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?
TY - JOUR. T1 - Interhelical interactions in the gp41 core. T2 - Implications for activation of HIV-1 membrane fusion. AU - Wang, Shilong. AU - York, Joanne. AU - Shu, Wei. AU - Stoller, Marisa O.. AU - Nunberg, Jack H.. AU - Lu, Min. PY - 2002/6/11. Y1 - 2002/6/11. N2 - The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein complex (gp120-gp41) promotes viral entry by mediating the fusion of viral and cellular membranes. Formation of a stable trimer-of-hairpins structure in the gp41 ectodomain brings the two membranes into proximity, leading to membrane fusion. The core of this hairpin structure is a six-helix bundle in which three carboxyl-terminal outer helices pack against an inner trimeric coiled coil. Here we investigate the role of these conserved interhelical interactions on the structure and function of both the envelope glycoprotein and the gp41 core. We have replaced each of the eight amino acids at the buried face of the carboxyl-terminal helix with a representative ...
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
The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance of the problem and decades of theory development, computer simulations, and laboratory experiments. Information about the correctly folded state of most proteins is likely to be present in their sequences, and yet many proteins fail to attain native structure after overexpression in a non-native environment or upon experimental denaturation and refolding. We hypothesize that correct protein folding in vivo is an active, energy-dependent process that most likely applies torque force co-translationally to all proteins and possibly also post-translationally to many proteins in every cell. When a site on an unfolded polypeptide is rotationally constrained, torsion applied at another site would induce twisting of the main chain, which would initiate the formation of a local secondary structure, such as
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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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Alpha helix   A common motif in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring,
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 ...
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[vague] 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) ...
List of notable protein secondary structure prediction programs List of protein structure prediction software Protein structure ... prediction (Structural bioinformatics software, Protein structure, Protein methods). ...
HSSP (Homology-derived Secondary Structure of Proteins) is a database that combines structural and sequence information about ... 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 ...
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 ...
In protein structure, STRIDE (Structural identification) is an algorithm for the assignment of protein secondary structure ... DSSP Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23(4):566-79. doi:10.1002/ ... 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 ...
"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 ...
"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. " ...
"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 ...
"Protein structure: Primary, secondary, tertiary & quatrenary (article)". Khan Academy. Retrieved 28 September 2022. Stratmann ... 2002), I.3. Proteins: The Shape and Structure of Proteins Alberts et al. (2002), I.3. Proteins: Protein Function Archived 25 ... without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly ... Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and ...
Salamov A.A.; Solovyev V.V. (199). "Protein secondary structure prediction using local alignments". J. Mol. Biol. 268 (1): 31-3 ... 200). "Community structure and metabolism through reconstruction of microbial genomes from the environment". Nature (42): 37 - ... Solovyev V.V. (1993). "Fractal graphical representation and analysis of DNA and Protein sequences". BioSystems (3): 137-160. - ...
Cid, Hilda; Bunster, Marta; Arriagada, Eugenio; Campos, María (1982). "Prediction of secondary structure of proteins by means ... Shu, Jian-Jun; Yong, Kian Yan (2017-04-15). "Fourier-based classification of protein secondary structures". Biochemical and ... "Quantitative theory of hydrophobic effect as a driving force of protein structure". Protein Science. 23 (4): 387-399. doi: ... Among their first research was the development of the secondary structures prediction method by means of hydrophobicity ...
"JPred: A Protein Secondary Structure Prediction Server". Retrieved 2021-12-17. Kumar, Prof. T. Ashok ... "AlphaFold Protein Structure Database". Retrieved 2021-12-17. "iCn3D: Web-based 3D Structure Viewer". www. ... "Protein BLAST: search protein databases using a protein query". Retrieved 2021-12-17. (CS1 errors: ... "CFSSP: Chou & Fasman Secondary Structure Prediction Server". Retrieved 2021-12-17. "Bioinformatics Toolkit". ...
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. (Articles with short description, Short ... 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 ...
Table 3. Table of WDCP protein Isoforms and Protein Information. The secondary structure of WDCP Protein Isoform 1 consists of ... "abi GOR IV Protein Secondary Structure Prediction Method". Rhone-Alpes Bioinformatic Pole Gerland Site. Prabi-Gerland. ... The mRNA secondary structures of the UTR regions exhibited a high number of predicted stem-loop structures in the WDCP ... SUMOylation can affect protein-protein interactions and affect protein ubiquitination. Palmitoylation is the addition of a ...
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_ ...
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/ ... The Chou-Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed ...
... (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 ...
The supersecondary structure refers to a specific combination of secondary structure elements, such as β-α-β units or a helix- ... The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a ... A protein structure database is a database that is modeled around the various experimentally determined protein structures. The ... Structure similarity can then be used to group proteins together into protein superfamilies. If shared structure is significant ...
... the tertiary structure, and the quartenary structure. Protein secondary structure prediction is a main focus of this subfield ... as tertiary and quartenary structures are determined based on the secondary structure. Solving the true structure of a protein ... where they conform into a three-dimensional structure, including the primary structure, the secondary structure (alpha helices ... Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". ...
A supersecondary structure is a compact three-dimensional protein structure of several adjacent elements of a secondary ... Protein folding Secondary structure Structural motif "Helix Supersecondary Structures". Retrieved ... Connecting loops can be long and include other secondary structures. The Greek key motif has its name because the structure ... This structure can be seen in almost all proteins with parallel strands. The loops connecting the beta strands and alpha helix ...
"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 ...
Circular dichroism experiments have shown that the secondary structure of dirigent protein from Forsythia intermedia is ... Halls SC, Lewis NG (July 2002). "Secondary and quaternary structures of the (+)-pinoresinol-forming dirigent protein". ... The tertiary structure has not been solved, but the protein has been confirmed to be dimeric. Each dimer has a single binding ... Dirigent proteins are members of a class of proteins which dictate the stereochemistry of a compound synthesized by other ...
The secondary structure of transmembrane protein 179 is predicted to be made up of mostly alpha helix (52.36%) with some ... Both the human and frog proteins have the repetitive structure of "LAFL" appearing twice in their protein which suggests that ... "Protein BLAST: search protein databases using a protein query". Retrieved 2019-03-03. Sievers F, Wilm A ... Transmembrane protein 179 is a protein that in humans is encoded by the TMEM179 gene. The function of transmembrane protein 179 ...
"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 ...
"Protein secondary structure and homology by neural networks The α-helices in rhodopsin." FEBS letters 241, (1988): 223-228 Rost ... "Predicting the secondary structure of globular proteins using neural network models." Journal of molecular biology 202, no. 4 ( ... "Prediction of protein secondary structure at better than 70% accuracy." Journal of molecular biology 232, no. 2 (1993): 584-599 ... From 1988 onward, the use of neural networks transformed the field of protein structure prediction, in particular when the ...
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. ...
... a secondary structure motif of proteins Hairpins (film), a 1920 film directed by Fred Niblo Hairpin, in music, the nickname for ...
The structure of PANO1 is 82% disordered meaning the protein is able to move around easily. The secondary structure reveals a ... "Protein BLAST: search protein databases using a protein query". Retrieved 2021-08-01. (CS1 maint: url- ... A predicted 3' UTR structure was generated using Unafold and depicts predicted stem loop structures. Two stem loop structures ... Stimulating protein 1, CCAAT/enhancer binding protein, GC box elements and HMG box-containing protein 1. Like previously ...
