structure is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule. (
  • Abstract Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. (
  • Background: Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. (
  • abstract = "The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy (1H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. (
  • We choose a window of size 17 based on the statistical correlation found between the secondary structure of a given residue position and the eight residues on either side of the prediction point [2]. (
  • The API returns indicators of hydrogen-bonded residues detected within the input data for use in secondary structure prediction. (
  • This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. (
  • In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn 2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. (
  • Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. (
  • To answer this question, we developed a method of trapping the polypeptide chain of a translocating protein within the channel and determined the minimum number of residues that could traverse it. (
  • One might naively suppose that since proteins are all composed of the same 20 types of amino acid residues, they would be more or less alike in their properties. (
  • Protein structures are governed primarily by hydrophobic effects and by interactions between polar residues and other types of bonds. (
  • It is commonly believed that protein core residues are immutable and generally optimized for energy, while on the contrary, surface residues are variable and hence unimportant for stability. (
  • But, it is now becoming clear that mutations of both core and surface residues can increase protein stability, and that protein cores are more ¯exible and thus more tolerant to mutation than expected. (
  • Thus primary structure involves only the covalent bonds linking residues together. (
  • There is no theoretical maximum size, but the largest protein so far discovered has about 30,000 residues. (
  • The term secondary structure refers to the interaction of the hydrogen bond donor and acceptor residues of the repeating peptide unit. (
  • The method is based on the information theory, and an assumption that information function of a protein chain can be approximated by a sum of information from single residues and pairs of residues. (
  • We find that amino acids that form disordered regions, such as random coils, are far more likely to be under positive selection than expected from their proportion in the proteins, and residues in helices and beta-structures are subject to less positive selection than predicted. (
  • For example, 19% of all native helices in the total set of proteins have statistical weights between 0.5 and 0.6 in these simulations, as indicated by the red bar in bin 0.5-0.6. (
  • The most common secondary structures are alpha helices and beta sheets. (
  • Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. (
  • Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. (
  • Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a high-level classification which remains popular today. (
  • Recently, other proteins, able to bind Ca 2+ containing the abovementioned motif but lacking one or both helices, have been described [ 8 ]. (
  • Strikingly, predictive accuracy seems to be most dependent upon the type of secondary structure, with helices being the most accurately predicted by Δδ values using five different RCCS tables. (
  • Avbelj F, Kocjan D, Baldwin RL (2004) Protein chemical shifts arising from alpha-helices and beta-sheets depend on solvent exposure. (
  • Every protein family has a set of characteristic secondary structure elements (SSEs, namely helices and ß-strands). (
  • Finally, specific 15 N-labeled amide sites on a protein embedded inside oriented bilayers can be used to probe the alignment of the helices with respect to the bilayer normal [2]. (
  • one "four-helical supersecondary structure" and four "polypeptide double helices" (antiparallel beta-pleated sheets) which are considered important in RNA binding. (
  • This thesis involves analyses of 3₂-helices, a-helices and of the change in residual entropy of a protein upon chemical modification. (
  • By a statistical analysis of 258 nucleic acid binding proteins from the protein data bank, 5% of their amino acids were found to exist as 3₂-helices. (
  • The third K homology domain, Epstein-Barr nuclear antigen- 1 and the homeodomain from the Drosophila paired protein contained 3₂-helices involved in nucleic acid recognition. (
  • For proteins, this has come to mean the specification of regular polypep- tide hack bone folding patterns: helices, pleated sheets, and turns. (
  • Some fibrous proteins, including alpha-keratin, are almost completely comprised of alpha-helices. (
  • Transmembrane proteins contain alpha-helices due to their hydrophobic properties. (
  • Linus Pauling correctly guessed the formation of helices and strands (14, 15) (and falsely hypothesized other structures). (
  • Conversely, proline, because it contains a secondary amino group, forms rigid peptide bonds that cannot be accommodated in either alpha or beta helices. (
