Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Molecular Conformation: The characteristic three-dimensional shape of a molecule.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Deuterium Exchange Measurement: A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Optical Rotatory Dispersion: The method of measuring the dispersion of an optically active molecule to determine the relative magnitude of right- or left-handed components and sometimes structural features of the molecule.Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Kinetics: The rate dynamics in chemical or physical systems.Solutions: The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Silica Gel: A non-crystalline form of silicon oxide that has absorptive properties. It is commonly used as a desiccating agent and as a stationary phase for CHROMATOGRAPHY. The fully hydrated form of silica gel has distinct properties and is referred to as SILICIC ACID.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Myoglobin: A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Spectrum Analysis, Raman: Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Anilino Naphthalenesulfonates: A class of organic compounds which contain an anilino (phenylamino) group linked to a salt or ester of naphthalenesulfonic acid. They are frequently used as fluorescent dyes and sulfhydryl reagents.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Spectroscopy, Fourier Transform Infrared: A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Protein Stability: The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Muramidase: A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 22.214.171.124.Apoproteins: The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Hydrogen: The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.Prions: Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL.Guanidine: A strong organic base existing primarily as guanidium ions at physiological pH. It is found in the urine as a normal product of protein metabolism. It is also used in laboratory research as a protein denaturant. (From Martindale, the Extra Pharmacopoeia, 30th ed and Merck Index, 12th ed) It is also used in the treatment of myasthenia and as a fluorescent probe in HPLC.Solvents: Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)Bacteriorhodopsins: Rhodopsins found in the PURPLE MEMBRANE of halophilic archaea such as HALOBACTERIUM HALOBIUM. Bacteriorhodopsins function as an energy transducers, converting light energy into electrochemical energy via PROTON PUMPS.Spectrophotometry, Infrared: Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Static Electricity: The accumulation of an electric charge on a objectSpectrophotometry, Ultraviolet: Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Schiff Bases: Condensation products of aromatic amines and aldehydes forming azomethines substituted on the N atom, containing the general formula R-N:CHR. (From Grant & Hackh's Chemical Dictionary, 5th ed)Bacterial Proteins: Proteins found in any species of bacterium.Amyloid: A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease.Biophysics: The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.Horses: Large, hoofed mammals of the family EQUIDAE. Horses are active day and night with most of the day spent seeking and consuming food. Feeding peaks occur in the early morning and late afternoon, and there are several daily periods of rest.Deuterium: Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Biophysical Phenomena: The physical characteristics and processes of biological systems.PhotochemistryCrystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Spectrum Analysis: The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Hydrostatic Pressure: The pressure due to the weight of fluid.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Fluorescence Resonance Energy Transfer: A type of FLUORESCENCE SPECTROSCOPY using two FLUORESCENT DYES with overlapping emission and absorption spectra, which is used to indicate proximity of labeled molecules. This technique is useful for studying interactions of molecules and PROTEIN FOLDING.Prion Diseases: A group of genetic, infectious, or sporadic degenerative human and animal nervous system disorders associated with abnormal PRIONS. These diseases are characterized by conversion of the normal prion protein to an abnormal configuration via a post-translational process. In humans, these conditions generally feature DEMENTIA; ATAXIA; and a fatal outcome. Pathologic features include a spongiform encephalopathy without evidence of inflammation. The older literature occasionally refers to these as unconventional SLOW VIRUS DISEASES. (From Proc Natl Acad Sci USA 1998 Nov 10;95(23):13363-83)DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Protons: Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Chymotrypsin: A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Energy Transfer: The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Chemistry, Physical: The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.Physicochemical Phenomena: The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.Amides: Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Mutant Proteins: Proteins produced from GENES that have acquired MUTATIONS.Molecular Chaperones: A family of cellular proteins that mediate the correct assembly or disassembly of polypeptides and their associated ligands. Although they take part in the assembly process, molecular chaperones are not components of the final structures.Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 126.96.36.199.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Spectrometry, Mass, Electrospray Ionization: A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Electron Spin Resonance Spectroscopy: A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.Ions: An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.Hemeproteins: Proteins that contain an iron-porphyrin, or heme, prosthetic group resembling that of hemoglobin. (From Lehninger, Principles of Biochemistry, 1982, p480)Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.Microscopy, Atomic Force: A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical position is recorded as a spring attached to the probe rises and falls in response to peaks and valleys on the surface. These deflections produce a topographic map of the sample.Heme: The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Fourier Analysis: Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)Urea: A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Glycosylation: The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Carbohydrate Conformation: The characteristic 3-dimensional shape of a carbohydrate.