A third small domain at the C-terminal tail appears to have an ordered alpha helical secondary structure and may be involved in ... Like the other structural proteins, the gene encoding the N protein is located toward the 3' end of the genome. N protein is ... In addition to its interactions with RNA, N forms protein-protein interactions with the coronavirus membrane protein (M) during ... protein is a protein that packages the positive-sense RNA genome of coronaviruses to form ribonucleoprotein structures enclosed ...
Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular ... motifs need not be associated with a distinctive secondary structure. "Noncoding" sequences are not translated into proteins, ... for representing the protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins ... Mammalian Motif Finder MochiView Multiple EM for Motif Elicitation Nucleic acid sequence Protein primary structure Protein I- ...
They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation ... This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala- ... "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein". EMBO ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ...
... may refer to: Homology-derived Secondary Structure of Proteins, a protein database Port Sudan Military Airport, ICAO ...
These cells have proteins that make up the characteristics of the tumor. These proteins arise from blood vessels, nerve cells ... It is a cone shaped structure dorsal to the midbrain tectum. The tumor appears to be derived from the specialized ependymal ... The critical diagnosis of this neoplasm is often difficult because of its similarity with other primary or secondary papillary ... The tumor cells may differ in their structure and function, but they all have normal function, which is directed by the ...
Pyramid structure can vary across ecosystems and across time. In some instances biomass pyramids can be inverted. This pattern ... Aquatic producers, such as planktonic algae or aquatic plants, lack the large accumulation of secondary growth as exists in the ... "Organisms usually extract energy in the form of carbohydrates, lipids, and proteins. These polymers have a dual role as ... At different levels in the hierarchy of life, such as the stability of a food web, "the same overall structure is maintained in ...
It has secondary chloroplasts, and is a mixotroph able to feed by photosynthesis or phagocytosis. It has a highly flexible cell ... Russell, A. G.; Watanabe, Y; Charette, JM; Gray, MW (2005). "Unusual features of fibrillarin cDNA and gene structure in Euglena ... gracilis: Evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs ...
As a result, structural proteins, resulting from polypeptide products of gag and gag-pol genes, that are necessary for the HIV ... On February, 1989, Manuela Navia, Paula Fitzgerald, et al., published a paper that showed the three-dimensional structure of ... brands, Piperazines, 3-Pyridyl compounds, Secondary alcohols, Tert-butyl compounds). ... and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and ...
Vascular fold-like structures called laminae suspend the distal phalanx from the hoof wall. The skeleton of the horse has three ... As tendons develop they lay down collagen, which is the main structural protein of connective tissue. As tendons pass near bony ... The stallion's reproductive system is responsible for his sexual behavior and secondary sex characteristics (such as a large ... Ligaments attach bone to bone or bone to tendon, and are vital in stabilizing joints as well as supporting structures. They are ...
Some viruses can encode proteins that bind to double-stranded RNA (dsRNA) to prevent the activity of RNA-dependent protein ... Nagata S, Mantei N, Weissmann C (October 1980). "The structure of one of the eight or more distinct chromosomal genes for human ... Ishikawa T (October 2008). "Secondary prevention of recurrence by interferon therapy after ablation therapy for hepatocellular ... the E7 protein of Human papillomavirus (HPV), and the B18R protein of vaccinia virus. Reducing IFN-α activity may prevent ...
... which leads to change in folding and the secondary structure of miR-137. This alteration is believed to cause inefficient ... By suppressing Jarid1b protein level, miR-137 is believed to play a role in modulating the differentiated state of mouse ESCs. ... miR-137 is located on chromosome 1p22 within the non-protein-coding RNA gene AK094607. It is transcribed as a non-coding ... This binding in turn results in an inhibition of translation of the target protein or degradation of the target messenger RNA. ...
Spider monkeys (Ateles geoffroyi) also feed on the leaves, which contain 11% protein and 4% sugars and remain similar in ... insipida is also found in secondary forest. Ficus yoponensis is found in Central and South America from Chiapas in Mexico in ... ecology and population structure". Proceedings of the Royal Society B: Biological Sciences. 269: 2257. doi:10.1098/rspb. ...
A proposed structure for the protein can be found in the images for proposed structures. The secondary structure for the ... The predicted structures are below for both proteins. MENTHA interacting proteins for FAM178B. STRING interacting proteins for ... The tertiary structure of the protein may assume a coiled coil structure. FAM178B is most highly expressed in the skeletal ... There is currently no known structure for the protein. ZNF598 is a zinc finger protein and the value is .13. It plays a key ...
According to an analysis of the secondary protein structure, TTC39B is most likely to be expressed in the endoplasmic reticulum ... The TTC39B protein folds into an alpha-alpha super helix. 40% of its structure matches with d1w3ba, the superhelical domain of ... Tetratricopeptide repeat protein 39B is a protein that in humans is encoded by the TTC39B gene. TTC39B is also known as C9orf52 ... "Tetratricopeptide repeat protein 39B isoform 1 [Homo sapiens] - Protein - NCBI". "NCBI". Retrieved 9 May 2013.[permanent dead ...
... ions from the cell provides the driving force for several secondary active transporters such as membrane transport proteins, ... Thyroid hormone V-ATPase Clausen MV, Hilbers F, Poulsen H (June 2017). "The Structure and Function of the Na,K-ATPase Isoforms ... Protein-protein interactions play a very important role in Na⁺-K⁺ pump-mediated signal transduction. For example, the Na⁺-K⁺ ... this membrane protein can also relay extracellular ouabain-binding signalling into the cell through regulation of protein ...
Folded tRNAs therefore act as secondary structure punctuations. The promoters for the initiation of the transcription of the ... mtDNA is packaged with proteins which appear to be as protective as proteins of the nuclear chromatin. Moreover, mitochondria ... InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. (apparently ... an annotated database and analysis platform of protein-protein interactions for human mitochondria". BMC Genomics. 12: 335. doi ...
Developing sperm carrying a Y chromosome can be supplied with essential proteins encoded by genes on the X chromosome. de ... There is also a comparative germ cell nest structure in the developing spermatogonia, with interconnected intracellular ... two haploid secondary spermatocytes, and in the second round into four haploid (23 chromosomes in the human) spermatids. These ... Haglund, Kaisa; Nezis, Ioannis P.; Stenmark, Harald (2011-01-01). "Structure and functions of stable intercellular bridges ...
At this point, the secondary axon leaves its nucleus and passes anteriorly and medially. The collection of secondary axons that ... The spinal cord is a long, thin, tubular structure made up of nervous tissue, which extends from the medulla oblongata in the ... Meanwhile, the overlying ectoderm secretes bone morphogenetic protein (BMP). This induces the roof plate to begin to secrete ... After synapsing, secondary axons decussate and ascend in the anterior lateral portion of the spinal cord as the spinothalamic ...
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 ...