  • Our results demonstrate that protein structures with a greater degree of organization and strong hydrophobicity, represented here as helices and beta-structures, are less tolerant to molecular adaptation than disordered, hydrophilic regions, across a diverse set of proteins. (
  • The relative orientation of the consecutive amide planes often forms repetitive patterns resulting in periodic and chiral sub-structures (e. g. α-helices, β-sheets, etc.) called secondary structure. (
  • M. M. Bradford, "A Rapid and Sensitive Method for the Quantization of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding," Analytical Biochemistry. (
  • A. Dong, P. Huang and W. S. Caughey, "Protein Seconddary Structures in Water from the Second Derivative Amide I Infrared Spectra," Biochemistry, Vol. 29, 1990, pp. 3303-3308. (
  • The function of proteins depends on their structure, and defining the structure of individual proteins is a large part of modern Biochemistry and Molecular Biology. (
  • Home » Biochemistry » What are the Secondary Structure of Proteins? (
  • In addition to general chemistry texts, information about protein structure can be found in texts for biochemistry, organic chemistry, general biology, genetics, and molecular biology. (
  • Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. (
  • Using CS-CHEMeleon, Δδ predicted versus experimentally determined secondary structures were compared for large datasets of membrane and non-membrane proteins as a function of RCCS dataset, Δδ threshold, nucleus, localized parameter averaging and secondary structure type. (
  • We report the complete solid-state MAS NMR resonance assignment of a medium-sized, trimeric membrane protein, YadA-M. The protein YadA (Yersinia adhesin A) is an important virulence factor of enteropathogenic Yersinia species (such as Yersinia enterocolitica and Yersinia pseudotuberculosis). (
  • S. Abu-Baker and G. Lorigan, "Solid-State NMR Spectroscopic Approaches to Investigate Dynamics, Secondary Structure and Topology of Membrane Proteins," Open Journal of Biophysics , Vol. 2 No. 4, 2012, pp. 109-116. (
  • P. C. Dave, E. K. Tiburu, K. Damodaran and G. A. Lorigan, "31P and 2H Solid-State NMR Spectroscopic Studies of the Transmembrane Domain of the Membrane-Bound Protein Phospholamban," Biophysical Journal, Vol. 86, 2004, pp. 1564-1573. (
  • The pro-tein secondary structure and thermal stability of the plasma membrane of wheat root have been characterized in D 2 O buffer from 20°C to 90°C by Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). (
  • X. Zhao, Y. Shi, L. Chen, F. Sheng and H. Zhou, "Secondary Structure Changes and Thermal Stability of Plasma Membrane Proteins of Wheat Roots in Heat Stress," American Journal of Plant Sciences , Vol. 2 No. 6, 2011, pp. 816-822. (
  • J. L. R. Arrondo and F. M. Go?i, "Structure and Dynamics of Membrane Proteins as Studied by Infrared Spectroscopy," Progress in Biophysics & Molecular Biology, Vol. 72, 1999, pp. 367-405. (
  • Mutant Escherichia coli strains in which export of the LamB protein (coded for by the lamB gene) to the outer membrane of the cell is prevented have been described previously. (
  • We have isolated pseudorevertants that restore export of functional LamB protein to the outer membrane. (
  • Structure determination of membrane proteins with magic angle spinning NMR is rapidly developing. (
  • The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni , may play an important role in the adaptation of the organism to various host environments. (
  • It was shown that the single-copy cmp locus encoded a protein with characteristics of bacterial outer membrane proteins. (
  • Many gram-negative bacteria have one or more predominant outer membrane proteins (OMPs). (
  • As the major components of the gram-negative bacterial outer membrane, pore-forming proteins also play a role in bacterial pathogenesis, such as adherence, invasion, and serum resistance ( 35 , 44-46 ). (
  • Though there are limitations, this work has demonstrated that a basic analysis of AAC is a useful tool to use in combination with other computational and experimental methods for classifying and investigating function and ligand specificity in a large group of transport or other membrane proteins, including those that are molecular targets for development of new drugs. (
  • Outside the membrane, the transmembrane proteins adopt a non-helical structure and many times the alpha-helix is broken by a proline residue. (
  • Many times, beta-barrels can be found in proteins that span the membrane. (
  • The purpose of this server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions. (
  • A simple approach to membrane protein secondary structure and topology based on NMR spectroscopy. (
  • This paper describes a simple, qualitative approach for the determination of membrane protein secondary structure and topology in lipid bilayer membranes. (
  • The approach is based on the observation of wheel-like resonance patterns observed in the NMR 1H-15N/15N polarization inversion with spin exchange at the magic angle (PISEMA) and 1H/15N heteronuclear correlation (HETCOR) spectra of membrane proteins in oriented lipid bilayers. (
  • Therefore, the Pisa wheels provide a sensitive, visually accessible, qualitative index of membrane protein secondary structure and topology. (
  • A solid-state NMR index of helical membrane protein structure and topology. (