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Lysine: An essential amino acid. It is often added to animal feed.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Cell Line: Established cell cultures that have the potential to propagate indefinitely.X-Ray Diffraction: The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Cytochrome c Group: A group of cytochromes with covalent thioether linkages between either or both of the vinyl side chains of protoheme and the protein. (Enzyme Nomenclature, 1992, p539)Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Epitopes: Sites on an antigen that interact with specific antibodies.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Aspartic Acid: One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Light: That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.Zinc: A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Molecular Weight: The sum of the weight of all the atoms in a molecule.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Serum Albumin, Bovine: Serum albumin from cows, commonly used in in vitro biological studies. (From Stedman, 25th ed)Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Crystallography: The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Hemoglobins: The oxygen-carrying proteins of ERYTHROCYTES. They are found in all vertebrates and some invertebrates. The number of globin subunits in the hemoglobin quaternary structure differs between species. Structures range from monomeric to a variety of multimeric arrangements.Calcium: A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Electron Transport: The process by which ELECTRONS are transported from a reduced substrate to molecular OXYGEN. (From Bennington, Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984, p270)Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Iron: A metallic element with atomic symbol Fe, atomic number 26, and atomic weight 55.85. It is an essential constituent of HEMOGLOBINS; CYTOCHROMES; and IRON-BINDING PROTEINS. It plays a role in cellular redox reactions and in the transport of OXYGEN.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.Allosteric Regulation: The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.Trifluoroethanol: A non-aqueous co-solvent that serves as tool to study protein folding. It is also used in various pharmaceutical, chemical and engineering applications.Scattering, Small Angle: Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Stereoisomerism: The phenomenon whereby compounds whose molecules have the same number and kind of atoms and the same atomic arrangement, but differ in their spatial relationships. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Structural Homology, Protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Lipid Bilayers: Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Allosteric Site: A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.Calorimetry: The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Isomerism: The phenomenon whereby certain chemical compounds have structures that are different although the compounds possess the same elemental composition. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Oligopeptides: Peptides composed of between two and twelve amino acids.Micelles: Particles consisting of aggregates of molecules held loosely together by secondary bonds. The surface of micelles are usually comprised of amphiphatic compounds that are oriented in a way that minimizes the energy of interaction between the micelle and its environment. Liquids that contain large numbers of suspended micelles are referred to as EMULSIONS.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Drug Design: The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.Cross-Linking Reagents: Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.Alanine: A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Cryoelectron Microscopy: Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Histidine: An essential amino acid that is required for the production of HISTAMINE.Adenosine Diphosphate: Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Protein Subunits: Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Gramicidin: A group of peptide antibiotics from BACILLUS brevis. Gramicidin C or S is a cyclic, ten-amino acid polypeptide and gramicidins A, B, D are linear. Gramicidin is one of the two principal components of TYROTHRICIN.Protein Interaction Domains and Motifs: Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Motion: Physical motion, i.e., a change in position of a body or subject as a result of an external force. It is distinguished from MOVEMENT, a process resulting from biological activity.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.Scattering, Radiation: The diversion of RADIATION (thermal, electromagnetic, or nuclear) from its original path as a result of interactions or collisions with atoms, molecules, or larger particles in the atmosphere or other media. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Fluorescence: The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.Fluorescence Polarization: Measurement of the polarization of fluorescent light from solutions or microscopic specimens. It is used to provide information concerning molecular size, shape, and conformation, molecular anisotropy, electronic energy transfer, molecular interaction, including dye and coenzyme binding, and the antigen-antibody reaction.Protein Unfolding: Conformational transitions of the shape of a protein to various unfolded states.Biocatalysis: The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.Mathematics: The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.DNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.