The NH2 terminus contains two hydrophobic segments whose secondary structure is believed to be helical. Evidence suggests that ... Wang LH, Kulmacz RJ (2002). "Thromboxane synthase: structure and function of protein and gene". Prostaglandins and Other Lipid ... Wang LH, Kulmacz RJ (2003). "Thromboxane synthase: structure and function of protein and gene". Prostaglandins Other Lipid ... However, this protein is considered a member of the cytochrome P450 superfamily on the basis of sequence similarity rather than ...
It is a structure of the epidermis containing three different cell types: anchor cells, adhesive glands and releasing glands. ... They are absent in the clade Neodermata, most likely due to a secondary loss of this feature because their epidermis is turned ... flatworm Macrostomum lignano relies on a duo-gland system and is mediated by a cell type-specific intermediate filament protein ...
The mRNA secondary structure for C17orf78 was found by the online tool RNAfold show a moderate affinity for stem-loop (hairpin ... C17orf78 is also potentially a transmembrane protein due to the presence of a transmembrane region. C17orf78 secondary ... Uncharacterized protein C17orf78 is a protein encoded by the C17orf78 gene in humans. The name denotes the location of the ... "I-TASSER server for protein structure and function prediction". Retrieved 2020-05-21. " ...
... 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')-this ... and contains less protein and lipid than ordinary table rice. Sake rice is used only for making sake, because some say it is ...
Protein Structure and Molecular Enzymology. 996 (1-2): 82-8. doi:10.1016/0167-4838(89)90098-8. PMID 2736261. Lund T, Geurts van ... secondary to a constitutive achlorhydria. This finding facilitates the diagnosis of patients with this neurogenetic disorder. ... Wiborg O, Berglund L, Boel E, Norris F, Norris K, Rehfeld JF, Marcker KA, Vuust J (February 1984). "Structure of a human ... In 1964 the structure of gastrin was determined. GRCh38: Ensembl release 89: ENSG00000184502 - Ensembl, May 2017 GRCm38: ...
... and secondary prevention cohorts (CARE and PROVE IT-TIMI 22). Click on genes, proteins and metabolites below to link to ... Rudenko G, Henry L, Henderson K, Ichtchenko K, Brown MS, Goldstein JL, Deisenhofer J (December 2002). "Structure of the LDL ... This protein belongs to the LDLR family and is made up of a number of functionally distinct domains, including 3 EGF-like ... e.g. a truncation of the receptor protein at residue number 660 leads to domains 3,4 and 5 of the EGF precursor domain being ...
... and protein folding and sorting. These processes play into the larger part of cell structure and metabolism. Magnesium is the ... Magnesium has also been noted as a possible secondary messenger for neural transmissions. Magnesium acts as an allosteric ... Both proteins are tetramer complexes with iron protein complexes called hemes built into each subunit of the tetramer. The ... Calcium also plays a part in bone structure as the rigidity of vertebrae bone matrices are akin to the nature of the calcium ...
Home » APIs » PREDATOR protein secondary structure prediction. PREDATOR protein secondary structure prediction API - Developers ... 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 ...
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 ...
Solovyev, V & Shindyalov, IN 2002, Properties and Prediction of Protein Secondary Structure. in T Jiang, T Smith, Y Xu & M ... Properties and Prediction of Protein Secondary Structure. In Jiang T, Smith T, Xu Y, Zhang M, editors, Current Topics in ... Solovyev, V., & Shindyalov, I. N. (2002). Properties and Prediction of Protein Secondary Structure. In T. Jiang, T. Smith, Y. ... Solovyev, Victor ; Shindyalov, I.N. / Properties and Prediction of Protein Secondary Structure. Current Topics in Computational ...
Although P5 has been proposed as a fimbrial protein composed of coiled coils, both structural analysis by circular dichroism of ... analysis of the multiply aligned sequences predict a high proportion of β strand with no evidence of coiled coil structure. A ... which are highly conserved and align with the transmembrane region predicted for the homologous Escherichia coli protein, OmpA ... P5 outer-membrane protein from a range of clinical isolates is presented and represents the first analysis of the heterogeneity ...
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What is primary and secondary structure of protein?. The primary structure is comprised of a linear chain of amino acids. The ... DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). ... Which is a type of secondary structure?. The most common types of secondary structures are the α helix and the β pleated sheet ... it cannot guess the secondary structure for a mutated protein for which you dont have the 3D structure. And, again, DSSP does ...
Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
PCC 6803" , in Secondary structure estimation of recombinant psbH, encoding a photosynthetic membrane protein of cy, Vol. 43, ... Secondary structure estimation of recombinant psbH, encoding a photosynthetic membrane protein of cyanobacterium Synechocystis ... Non-labelled protein was used for secondary structure estimation by de-convolution from circular dichroism (CD) spectra. ... Non-labelled protein was used for secondary structure estimation by de-convolution from circular dichroism (CD) spectra. ...
Visualization and classification of protein secondary structures using Self-Organizing Maps. Christian Grevisse, Ian Muller, ...
Here we report the effects of in vivo expression of CFDP1, the human BCNT protein, in Drosophila melanogaster. We show that ... Investigating cellular functions and mechanism of action of BCNT proteins is challenging, because they have been implicated in ... evidences suggesting that homodimerization mediated by the BCNT domain is integral to the chromatin functions of BCNT proteins. ... protein family is widely distributed in eukaryotes and is characterized by a highly conserved C-terminal domain. This family ...
keywords = "Hydrogen bonds, Protein folding, Protein stability, Secondary structure",. author = "Domenico Bordo and Patrick ... The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. In: ... The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. / Bordo, ... title = "The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins", ...
... membrane protein structure, structure prediction, protein structure prediction, protein secondary structure, protein secondary ... Membrane Protein Secondary Structure Prediction Server Transmembrane, transmembrane structure, protein transmembrane structure ... structure prediction, membrane protein structure prediction, membrane protein secondary structure prediction, preference ... We have a list of other web servers for membrane protein secondary structure prediction. If you are maintaing the similar ...
What are 5 key functions of water inside and outside of cells? What is the structure of a water molecule? How are water ...
What is the secondary structure of a protein? What is tertiary for that matter? This article answers these questions and more. ... Levels of Protein Structure. We have already discovered that the primary structure of a protein is the sequence of amino acids ... Tertiary Structure. The structure of a protein in 3D space is what defines its function:. *A hormone must fit its receptor ... The secondary structures have now folded to occupy a specific 3D space - this is tertiary structure and is vital to the ...
The display of protein secondary structure data along a 1D sequence is important for showing stru ... Secondary structure variance on PDBe-KB aggregated views of proteins 2022-10-06. ... PDBe is a founding member of the Worldwide Protein Data Bank (wwPDB) which collects, organises and disseminates data on ... Like the coral in our warming seas, some colourful proteins can be bleached in harsh environmental conditions - but thankfully ...
With the far-UV system it is possible to detect variations in the ordered structures present in the protein structure, such as ... which are related to the protein tertiary structure, confirmed the effects of the different polyphenols on VVTL1 protein. In ... Among other things, this technique allows to follow fine variations in the protein structure and conformation in the presence ... Once determined that the tested polyphenols influenced the protein structure which is indicative of their interaction, the ...