  • The accuracy in predicting the content of three secondary structure types is comparable to that of circular dichroism spectroscopy. (
  • Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Δδ) values, measured as the difference between experimental and random coil chemical shifts (RCCS). (
  • This review traces the evolution of multivariate methods and their application to secondary structure composition analyses of proteins by DUVRR spectroscopy from the first experiments using two-wavelengths, and culminating with recent studies utilizing time-resolved DUVRR measurements. (
  • From the perspective of the perpetuated lipids, 2 H solid-state NMR spectroscopy can be used to probe the effect of embedded proteins on the order and dynamics of the acyl chains of phospholipid bilayers [8-13]. (
  • Moreover, 31 P solid-state NMR spectroscopy can be used to investigate the interaction of peptides, proteins and drugs with phospholipid head groups [11-14]. (
  • The secondary structure of 13 C = O site-specific isotopically labeled peptides or proteins inserted into lipid bilayers can be probed utilizing 13C CPMAS solid-state NMR spectroscopy [15-18]. (
  • E. Goormaghtigh, V. Raussens and J. M. Ruysschaert, "Attenuated Total Refection Infrared Spectroscopy of Proteins and Lipids in Biological Membranes," Biochimica et Biophysica Acta, Vol. 1422, 1999, pp. 105-185. (
  • Particularly, the combination of IR and UV hole burning spectroscopy with molecular beam techniques has recently yielded detailed information on the structure of low energy conformations of a variety of biomolecules, among which several small peptides. (
  • Quantitative analysis of adsorbed proteins by X-ray photoelectron spectroscopy. (
  • The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy ( 1 H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. (
  • Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and 3 J(HNα) coupling constants. (
  • Secondary structure composition of two homologous proteins, alpha-fetoprotein and serum albumin, has been compared using circular dichroism and Fourier-transform infrared spectroscopy. (
  • Scientists from the University of Strathclyde, UCB Pharma and STFC's Central Laser Facility have used 2D-IR spectroscopy to quantify changes in the secondary structure of the multifunctional calcium-binding messenger protein Calmodulin (CaM). (
  • Making use of the ULTRA laser facility at the Central Laser Facility (CLF), the research team has been able to measure subtle protein conformational changes in solution - as a function of temperature and Calcium (Ca 2+ ) concentration - using 2D-IR spectroscopy in combination with multivariate analysis. (
  • By measuring the thermal stability and Ca 2+ - binding transition of human CaM with IR absorption and 2D-IR spectroscopy, the team have proved that 2D-IR can be used to reliably quantify relative changes in secondary structure elements in proteins by measuring subtle changes in the 2D-IR spectra of the amide I IR absorption band. (
  • Not only can ultrafast 2D-IR spectroscopy of unlabelled proteins help scientists paint a broader picture of conformational change but it can also help create a platform for spatially targeted studies. (
  • Correspondingly, ultraviolet NCD spectroscopy of peptide-bond excitations is a well-established method for the determination of the secondary structure of proteins. (
  • Recently, our group participated in the secondary structure analysis of the uracil-DNA-degrading factor by using vacuum ultraviolet NCD spectroscopy. (
  • FTIR spectra of each solution were obtained using attenuated total reflectance, and amide-I peaks were analyzed to provide secondary structure information. (
  • W. K. Surewicz and H. H. Mantsch, "New Insight into Protein Secondary Structure from Resolution-Enhanced Infrared Spectra," Biochimica et Biophysica Acta. (
  • Specifically, using time dependent density functional theory calculations, we examine the absorption spectra of naturally charged amino acids (Lys, Glu, Arg, Asp and His), extracted from solution phase protein structures generated by classical molecular dynamics simulations, and phosphorylated amino acids (Tyr, Thr and Ser) from experimentally determined protein structures. (
  • Our results provide a foundation for the development of spectroscopic markers based on the recently proposed Protein Charge Transfer Spectra (ProCharTS) which are relevant for the study of DNA-binding or intrinsically disordered proteins that are rich in charged amino acids. (
  • Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the protein's secondary structure. (
  • This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software. (
  • Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. (
  • The performance of three popular methods for estimating protein secondary structure fractions from CD spectra (implemented in software packages CONTIN, SELCON3, and CDSSTR) and a variant of CONTIN, CONTIN/LL, that incorporates the variable selection method in the locally linearized model in CONTIN, were examined using the five reference sets described here, and a 22-protein reference set. (
  • The optimization of protein secondary structure determination with infrared and circular dichroism spectra. (