Endocytosis: EH domains lend a hand. (1/52898)A number of proteins that have been implicated in endocytosis feature a conserved protein-interaction module known as an EH domain. The three-dimensional structure of an EH domain has recently been solved, and is likely to presage significant advances in understanding molecular mechanisms of endocytosis. (+info)
Membrane fusion: structure snared at last. (2/52898)The structure of the core of the neuronal 'SNARE complex', involved in neurotransmitter release, has been determined recently. Its topological similarity to viral fusion proteins suggests how the SNARE complex might facilitate membrane fusion. (+info)
Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. (3/52898)Transcription factors that are bound specifically to DNA often interact with each other over thousands of base pairs  . Large DNA loops resulting from such interactions have been observed in Escherichia coli with the transcription factors deoR  and NtrC , but such interactions are not, as yet, well understood. We propose that unique protein complexes, that are not present in solution, may form specifically on DNA. Their uniqueness would make it possible for them to interact tightly and specifically with each other. We used the repressor and operators of coliphage lambda to construct a model system in which to test our proposition. lambda repressor is a dimer at physiological concentrations, but forms tetramers and octamers at a hundredfold higher concentration. We predict that two lambda repressor dimers form a tetramer in vitro when bound to two lambda operators spaced 24 bp apart and that two such tetramers interact to form an octamer. We examined, in vitro, relaxed circular plasmid DNA in which such operator pairs were separated by 2,850 bp and 2,470 bp. Of these molecules, 29% formed loops as seen by electron microscopy (EM). The loop increased the tightness of binding of lambda repressor to lambda operator. Consequently, repression of the lambda PR promoter in vivo was increased fourfold by the presence of a second pair of lambda operators, separated by a distance of 3,600 bp. (+info)
Probing interactions between HIV-1 reverse transcriptase and its DNA substrate with backbone-modified nucleotides. (4/52898)BACKGROUND: To gain a molecular understanding of a biochemical process, the crystal structure of enzymes that catalyze the reactions involved is extremely helpful. Often the question arises whether conformations obtained in this way appropriately reflect the reactivity of enzymes, however. Rates that characterize transitions are therefore compulsory experiments for the elucidation of the reaction mechanism. Such experiments have been performed for the reverse transcriptase of the type 1 human immunodeficiency virus (HIV-1 RT). RESULTS: We have developed a methodology to monitor the interplay between HIV-1 RT and its DNA substrate. To probe the protein-DNA interactions, the sugar backbone of one nucleotide was modified by a substituent that influenced the efficiency of the chain elongation in a characteristic way. We found that strand elongation after incorporation of the modified nucleotide follows a discontinuous efficiency for the first four nucleotides. The reaction efficiencies could be correlated with the distance between the sugar substituent and the enzyme. The model was confirmed by kinetic experiments with HIV-1 RT mutants. CONCLUSIONS: Experiments with HIV-1 RT demonstrate that strand-elongation efficiency using a modified nucleotide correlates well with distances between the DNA substrate and the enzyme. The functional group at the modified nucleotides acts as an 'antenna' for steric interactions that changes the optimal transition state. Kinetic experiments in combination with backbone-modified nucleotides can therefore be used to gain structural information about reverse transcriptases and DNA polymerases. (+info)
A hyperstable collagen mimic. (5/52898)BACKGROUND: Collagen is the most abundant protein in animals. Each polypeptide chain of collagen is composed of repeats of the sequence: Gly-X-Y, where X and Y are often L-proline (Pro) and 4(R)-hydroxy-L-proline (Hyp) residues, respectively. These chains are wound into tight triple helices of great stability. The hydroxyl group of Hyp residues contributes much to this conformational stability. The existing paradigm is that this stability arises from interstrand hydrogen bonds mediated by bridging water molecules. This model was tested using chemical synthesis to replace Hyp residues with 4(R)-fluoro-L-proline (Flp) residues. The fluorine atom in Flp residues does not form hydrogen bonds but does elicit strong inductive effects. RESULTS: Replacing the Hyp residues in collagen with Flp residues greatly increases triple-helical stability. The free energy contributed by the fluorine atom in Flp residues is twice that of the hydroxyl group in Hyp residues. The stability of the Flp-containing triple helix far exceeds that of any untemplated collagen mimic of similar size. CONCLUSIONS: Bridging water molecules contribute little to collagen stability. Rather, collagen stability relies on previously unappreciated inductive effects. Collagen mimics containing fluorine or other appropriate electron-withdrawing substituents could be the basis of new biomaterials for restorative therapies. (+info)
How do peptide synthetases generate structural diversity? (6/52898)Many low-molecular-weight peptides of microbial origin are synthesized nonribosomally on large multifunctional proteins, termed peptide synthetases. These enzymes contain repeated building blocks in which several defined domains catalyze specific reactions of peptide synthesis. The order of these domains within the enzyme determines the sequence and structure of the peptide product. (+info)
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. (7/52898)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. (8/52898)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)
NMR paper Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR. - BioNMR
The following examples show how to set up alternate conformations for structure factor calculations as well as for empirical energy calculations. The first step is to append the alternate conformations to the current molecular structure file. In this particular case, one wants to generate alternate conformations for the side chains of residues 1 and 7. alternate.inp Now one has to go to the graphics and move the alternate conformations into the correct positions. In subsequent protocols, one has to insert the following statement after reading the molecular structure file ...