... chemical environments promotes quantitative conversion of parallel beta sheet structures to the anti-parallel beta structures, ... a characteristic indicator of amyloid protein aggregation. Pressure effects on aggregation kinetics in a series of co-solvents ... Pressure-perturbation of protein secondary structure coupled with Microfluidic Modulation Spectroscopy - a powerful platform ... Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure ...
... proteins was carried out using a combination of criteria: atom--atom contact compatibility, position occupancy rate, ... The non-Ig structures were used as templates to analyze sandwich-like interfaces of unresolved homologous proteins using a ... Protein--protein recognition: juxtaposition of domain and interface cores in immunoglobulins and other sandwich-like proteins J ... The geometric wedding of the domain and interface cores supports the concept of a rigid-like substructure on the protein ...
Thermostable Alanine Racemase from Bacillus Stearothermophilus: DNA and Protein Sequence Determination and Secondary Structure ... Thermostable Alanine Racemase from Bacillus Stearothermophilus : DNA and Protein Sequence Determination and Secondary Structure ... Thermostable Alanine Racemase from Bacillus Stearothermophilus : DNA and Protein Sequence Determination and Secondary Structure ... DNA and Protein Sequence Determination and Secondary Structure Prediction†, Biochemistry, vol. 27, no. 4, pp. 1311-1316. https ...
Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins ... Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER. ... Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER. ... In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein ...
... to 240-nm region indicates that the protein has a) a considerable content of ... The circular dichroism (C.D.) spectrum of C-reactive protein in the 200- ... Comparison of the Secondary Structures and Binding Sites of C-Reactive Protein and the Phosphorylcholine-Binding Murine Myeloma ... N. Martin Young, Ross E. Williams; Comparison of the Secondary Structures and Binding Sites of C-Reactive Protein and the ...
Secondary structures thus plays an important role and can be visualized through different tools in form of cartoons, tubes, etc ... Secondary structure of a protein is important to predict the function as well as to find out evolutionary relationship. ... View the structure of a protein, with a perfect representation where you can clearly differentiate the secondary structure of ... Differentiate two proteins Thrombin (PDB ID 1PPB) and trypsin(PDB ID 2PTN) in case of a secondary structure with number of ...
Dive into the research topics of Effects of calcium and protons on the secondary structure of the nodulation protein NodO from ... Effects of calcium and protons on the secondary structure of the nodulation protein NodO from Rhizobium leguminosarum biovar ... Effects of calcium and protons on the secondary structure of the nodulation protein NodO from Rhizobium leguminosarum biovar ... title = "Effects of calcium and protons on the secondary structure of the nodulation protein NodO from Rhizobium leguminosarum ...
The Escherichia coli outer membrane protein OmpA acquires secondary structure prior to its integration into the membrane. ... Tumor protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, ... As no experimental structure of TRPM3 is available, we built a homology model of the channel in complex with PI(4,5)P2 via ... Almost all proteins that reside in the outer membrane (OM) of Gram-negative bacteria contain a membrane-spanning segment that ...
Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of `Magnetic ... The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data ... from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists ... and disseminate experimental constraints associated with NMR structures to the research community from a searchable resource in ...
Prediction of secondary structure in proteins is vital to the understanding of how proteins function within the body. The ... there is no way to quickly and accurately model the secondary structure folding. Current methods involve inferring structure ... folding of the primary structure into the secondary, which occurs in the milliseconds after translation of the primary protein ... TaABF and TaWD40, both wheat proteins, have been shown to interact with ABA-responsive protein kinase, PKABA1. AFN1, an oat ...
The target student population includes those in both Secondary and Higher Education. ... This page is a subset of reference material about cell structures. It gives an overview of membrane proteins, with particular ... The user will learn about membrane proteins, their structures, and how they contribute towards cell function. ... There are no prerequisites for this site, although some knowledge of cell structure and function will enhance the learning ...
Both BoNT/A1 and BoNT/A2 utilize three isoforms of synaptic vesicle protein SV2 (SV2A, B, and C) as their protein receptors. We ... The structure is similar to previously reported BoNT/A-SV2C complexes, but a shift of the receptor-binding segment in BoNT/A2 ... here present a high resolution (2.0 Å) co-crystal structure of the BoNT/A2 receptor-binding domain in complex with the human ... Krissinel, E.; Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three ...
  • The API returns indicators of hydrogen-bonded residues detected within the input data for use in secondary structure prediction. (
  • Based on the described research achievements, now we open the protein secondary structure prediction website, for the aim of improving the research communication and international technology service in Internet which concludes providing protein secondary structure predicting results free, receiving academic discussion and improving scientific research level. (
  • Solovyev, V & Shindyalov, IN 2002, Properties and Prediction of Protein Secondary Structure . (
  • Membrane protein sequence is the minimal input required by the prediction program. (
  • In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein structures we have used the known Q3 (alpha-helix,beta-strands and irregular turns/loops) secondary structure information, along with residue-residue contact information as restraints for MODELLER. (
  • An improved sequence-based prediction protocol for protein-protein interactions using amino acids substitution matrix and rotation forest ensemble classifiers. (
  • Improved performance in protein secondary structure prediction by inhomogeneous score combination. (
  • 1999. " Ab Initio Protein Structure Prediction With Molego " . (
  • 1998. " Implementing Genetic Algorithms With Sterical Constraints For Protein Structure Prediction " . (
  • 2000. " Protein Structure Prediction Using Combinatorial Optimization " . (
  • 1998. " Protein Structure Prediction With Combinatorial Optimization " . (
  • In Third Community Wide Experiment On The Critical Assessment Of Techniques For Protein Structure Prediction, Casp3 , 77. (
  • These cover the prediction of secondary structure, disordered regions, transmembrane helices, signal peptides and GO annotations. (
  • Predicting the secondary structure of globular proteins using neural network models. (
  • In this study spectra of five different globular proteins were compared in the solid and solution states recorded with several sampling techniques. (
  • 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. (
  • Among other things, this technique allows to follow fine variations in the protein structure and conformation in the presence of other molecules, thus giving information on the occurrence of interactions. (
  • Pressure effects on protein conformation are explained by hydration of solvent-excluded cavities that are populated with solvent upon unfolding. (
  • The Laboratory of Protein Conformation and Dynamics integrates complementary biophysical and biochemical techniques to understand the molecular mechanisms of amyloid formation. (
  • Dr. Lee focuses her research efforts on studying changes in protein conformation and dynamics important for the mechanisms by which amyloid structures assemble under normal and pathological conditions. (
  • This is the first folding level of protein conformation. (
  • Our study also revealed that the amide I, II, and III bands differ in their sensitivities to changes in protein conformation: For example, strong bands in the region 1620-1630 and 1685-1695 cm(-1) were seen in the amide I region of aggregated protein spectra. (
  • 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. (
  • Demonstrated more accurate determination of the secondary structure of single protein molecules than conventional bulk vibrational spectroscopy. (