  • Protein concentration is not an absolute prerequisite for the determination of secondary structure from circular dichroism spectra: a new scaling method. (
  • Evaluation of the information content in infrared spectra for protein secondary structure determination. (
  • However, analysis of hybrid IR-CD spectra gives more accurate values for secondary structure composition for both AFP and SA and shows that the secondary structures of these proteins are the same. (
  • The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. (
  • Protein secondary structure is an important consideration when studying protein folding, protein stability, or enzyme activity. (
  • Both these parameters provide important information about the stability of the protein under study. (
  • Part of the long-term goal of understanding the formation, function and stability of proteins requires that all conformations be accurately assigned and structurally understood. (
  • How to quantify the "stability" of a protein complex? (
  • 2D NMR Analysis of the Effect of Asparagine Deamidation Versus Methionine Oxidation on the Structure, Stability, Aggregation, and Function of a Therapeutic Protein. (
  • Hydrogen bonding is a central feature in protein structure but only make minor contributions to protein stability. (
  • 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. (
  • So, in order to form the tertiary structure, the polypeptide chain bends and twists, achieving the lowest energy state with a high stability. (
  • Recent research on secondary structure prediction is mainly based on widely known machine learning techniques, such as Artificial Neural Networks and Support Vector Machines. (
  • Ibrahim, A. and Yasseen, I. (2017) Using Neural Networks to Predict Secondary Structure for Protein Folding. (
  • In our work, we have used five different structures of Neural Networks including (Feed Forward NN, Learning vector quantization NN, Probabilistic NN). (
  • A simple and fast secondary structure prediction method using hidden neural networks. (
  • Deep neural networks are good at capturing the global information in the whole protein, which are widely believed to be crucial for the prediction. (
  • Neural networks tend to work for secondary structure prediction due to the pattern recognition nature of the task. (
  • Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. (
  • Bioinformatics involves the technology that uses computers for storage, retrieval, manipulation, and distribution of information related to biological macromolecules such as DNA, RNA, and proteins. (
  • We used this dataset from bioinformatics information Lab from University of Missouri, United States of America, it is contains 1854 protein. (
  • The effect of long‐range interactions on the secondary structure formation of proteins. (
  • Motivation: Proteinâ€"protein interactions play vital functional roles in various biological phenomena. (
  • Quaternary Strut1ure Subunit Interactions Symmetry in Proteins C. Determination of Subunit Composition Appendix: Viewing Stereo Pictures The properties of a protein are largely determined by its three-dimensional structure. (
  • Tertiary structure is the three-dimensional shape of the protein determined by regions stabilized by interactions between the side chains. (
  • Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed ßa protein. (
  • This will eliminate many of the ionic interactions that were necessary for maintenance of the folded shape of the protein. (
  • We carry out a comprehensive study of long-range interactions on a large data set of non-homologous proteins. (
  • Our study reveals that the long-range interactions between amino acids far apart are common in protein folding, and play an important role on the formation of secondary structure. (
  • The interactions between the side-chains of amino acids are responsible for the formation of the tertiary structure. (
  • The presented structure analysis and modelling of co-substrate interactions provide valuable insight into the function of MmuM in both methionine biosynthesis and cofactor repair. (
  • Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. (
  • Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. (
  • Beger RD, Bolton PH (1997) Protein phi and psi dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures. (
  • SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. (
  • Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. (
  • Also, solid-state NMR spectroscopic studies can be utilized to ascertain pertinent informa- tion on the backbone and side-chain dynamics of 2 H- and 15 N-labeled proteins, respectively, in phospholipid bilayers [19-26]. (
  • Kountouris, P., Hirst, J.D.: Prediction of backbone dihedral angles and protein secondary structure using support vector machines. (
  • Secondary structure protein refers to regular repeative sub-structures on the protein backbone. (
  • Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. (
  • Furthermore, the protein backbone also exhibits CT transitions in the far UV range. (
  • Hence, the IR signature of the Amide bands and the mid-IR fingerprint of the backbone bands are quite complementary and offer a very detailed description of the secondary structure of peptides. (
  • Secondary structure is comprised of regions stabilized by hydrogen bonds between atoms in the polypeptide backbone. (
  • The secondary structure arises from the hydrogen bonds formed between atoms of the polypeptide backbone. (
  • Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? (
  • To explore this question, backbone dihedral angles were extracted from the known three-dimensional structure of 2,439 proteins and mapped into 36 labeled, 60° × 60° bins, called mesostates. (
  • This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups. (
  • The statistical bias toward native secondary structure in helix (red), strand (green), turn (blue), and generalized turn (black) for all segments in Table 2 is parceled into bins, with statistical weights that range from 0.0 to 1.0 in increments of 0.1. (
  • Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three dimensional structure, as well as its function. (
  • Other extended structures such as the polyproline helix and alpha sheet are rare in native state proteins but are often hypothesized as important protein folding intermediates. (
  • There are eight types of secondary structure that DSSP defines: G = 3-turn helix (310 helix). (
  • It is contains 28.3% α-helix (H), 21.3% β-sheet (E) and 50.4% coil (C). The second dataset is formed of proteins from four different classes. (
  • Certainly, tertiary structure must be lost, but given that the stem is wide enough to accommodate an α helix with its side chains, it is not clear to what extent secondary structure is preserved. (
  • Reported correlation coefficients for secondary structure content prediction by CD are typically in the range of r = 0.92-0.97 for α-helix (H), r = 0.80-0.90 for β-sheet (E) [ 4 , 6 ]. (
  • Here the content-balancing means that the evaluation is independent of the contents of helix, strand and coil in the protein being predicted. (
  • Ne-=-ither the turn nor the helix-in-solution methods have yet been combined with other secondary structure prediction methods. (
  • Various types of secondary structures have been discovered, but by far the most common is the orderly repeating forms known as the a-helix and the b sheet. (
  • The structure of a b sheet is very different from the structure of an a-helix. (
  • Again, the polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the a-helix, these bonds are formed between neighbouring polypeptide (b) strands. (
  • The two most important secondary structure of proteins, the alpha helix, and the beta sheet were predicted by the American chemist Linus Pauling in the early 1950s. (
  • Two secondary structure of proteins, the alpha helix, and the beta pleated sheet fulfill these criteria well. (
  • The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the X-ray structure. (
  • The main difference between primary secondary and tertiary structure of protein is that the primary structure of a protein is linear and the secondary structure of a protein can be either an α-helix or β-sheet whereas tertiary structure of a protein is globular . (
  • The secondary structure of a protein is either an α-helix or β-sheet formed from its primary structure. (
  • The two main secondary structures are the alpha helix and the anti-parallel beta-pleated sheet. (
  • For a polypeptide consisting of a single conformational folding pattern (e.g., an alpha helix only), the secondary and tertiary structure may be one and the same. (
  • The importance of an antiparallel DNA double helix structure is because of its hydrogen bonding between the complementary nitrogenous base pairs. (
  • in 1951 (before any protein structure had ever been experimentally determined). (
  • Protein folding in vivo is mediated by helper proteins, the molecular chaperones, of which Hsp60 and its Escherichia coli variant GroEL are some of the best characterized. (
  • The mmuM gene product from Escherichia coli is an archetypal HMT family protein and contains a predicted zinc-binding motif in the enzyme active site. (
  • The key biological molecules are carbohydrates, lipids, proteins and nucleic acids. (
  • Background Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. (
  • The aggregation of nonpolar side chains in the interior of a protein is favored by the increase in Entropy of the water molecules that would otherwise form cages around the hydrophobic groups. (
  • Basic building block of protein molecules. (
  • Proteins are the largest and most varied class of biological molecules, and they show the greatest variety of structures. (
  • Draw the Lewis structure for each of the following molecules or ions. (
  • The Lewis structure of molecules or ions, spatial orientation of electron pairs and the simple geometric structure indicating the approximate bond angles of that molecules or ions should be determined. (
  • GroEL seems to interact with non-native proteins, binding one or two molecules per 14-mer in a 'central cavity', but little is known about the conformational state of the bound polypeptides. (
  • As structure and function in biological molecules are so heavily linked, an understanding of the molecular mechanisms that occur under physiological conditions must be quantified. (
  • Organic molecules are often chiral, including the naturally occurring sugars and amino acids, the building blocks of nucleic acids and proteins. (
  • 2013). Hydrophobic enhancement of Dopamediated adhesion in a mussel foot protein. (