  • As examples to demonstrate the capabilities of this technique, single molecules of two different protein species, apoferritin and thyroglobulin, were successfully measured, and their secondary structures were accurately determined from the high-quality AFM-IR spectra. (
  • In general, UV-light and oxygen are constantly attacking these molecules and rearranging their structures into molecular configurations unsuitable for their original purpose. (
  • For example, lyophilization in the absence of lyoprotectants caused spectral changes that could (partially) have been caused by the removal of hydrating water molecules rather than secondary structural changes. (
  • Preliminaries of the molecules of life and cell structures are investigated in this course. (
  • pH dependent fluorescence studies revealed the existence of electrostatic interaction between the protein and dye molecules. (
  • While storage and release of lipids are major functions of adipocytes, the adipocyte also uses specific lipid molecules for intracellular signaling and uses a host of protein factors to communicate with essentially every organ system in the body. (
  • GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors. (
  • Introduction G-protein combined receptors (GPCRs), known as seven-transmembrane (7TM) site receptors also, although diverse functionally, constitute the biggest integral membrane proteins family members in the human being genome [1]C[3]. (
  • These receptors are essential in human beings physiologically, taking part in the rules of all of our physiological activities such as for example neurotransmission, enzyme launch, inflammation or chemotaxis, aswell as our feeling of vision, taste and smell, by sensing endogenous or environmental stimuli through binding suitable ligands and AZD-3965 IC50 transducing related sign into cells typically through combined heterotrimeric G proteins. (
  • The Aedes aegypti G protein-coupled receptors AAEL024199 (AeCNMaR-1a) and AAEL018316 (AeCNMaR-1b) were identified as orthologs of the Drosophila melanogaster CNMa receptor (DmCNMaR). (
  • Our analytical standards of proteins, peptides, and amino acids offer accurate and reliable results in biomarker discovery, pharmaceutical research, clinical and diagnostic testing, top-down and bottom-up proteomics, and food authentication applications. (
  • Although P5 has been proposed as a fimbrial protein composed of coiled coils, both structural analysis by circular dichroism of purified P5 and computer analysis of the multiply aligned sequences predict a high proportion of β strand with no evidence of coiled coil structure. (
  • Intra-molecular side-chain:main-chain (sch:mch) and side-chain (sch:sch) hydrogen bonds observed in 44 well refined crystallographic protein structures with non-homologous sequences have been identified, classified and analysed to detect recurring structural patterns. (
  • The role of short-range hydrogen bonds in the formation and stabilization of a secondary structure and the importance of long-range hydrogen bonds as a cohesive force for different structural segments were also examined. (
  • The significance of hydrogen bonds as formers and stabilizers of a protein fold and the association of its secondary structural units was also considered through an examination of bond density and distribution throughout the protein tertiary structure. (
  • structural proteins must be shaped to maximise mechanical strength. (
  • Structural analysis of a non-redundant data set of 47 immunoglobulin (Ig) proteins was carried out using a combination of criteria: atom--atom contact compatibility, position occupancy rate, conservation of residue type and positional conservation in 3D space. (
  • IMSEAR at SEARO: Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER. (
  • This analysis also clearly indicates that even if we satisfy several true residue-residue contact distances, up to 30%of their sequence length with fully known secondary structural information, we end up predicting model structures much distant from their corresponding native structures. (
  • Despite these structural and binding-site differences, comparison of the amino-acid sequences of C-reactive protein and the hypervariable regions of the myeloma proteins suggests that the phosphorylcholine-binding sites of the two may still have features in common. (
  • The set of recalculated coordinates constitutes a unified database of protein structures in which potential user‐ and software‐dependent biases have been kept as small as possible and can be used by the structural biology community for further development of calculation protocols, validation tools, structure‐based statistical approaches and modeling. (
  • Here we study the relationship between amino acid residues encoded by edited codons and the structural characteristics of these residues within proteins, e.g., in protein-protein interfaces, elements of secondary structure, or protein structural cores. (
  • We find that the residues encoded by edited codons are significantly biased toward involvement in helices and protein structural cores. (
  • To begin to understand these differences, Dr. Lee is currently investigating the mechanisms of amyloid formation for two human proteins: α-synuclein, which is localized to nerve terminals and associated with Parkinson's disease, and Pmel17, which serves as structural scaffolding for melanin deposition in skin and eyes. (
  • Structural observations of endocytic pits by electron tomography revealed a dynamin-like structure indicative of a mode of scission analogous to that carried out by dynamin-1. (
  • Considering the differing sensitivity of the different amide modes to structural changes, it is advisable to utilize not only the amide I band, but also the amide II and III bands, to determine changes in protein secondary structure. (
  • Finally, it is important to realize that changes in these bands may not always correspond to secondary structural changes of the proteins. (
  • Surprisingly, we showed that secondary structural elements and N-glycosylation features were sufficient for model generation. (
  • structural analysis using circular dichroism showed that the purified FPR3 receptor was correctly folded with >50% -helix, which is similar to other known GPCR secondary structures. (
  • Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies in complex with the SARS-CoV-2 spike trimer or RBD. (
  • structural protein tests. (
  • The service predicts secondary protein structures by analyzing amino acid sequences submitted and detecting hydrogen-bonded residues within those structures. (
  • Secondary structure refers to regular, recurring arrangements in space of adjacent amino acid residues in a polypeptide chain. (
  • Loads DSSP output and assigns secondary structure states to the peptidic residues. (
  • In addition, the strong modification of the band at 230-250 nm, which indicates the contribute of the aromatic chromophore transition, suggests that the interaction likely involves the aromatic residues of the protein. (
  • The results shows that it is very difficult to obtain useful models even with 100% accurate secondary structure predictions and accurate residue contact predictions for up to 30% of residues in a sequence. (
  • No systematic patterns in converted sites were found on mRNAs, and the converted sites rarely encoded residues located at the active sites of proteins. (
  • Hence, only the edited form of an mRNA can be translated into a polypeptide with helix-preferring and core-forming residues at the appropriate positions, which is often required for a protein to form a functional three-dimensional (3D) structure. (
  • We have performed a novel analysis of the location of residues affected by RNA editing in proteins in plant organelles. (
  • We suggest that RNA editing may have conferring evolutionary advantage by acting as a mechanism to reduce susceptibility to DNA damage by allowing the increase in GC content in DNA while maintaining RNA codons essential to encode residues required for protein folding and activity. (
  • Earlier analysis [ 15 ] of the location of RNA targets within transcripts did not detect any rules to explain why particular residues within a protein sequence were affected by codon changes while other residues were not altered. (
  • In wheat mitochondrion ORF240, equivalent to cytochrome c biosynthesis protein, RNA editing converts a codon for one of the heme-binding residues to encode an amino acid appropriate for the heme interaction [ 18 ]. (
  • To determine the critical features guiding amyloid formation, Dr. Lee is characterizing how individual amino acid residues affect protein-protein interaction during the amyloid assembly process. (
  • Proteins are large biomolecules consisting of one or more long chains of amino acid residues. (