  • The hydrophobic effect is the major determination of original protein structure. (
  • This is due to the exposure of hydrophilic, acidic ad basic amino acids to the outside and hiding of the hydrophobic amino acids such as aromatic amino acids and the amino acids with alkyl groups in the core of the protein structure. (
  • Although Met is one of the less abundant proteinogenic amino acids, it has an indispensable role in the initiation of translation [ 2 ] and commonly contributes to the hydrophobic cores of proteins [ 3 ]. (
  • Hydrophobic interaction is the main stabilizing force for subunits in quaternary structure. (
  • In this work we investigate whether further progress may be achieved by incorporating the relative solvent accessibility (RSA) of an amino acid residue as a fingerprint of the overall topology of the protein. (
  • For cold-shock protein and the SH3 domain, we accurately reproduce the secondary structure elements and the topology of the 5-stranded beta-sheets, but not the barrel structure. (
  • Quaternary structure is the association between two or more polypeptides, but not every protein has a quaternary structure. (
  • In the natural course of making a protein, polypeptides are elongated by the addition of amino acids to the C-terminal end of the growing chain. (
  • There are four levels of structure found in polypeptides and proteins . (
  • Dandekar, T., Argos, P.: Folding the main chain of small proteins with the genetic algorithm. (
  • Even such small proteins contain hundreds of atoms and have molecular weights of over 5000 Daltons (Da). (
  • Using this approach, we demonstrate the applicability of the framework to the problem of reconstructing the overall protein fold for a number of commonly studied small proteins, based on only predicted secondary structure and contact map. (
  • Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to determine the accuracy of secondary structure assessment by calculating and comparing Δδ values for various RCCS datasets. (
  • Despite obvious RCCS variations between datasets, prediction of secondary structure was consistently similar. (
  • Fibrous proteins are usually important in forming biological structures. (
  • Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. (
  • Secondary structure motifs are selectively enhanced by different excitation wavelengths, a characteristic that inspired the first methods for quantifying secondary structures by DUVRR. (
  • As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined. (
  • The limited size of data set might due to the small number of non-homologous proteins with solved three-dimensional structures at that time. (
  • The method is based on Metropolis Monte Carlo simulations in a force field of empirical potentials that are designed to stabilize secondary structure elements in room-temperature simulations. (
  • Slow-digesting proteins stabilize blood sugar over longer periods and are anti-catabolic, which means they help prevent the breakdown of muscle. (
  • It appears that in all the inhibitors examined there is a region conserved in the vicinity of the active site, composed of one beta-turn with an adjacent beta-sheet structure, and a second beta-turn situated in the other part of the polypeptide chain and linked with the first one by disulphide bridge. (
  • In this structure, two different regions of a polypeptide chain lie side by side and are bound by hydrogen bonds. (
  • In some proteins, the linear polypeptide chain is cross-linked: Disulfide bonds. (
  • Extreme temperatures will result in the unfolding of a polypeptide chain leading to a change in structure and often a loss of function. (
  • In a b sheet, the polypeptide chain folds back on itself so that polypeptide strands like side by side, and are held together by hydrogen bonds, forming a very rigid structure. (
  • It forms the polypeptide chain of the protein. (
  • The tertiary structure of protein is the folded structure of the polypeptide chain into a 3D-structure. (
  • The primary structure may be thought of as a complete description of all of the covalent bonding in a polypeptide chain or protein. (
  • The tertiary structure of a polypeptide or protein is the three-dimensional arrangement of the atoms within a single polypeptide chain. (
  • Detailed consideration of the dynamic behavior or proteins and how they fold to their native structllfcs is deferred until Chapter 9. (
  • Many have intricate three-dimensional folding patterns that result in a compact form, but others do not fold up at all ("natively unstructured proteins") and exist in random conformations. (
  • To understand how proteins fold, we will start with the basics of structure, and progress through to structures of increasing complexity. (
  • The structure displays the main features of the canonical MH2 fold with two main differences: the addition of an α -helical region and the remodelling of a protein-interaction site that is conserved in the MH2 domain of Smads. (
  • Hua, S., Sun, Z.: A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. (
  • The GOR method of protein secondary structure prediction is described. (
  • Knowledge of protein structure plays a significant role in molecular biology, cell biology, pharmacology and medical science. (
  • The random coil is not a true secondary structure, but is the class of conformations that indicate an absence of regular secondary structure. (
  • The ability of this encoding to capture protein native conformations was tested using an evolutionary algorithm as the inference procedure for discovering L-systems. (
  • It is an attempt to objectively classify the whole set of conformations occurring in protein structures described by small overlapping fragments. (
  • Hydrogen bonds fine tune the tertiary structure by selecting the unique structure of a protein from among a relatively small number of hydrophobically stabilized conformations. (
  • The first dataset is obtained from matlab math work [5] and from thesis [3] , it is contain 114 protein samples which are divided into training dataset with 75 protein samples and testing dataset with 44 protein sample. (
  • We suggest caution when using Δδ-based restraints in structure calculations as the underlying dataset may be biased. (
  • The reported values vary because of differences in the reference dataset, secondary structure assignment and prediction algorithms used. (
  • Homology of the predicted secondary structures of the N-terminal fragments of preproteins. (
  • Using the predicted RSA, we were able to improve the performance of our secondary structure prediction by up to 1.4% and achieved the overall per-residue accuracy between 77.0% and 78.4% for the 3-state classification problem on different control sets comprising, together, 603 proteins without homology to proteins included in the training. (
  • This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of this, HSSP is also a database of homology-based implied protein structures. (
  • PSS transition sites can be utilized in Homology Modeling (HM) to define the boundary of secondary structure elements. (
  • I've been reading lately about primary (which I understand completely) and secondary (which I do not understand that well since I'm not very good at chemistry) structure of proteins. (
  • Data from the paper [1] , published in the Journal Analytical Chemistry indicates that secondary structure transitions, along with thermally induced alterations in the coupling between vibrations in the protein, alters the 2D-IR signal. (
  • The Rost-Sander data set [1] consists of proteins whose structures span a relatively wide range of domain types, composition and length. (
  • There are four different structure types of proteins, namely the Primary, Secondary, Tertiary and Quaternary structures. (
  • The primary structure of a polypeptide of protein determines its secondary, tertiary, and quaternary structures. (
  • We have trained a two-layered feed-forward neural network on a non-redundant data base of 130 protein chains to predict the secondary structure of water-soluble proteins. (
  • Tertiary structure or the globular form of proteins is water-soluble under physiological conditions. (
  • Most defined secondary structures found in proteins are one or the other type. (
  • It appears that the occurrence of motifs and sub-structures is an important component in protein folding, and these sub-structures may be captured by a grammar-based encoding. (
  • Nevertheless, motifs need not be associated with a distinctive secondary structure. (
  • Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. (
  • The inclusion of protein family information in this form increases the prediction accuracy by six to eight percentage points. (
  • Over past decades, the prediction accuracy of protein secondary structure has gained some improvements, largely due to the successful application of machine learning tools such as neural network (NN) and support vector machine (SVM). (
  • It implies that cross-validation technique, where test proteins are removed from the training set, is a more realistic evaluation of protein secondary structure prediction accuracy to be obtained [ 3.0.CO;2-4" href="/articles/10.1186/1471-2105-7-S4-S14#ref-CR16" id="ref-link-section-d3236e478">16 ]. (
  • In this work, we introduce computational methods for extracting and visualizing the secondary structure consensus for a given protein family. (
  • Computational prediction of secondary and supersecondary structures. (
  • Many different computational approaches for protein structure comparison apply the secondary structure elements. (
  • Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. (
  • The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. (
  • Employing advanced computational techniques for protein structure prediction at secondary and tertiary levels provides alternative ways to accelerate the prediction process and overcome the extremely low percentage of protein structures that have been determined. (
  • H spin diffusion with MAS NMR is demonstrated for a helical transmembrane model protein complex. (
  • To gain accurate analysis of your secondary and tertiary protein structure, contact us today. (
  • In the case of proteins the amino acids are connected by peptide bonds, which have partial double bond character rendering the amide group planar. (
  • PSSP provides a significant first step toward the tertiary structure prediction, as well as offering information about protein activity, relationship, and function. (
  • Loops are almost invariably situated at the protein surface where they are poised to assume important roles in molecular function and biological recognition. (