  • A hypothetical protein yjaB of these bacteria, consisting of 147 residues was picked out for in silico analysis. (
  • Alignment of the P5 sequences identified regions which are highly conserved and align with the transmembrane region predicted for the homologous Escherichia coli protein, OmpA. (
  • primary structure, in turn determined by DNA sequences) is vital to its function - but this shape can be distorted. (
  • RNA editing often increases the percent identity of the encoded amino acid sequence to the homologous sequences, implying an important role for RNA editing in the function of encoded proteins. (
  • The used Sequences for this were the "aligned" secondary structure sequences. (
  • This work uses unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity, and finds that without prior knowledge, information emerges in the learned representations on fundamental properties of proteins such as secondary structure, contacts, and biological activity. (
  • Random forest models that take as input a set of respiratory viral sequences can classify the protein as "spike" vs. non-spike based on predicted secondary structure elements alone (with 97.3% correctly classified) or in combination with N-glycosylation related features (with 97.0% correctly classified). (
  • With ChIP, the experimenter can determine if a specific protein binds to the exact sequences of a gene in residing cells by combining it with PCR (ChIP-PCR), microarray (ChIP-chip), or sequencing (ChIP-Seq) strategies. (
  • Duim B. , Bowler L. D. , Eijk P. P. , Jansen H. M. , Dankert J. , van Alphen L. Molecular variation in the major outer membrane protein P5 gene of nonencapsulated Haemophilus influenzae during chronic infections. (
  • Bordo, D & Argos, P 1994, ' The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins ', Journal of Molecular Biology , vol. 243, no. 3, pp. 504-519. (
  • While the ability to bind proteins is well known for tannins, which are polymers of several catechin units (fig. 1) less information is available on the interaction with proteins of polyphenols with a lower molecular weight. (
  • As no experimental structure of TRPM3 is available, we built a homology model of the channel in complex with PI(4,5)P 2 via molecular modeling. (
  • Effects of the oncogenic V664E mutation on membrane insertion, structure, and interactions of the Neu transmembrane domain: Mechanistic insights revealed from biophysical analyses and molecular dynamics simulation. (
  • This event is prevented by small Heat Shock Proteins (sHSPs) acting as molecular chaperones. (
  • Small heat shock proteins (sHSPs) are a ubiquitous family of molecular chaperones that play a vital role in maintaining protein homeostasis in cells. (
  • The molecular interaction between hemoglobin (HHb), the major human heme protein, and the acridine dyes acridine orange (AO) and 9-aminoacridine (9AA) was studied by various spectroscopic, calorimetric and molecular modeling techniques. (
  • The process can also be templated by a guest molecule that itself has an asymmetrical structure, which paves the way to molecular imprinting techniques at the level of single polymer chains. (
  • The results suggest that the molecular chains in the materials tested are primarily randomly coiled and lacking in regular structure, and are able to easily change between many transient conformations. (
  • There are three common secondary structures in proteins, namely alpha helices, beta sheets, and turns. (
  • The major secondary structures are α-helices and β-structures. (
  • With the far-UV system it is possible to detect variations in the ordered structures present in the protein structure, such as α-helices and β-sheets. (
  • View the structure of a protein, with a perfect representation where you can clearly differentiate the secondary structure of protein and report the number of helices and the beta strands, also report whether structure contains loops or not. (
  • Differentiate two proteins Thrombin (PDB ID 1PPB) and trypsin(PDB ID 2PTN) in case of a secondary structure with number of helices and beta sheets? (
  • Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90 o angle. (
  • AROS konnte als ein flexibles Protein ohne stabile Tertiärstruktur aber mit Sekundärstrukturelementen wie α Helices charakterisiert werden. (
  • This structure is extremely important - in the case of enzymes, any change to the shape of the molecule will deactivate the enzyme. (
  • Trehalose can help enzymes and proteins preserve their activity when lyophilized (freeze-dried) together. (
  • Other sugars and polyols have been explored as a partner chemical that provides many hydrogen bonding sites that stabilize the complex 3-D structure of proteins, enzymes, and nucleic acids in the absence of water but trehalose seems to be one of the best. (
  • The recombinant protein was purified and using MALDI-TOF MS determined to have a mass of 16,428 Da. (
  • The secondary structure contains regions of amino acid chains that are stabilized by hydrogen bonds from the polypeptide backbone. (
  • The human craniofacial development protein 1 (CFDP1) is a 299 amino acid long polypeptide which belongs to the evolutionarily conserved family of Bucentaur (BCNT) proteins ( Fig. 1 ) characterized by a highly conserved C- terminal BCNT domain 1 , 2 . (
  • When more than one polypeptide chain join forces for a common cause, quaternary structure is born. (
  • They are classified as integral, peripheral membrane proteins and polypeptide toxins. (
  • The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. (
  • The purpose of this server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions. (
  • These hydrogen bonds create alpha-helix and beta-pleated sheets of the secondary structure. (
  • When the chain coils, the structure is called an alpha helix . (
  • The results show that one can obtain better models for the proteins which have high percent of alpha-helix content. (
  • He called one configuration the alpha helix-later used by James Watson and Francis Crick to explain the structure of DNA. (
  • Gap junction proteins are present in both vertebrates and invertebrates permitting direct and indirect cellular communication. (
  • Recent evidences suggest that gap junction proteins play a critical role in bacterial and viral infections. (
  • Hydrophobic and Hydrophilic interactions - in the water based environment of the cell, the protein will fold so that water is excluded from hydrophobic regions (e.g. in the centre of the structure), with hydrophilic regions facing outwards in contact with water. (
  • All these compounds were tested for their interactions with the main wine protein, Vitis Vinifera Thaumatin-Like-1 protein (VVTL1) which was purified from wine. (
  • In addition, considering the importance of the protein denaturation for haze formation in wines, the effect of such interactions with polyphenols on the stability of the protein was studied by both thermal and UV-photo induced denaturation experiments. (
  • These subsets, with an average of 12 conserved positions and a contact surface of 630 A(2), delineate the inter- and intra-domain core, a refined instrument with a reduced target for analysis of sheet--sheet interactions in sandwich-like proteins. (
  • Emerging methods such as neutron reflectometry are also employed to investigate protein-lipid interactions. (
  • They are involved in protein-protein interactions. (
  • Protein structure and activity in solution is largely determined by its interactions with the surrounding water. (
  • IL2-TRAIL peptide showed cytotoxicity in relapsed patient samples and was more effective than TRAIL or IL2-TRAIL proteins. (
  • Students can build three amino acids simultaneously with this kit to investigate D and L isomers of amino acids, hydrogen bonding, dehydration synthesis, peptide formation, the meaning of "alpha amino acid", primary and secondary structures of proteins, and amines such as GABA and epinephrine. (
  • Students can build a five amino acids simultaneously with this kit to investigate D and L forms of amino acids, hydrogen bonding, dehydration synthesis, peptide formation, the meaning of "alpha amino acid", primary and secondary structure of proteins. (
  • Non-labelled protein was used for secondary structure estimation by de-convolution from circular dichroism (CD) spectra. (
  • The SRCD spectra of the different samples (VVTL1 protein alone and in the presence of the different polyphenols) were recorded in both the far and near UV regions. (
  • Far-UV SRCD spectra of VVTL1 protein alone or in presence of 2 eq. of polyphenols in model wine solution. (
  • Spectra in the near-UV region, which are related to the protein tertiary structure, confirmed the effects of the different polyphenols on VVTL1 protein. (
  • In the 240- to 320-nm region the two proteins have different CD spectra, and show little resemblance to the phosphorylcholine-binding murine myeloma proteins such as MOPC 167 IgA. (
  • This innovative experimental approach enabled the acquisition of AFM-IR spectra and maps from a single protein on a time scale of 1 s, with a ~10-20 signal-to-noise ratio. (
  • Changes in the amide bands in Fourier transform infrared spectra of proteins are generally attributed to alterations in protein secondary structure. (
  • Moreover, attenuated total reflectance spectra of proteins in H2O were not directly comparable to transmission spectra due to the anomalous dispersion effect. (
  • How do I run DSSP and assign the secondary structure? (
  • If you would like to run dssp and assign the secondary structure, use AssignDSSP () instead. (
  • What is DSSP in protein engineering? (
  • DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). (
  • DSSP does not predict secondary structure. (
  • Can DSSP predict the secondary structure of mutations? (
  • There's no magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you don't have the 3D structure. (
  • And, again, DSSP does not predict secondary structures, it just extracts this information from the 3D coordinates. (
  • search_method = *ksdssp mmtbx_dssp from_ca cablam Particular method to search protein secondary structure. (
  • In the following the secondary structure predictions were evaluated against the DSSP data. (
  • Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins have been explored to aid in modelling protein tertiary structures. (
  • To gain insight into NodO's secondary and tertiary structures, and their dependence upon Ca 2+ binding, we performed fluorescence experiments and FTIR spectroscopy. (
  • The human genes encoding these proteins are clustered at chromosomal region 6p21 and coexpressed in multiple tissues, including the pancreas. (
  • Although, providing the massive amount of data by recent genome sequencing projects but many of these genomes are still not fully annotated as well as consist of genes/proteins with unknown function and structure. (
  • In addition, a third protein family composed by proteins denominated pannexins is present in vertebrates and shows primary sequence homology to innexins. (
  • PAPbeta, a protein that binds to and is phosphorylated by the non-receptor tyrosine kinase PYK2, contains several modular signaling domains including a pleckstrin homology domain, an SH3 domain, ankyrin repeats and an ARF-GAP domain. (
  • Sequence similarity was brought in through Protein Data Bank and non-redundant database using BLASTp program of NCBI and a search for templates revealed that yjaB shares 97% homology to a protein of Escherichia coli, indicating this protein is evolutionary conserved and was found with acetyltransfarase. (
  • Current model of haze formation suggests the unfolding of these proteins, mainly due to inappropriate storage conditions, with the exposition of the hydrophobic sites, which make the proteins susceptible to aggregation. (
  • In this study, we demonstrate that pressure unfolding of human immunoglobulins in specific chemical environments promotes quantitative conversion of parallel beta sheet structures to the anti-parallel beta structures, a characteristic indicator of amyloid protein aggregation. (
  • Aggregation of proteins into amyloid structures is a hallmark of human diseases such as Alzheimer's, Parkinson's, and Hungtington's. (
  • Dr. Lee is also particularly interested in the effect of metal ions and the influence of different cellular membrane compartments on protein misfolding and aggregation. (
  • Aggregation can lead to loss of the activity of the molecule, may lead to hypersensitivity reactions in the patient, and can make future doses of the medication ineffective if the patient develops antibodies against the active protein," he explains. (
  • The non-Ig structures were used as templates to analyze sandwich-like interfaces of unresolved homologous proteins using a database merging structure and sequence conservation. (
  • This analysis further shows that MODELLER restrain optimization program can be useful only if we have truly homologous structure(s) as a template where it derives numerous restraints, almost identical to the templates used. (
  • Infrared spectroscopy, together with circular dichroism and fluorescence, is a popular methods of monitoring protein structure changes. (
  • The secondary structure of B. stearothermophilus alanine racemase was predicted from the results obtained by theoretical analysis and circular dichroism measurement. (
  • The circular dichroism (C.D.) spectrum of C-reactive protein in the 200- to 240-nm region indicates that the protein has a) a considerable content of α-helix, a feature not found in immunoglobulins, and, b) a very similar structure to amyloid P component. (
  • Elucidating protein secondary structure with circular dichroism and a self organising map neural network. (
  • Protein secondary structure is determined using circular dichroism spectroscopy, and transmission electron microscopy is used to visualize filament morphology. (
  • Circular dichroism analysis suggests the secondary structure of the protein to be predominantly beta-sheet. (
  • The binding-induced conformational change in the protein was investigated using circular dichroism, synchronous fluorescence, 3D fluorescence and FTIR spectroscopy results. (
  • The conformational properties of the wine protein alone were studied and then compared to that resulting from the presence of the different polyphenols tested. (
  • Investigating cellular functions and mechanism of action of BCNT proteins is challenging, because they have been implicated in human craniofacial development. (
  • These cellular specializations are formed by two protein families corresponding to connexins (vertebrates) and innexins (invertebrates). (
  • This soaking process allows amino acids and proteins in the cellular structure of each bean to develop which results in higher levels of acidity and complex fruit flavours in the cup - it is thought that this process of soaking contributes to the flavour profiles that Kenyan coffees are so famed for. (
  • Oxidant damage to cellular DNA, proteins (including the epigenome), and lipids can occur when reactive oxygen species escape cell antioxidant and repair mechanisms. (
  • RNA is similar in structure to DNA but is involved in different cellular functions. (
  • Graphical user interface is currently available under phenix.refine GUI, 'Refinement settings' tab, select 'Use secondary structure restraints' checkbox and click 'Select Atoms' button. (
  • By treating the protein alone with increasing temperatures (from 5 to 70°C), a drastic change in the SRCD spectrum was detectable starting from temperatures above 54°C were an increase in the unordered structure was observed, indicating protein denaturation. (
  • Results from thermal denaturation of rTerrelysin show that the protein maintained the beta-sheet confirmation up to 65 degrees C. Polyclonal antibody to rTerrelysin recognized a protein of approximately 16.5 kDa in mycelial extracts from A. terreus. (
  • abstract = "Porcine myofibrillar protein (MP) was oxidatively stressed in an iron-H2O2 radical-producing system then subjected to microbial transglutaminase (TGase, E:S=1:20) at 4°C. Changes in the MP secondary structure and cross-linking site on myosin (subfragments S1, S2, rod, light meromyosin, and heavy meromyosin) after TGase treatment were investigated. (
  • Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein show promise therapeutically and are being evaluated clinically. (
  • Abnormal values for CSF VDRL, cell count, and protein, as well as IgM antibodies, may be found in either congenital or acquired syphilis. (
  • Inhibition of the reaction of C-reactive protein with pneumococcal C substance by analogs of phosphorylcholine showed that C-reactive protein is much more specific for the phosphate moiety than the myeloma proteins. (
  • Für AROS konnte gezeigt werden, dass der mittlere Bereich des Proteins für die Inhibition verantwortlich ist. (
  • [ 8 ] ​ Glucocorticoid excess may lead to muscle weakness via inhibition of protein synthesis, increased protein catabolism and altered carbohydrate metabolism. (
  • This gene provides instructions for making a protein called the lamin B receptor. (
  • Without RNA editing, protein folding will not occur properly, thus affecting gene expression. (
  • Although, the number of omic techniques is ever expanding, the most developed omics technologies are high throughput DNA sequencing, transcriptomics (focused on gene expression), epigenomics (focused on epigenetic regulation of gene expression), proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of metabolites, the metabolome). (