  • The accurate assignment of the secondary structure of proteins from protein atom coordinates underlies the analysis of protein structure and function. (
  • Protein secondary structure (SS) prediction is important for studying protein structure and function. (
  • Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. (
  • Experiments on biomolecules in the gas phase, where the interaction with the environment is eliminated or controlled, provide fundamental insight into their structure and function. (
  • It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. (
  • Enzymatic function can be tied directly to the internal motions identified as the residual entropy of protein structure. (
  • The observed increase in fast motions identifies obvious structures known to be important in the redox mechanism and several unobvious structures that could indicate regions possibly coupled to protein function. (
  • Together these results identify important properties for understanding protein structure and function. (
  • In certain proteins or groups of proteins, the so-called spikes of high content for a specific amino acid type or combination of amino acids were identified and confirmed statistically, which in some cases could be directly related to function and ligand specificity. (
  • This was prevalent in proteins with a function of multidrug or metal ion efflux. (
  • Locations of specific amino acid types in some of the proteins that have crystal structures (EmrE, LacY, AcrB) were also considered to help link amino acid content with protein function. (
  • Nearly every function in living beings depends on proteins. (
  • Each of these proteins has its own structure and function. (
  • Yes, in fact several known proteins have different folding patterns for the same primary structure as part of their function. (
  • Metal ions may also function to internally cross link proteins. (
  • As a result the change in structure will cause a change or loss of function. (
  • The function of a protein is based on its structure. (
  • A 2DIR spectrum shows the change in the probe spectrum as a function of pump wavelength and provides information on how vibrations couple to other vibrations within the protein secondary structure as well as how excited vibrations lose their energy. (
  • The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. (
  • We also observed that projecting real-valued RSA into 2 discrete classes with the commonly used threshold of 25% RSA decreases the classification accuracy for secondary structure prediction. (
  • Another less commonly known secondary structure is the beta-barrel. (
  • Using the Snob program for information-theoretic Minimum Message Length (MML) intrinsic classification, we are able to take the protein dihedral angles as determined by X-ray crystallography, and cluster sets of dihedral angles into groups. (
  • As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. (
  • The side chains project outward and contact any solvent, producing a structure something like a bottle brush or a round hair brush. (
  • Here we use nuclear magnetic resonance techniques to show that the interaction of the small protein cyclophilin with GroEL is reversible by temperature changes, and all amide protons in GroEL-bound cyclophilin are exchanged with the solvent, although this exchange does not occur in free cyclophilin. (
  • There are several methods for formally defining protein secondary structure (e.g. (
  • Cuff and Barton 513 protein data set is used in training and testing the prediction methods under the same hardware, platforms, and environments. (
  • T. A. Cross, "Solid-State Nuclear Magnetic Resonance Characterization of Gramicidin Channel Structure," Methods in Enzymology, Vol. 289, 1997, pp. 672-696. (
  • Y. Nakazawa and T. Asakura, "Structure Determination of a Peptide Model of the Repeated Helical Dmoain in Samia Cynthia Ricini Silk Fibroin before Spinning by a Combination of Advanced Solid-State NMR Methods," Journal of the American Chemical Society, Vol. 125, No. 24, 2003, pp. 7230-7237. (
  • Most of the state-of-the-art methods for protein seconday structure prediction are complex combinations of discriminant models. (
  • A survey of machine learning methods for secondary and supersecondary protein structure prediction. (
  • Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. (
  • It is able to predict protein secondary structure as good as current popular methods. (
  • Potential for hydrogen bonds is associated with resulting secondary structures, providing a partial indicator that may be used in combination with outputs of other services. (
  • This structure is composed of antiparallel beta-strands, and it is twisted and coiled into a barrel so that the first strand hydrogen bonds to the last strand. (
  • Also, it is important to note that the hydrogen bonds between the binding atoms are weak, but the summation of all the hydrogen bonds allows the structure to maintain its shape. (
  • Hydrogen bonds formed between amino acids are responsible for the formation of the secondary structure of a protein while disulfide and salt bridges form the tertiary structure. (
  • In addition, hydrogen bonds also help in stabilizing the 3D-structure. (