  • 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. (
  • Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another. (
  • Hydrogen bonds in the antiparallel β-sheet were more stable than those in the parallel β-sheet, because the hydrogen bond structures of the antiparallel β-sheet were closer to those of the optimized hydrogen bonded formamide dimer. (
  • SARS-CoV-2, the virus that causes COVID-19, is an enveloped virus, meaning that its genetic material is packed inside an outer layer (envelope) of proteins and lipids. (
  • Overall, our findings highlight unanticipated evidences suggesting that homodimerization mediated by the BCNT domain is integral to the chromatin functions of BCNT proteins. (
  • It gives an overview of membrane proteins, with particular emphasis on peripheral and integral proteins. (
  • Further characterization of these proteins is important to understand details of chitin metabolism. (
  • To achieve AFM-IR characterization of a single protein molecule, an innovative approach was adopted in the experimental setup. (
  • Ahmed MS, Islam MA, Hossain MM, Nasreen M. An In Silico Approach for Characterization of an Acetyltransfarase Protein from Shigella flexneriSerotype 5b (strain 8401). (
  • They not only stabilize/protect the protein structure during freezing, primary drying, and secondary drying, but often also reduce the primary drying time. (
  • It is believed that tardigrades produce various "dry-tolerant proteins" that "are intrinsically disordered in water but develop secondary structures in the dehydrated state that allow them to stabilize DNA, proteins, and cell membranes. (
  • From the mesenchymal condensation of chondroprogenitors to the hypertrophic maturation of chondrocytes, chondrogenesis is sequentially regulated by cross-talk among transcription factors, growth factors, and chromatin structure{altering chromatin structure can alter chondrogenesis} . (
  • These include α1 acid glycoprotein, serum amyloid A, the C-reactive protein homolog pentraxin-3, the lipocalin 24p3, and a host of cytokines ( 17 ). (
  • Brookmeyer, R et al,2007).Alzheimer 's disease is a type of a protein misfolding disease, caused by accretion of abnormally folded amyloid-beta and tau proteins in the encephalon. (
  • Because the conditions during freezing and drying are different, the stresses on biologic drug substances are different, and combinations of excipients are often required to provide the protection and stabilization required for a given protein, monoclonal antibody, etc. (
  • Renowned as the #1 antibody event in the industry, this year's agenda boasts 15 dedicated topic streams, 3 unmissable training course add-on options and will bring together more than 700 of the antibody and protein community. (
  • In patients with idiopathic FSGS, investigational findings for an underlying etiology-such as systemic lupus erythematosus (serum complement C4/C3 levels, antinuclear antibody/anti-DNA titers), hepatitis B or C or HIV infection, vasculitis (antineutrophil cytoplasmic antibody titers, serum protein electrophoresis)-are generally negative. (
  • What is primary and secondary structure of protein? (
  • Following this observation similarity searches were conducted between dynamin-1 and Vps1p revealing conservation of primary and secondary structure between the two proteins within the GTPase domain, middle domain and GTPase effector domain. (
  • Evolved Matrix Operations for Post-processing Protein Secondary Structure Predictions. (
  • Subcellular localization predictions shows it is a cytoplasmic protein. (
  • NodO, a 30-kDa nodulation protein secreted by Rhizobium leguminosarum biovar viciae, belongs to a family of proteins produced by Gram-negative bacteria containing a variable number of glycine/aspartates nonapeptides. (
  • SGS combines biophysical techniques with more sensitive orthogonal approaches to provide you with a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation. (
  • High hydrostatic pressure is a thermodynamic driver causing unfolding of proteins orthogonal to the action of temperature or various chaotropic reagents. (
  • Pressure effects on proteins is highly reproducible and can be controlled very precisely. (
  • Recombinant Amb a 1 behaved quite different with regard to IgE reactivity in various experimental setups (i.e., immunoblot, ELISA and mediator-release assays), thus suggesting that a high-quality preparation of the protein would be needed for reproducible immunologic evaluation. (
  • The quaternary structure of the insulin hormone. (
  • The classic examples of proteins with quaternary structure are haemoglobin, collagen and insulin. (
  • The haem groups in the quaternary structure of the haemoglobin molecule combine with oxygen to form oxyhaemoglobin. (
  • Recently introduced Microfluidic Modulation Spectroscopy (MMS) represents a major advancement of infrared spectroscopy specifically developed to simplify protein structure analysis. (
  • These proteins can only function when all subunits are present. (
  • Proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. (
  • In the KDTICM application research such as biology information field, we have got the leading position in predicting protein secondary structure, and apply the KDTICM and its software ICCKDSS in eight fields such as electrolytic aluminum production, agriculture, medical information and etc. (
  • Moreover, functional studies suggest that in different organisms the BCNT proteins play a conserved role in chromatin regulation. (
  • In white wines, even if present at low concentration, proteins have considerable importance because they greatly affect wine stability. (
  • Once determined that the tested polyphenols influenced the protein structure which is indicative of their interaction, the effects of the same polyphenols on the thermal stability of VVTL1 protein were assessed. (
  • Excipients not only affect the stability of proteins and other biologics, they also determine the appropriate operating parameters for the lyophilization process. (
  • PDBe is a founding member of the Worldwide Protein Data Bank (wwPDB) which collects, organises and disseminates data on biological macromolecular structures. (
  • Channels formed by these proteins are essential in many biological processes. (
  • The work also suggests that engineers may be able to gain new insights into biological systems through the study of the structure-function relationships found in music and other art forms. (
  • In the end, whole results indicated the biological function of the target protein to be an acetyltransfarase. (
  • Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans. (
  • Finds more SS elements than other methods, works better when the structure is distorted. (
  • Bioinformatics approach is an alternative to laboratory-based methods that makes of algorithms and databases to predict protein function. (
  • One region of this protein, called the sterol reductase domain, plays an important role in the production (synthesis) of cholesterol. (
  • During cholesterol synthesis, the sterol reductase function of the lamin B receptor allows the protein to perform one of several steps that convert a molecule called lanosterol to cholesterol. (
  • Lyophilization subjects a protein to conditions such as freezing, temperature ramps, vacuum, and dehydration, all of which can disrupt the fragile protein structure leading to loss of activity, according to Anjali Joshi, director of formulation development with Recipharm. (
  • During lyophilization, removal of water can therefore cause destabilization of the protein structure," comments Joshi, referencing a review by Ohtake et al (1). (
  • The sequence of the non-typable Haemophilus influenzae (NTHi) P5 outer-membrane protein from a range of clinical isolates is presented and represents the first analysis of the heterogeneity in P5 from NTHi isolates from diverse anatomical sites. (
  • Secondary structure estimation of recombinant psbH, encoding a photosynthetic membrane protein of cyanobacterium Synechocystis sp. (
  • Wolfgang Sch fberger , "Secondary structure estimation of recombinant psbH, encoding a photosynthetic membrane protein of cyanobacterium Synechocystis sp. (
  • Inner nuclear membrane protein LBR preferentially interacts with DNA secondary structures and nucleosomal linker. (
  • We have already discovered that the primary structure of a protein is the sequence of amino acids, determined by information encoded in DNA. (
  • When the chain pleats, the structure is called a beta-pleated sheet .The amount of coiling or pleating depends on the primary structure (sequence of amino acids. (