Conformational control of nonplanar free base porphyrins: Towards bifunctional catalysts of tunable basicity
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo<...
TY - JOUR. T1 - Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. AU - Woods, Chanin T.. AU - Lackey, Lela. AU - Williams, Benfeard. AU - Dokholyan, Nikolay V.. AU - Gotz, David. AU - Laederach, Alain. PY - 2017/7/25. Y1 - 2017/7/25. N2 - When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular molecules sometimes alter the energy landscape, thereby changing the ensemble of likely low-energy conformations. The effects of these energy landscape changes on the conformational ensemble are particularly challenging to visualize for large RNAs. We have created a robust approach for visualizing the conformational ensemble of RNAs that is well suited for in vitro versus in vivo comparisons. Our method creates a stable map of conformational space for a given RNA sequence. We first identify single point ...
Prediction of the receptor conformation for iGluR2 agonist binding - Employees
TY - JOUR. T1 - Prediction of the receptor conformation for iGluR2 agonist binding. T2 - QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. AU - Sander, Tommy. AU - Liljefors, Tommy. AU - Balle, Thomas. N1 - Keywords: Protein flexibility, molecular docking, normal mode analysis, elastic network model, ensemble generation, iGluR2 receptor, domain closure. PY - 2008. Y1 - 2008. KW - Former Faculty of Pharmaceutical Sciences. U2 - 10.1016/j.jmgm.2007.11.006. DO - 10.1016/j.jmgm.2007.11.006. M3 - Journal article. VL - 26. SP - 1259. EP - 1268. JO - Journal of Molecular Graphics and Modelling. JF - Journal of Molecular Graphics and Modelling. SN - 1093-3263. IS - 8. ER - ...
DynDom - Protein Domain Motions
DynDom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending. It is fully automated.. You can use DynDom if you have two conformations of the same protein. These may be two X-ray structures, or structures generated using simulation techniques such as molecular dynamics or normal mode analysis.. The application of DynDom provides a view of the conformational change that is easily understood. The conformational change may be quite complicated in detail, but by using DynDom you can visualize it as involving the movement of domains as quasi-rigid bodies. The analysis of a conformational change in terms of domain movements only makes sense if the interdomain deformation is at least comparable to the intradomain deformation. You can use DynDom to assess this, but the results could be misleading if this is not the case.. DynDom allows you to visualize the domain motion in terms of the rotation of one domain relative to another. Here we see the ...
Supplementary data for article: Grozdanovic, M. M.; Drakulić, B. J.; Gavrović-Jankulović, M. Conformational Mobility of Active...
SWISS-MODEL Template Library | 1ht1
Conformational equilibria and intrinsic affinities define integrin activation | The EMBO Journal
Integrins undergo large‐scale conformational changes (Springer & Dustin, 2012). In the bent‐closed (BC) conformation, the integrin ectodomain folds at knees in the α‐ and β‐subunits so that the head and upper legs associate with the lower legs (Fig 1A). In two extended states, the extended‐closed (EC) and extended‐open (EO) conformations, extension of the α‐ and β‐knees raises the headpiece above the lower legs on cell surfaces (Fig 1A). In transition from EC to EO, that is, headpiece opening, the ligand‐binding metal ion‐dependent adhesion site (MIDAS) in the β‐subunit βI domain rearranges. This reshaping of the ligand‐binding site is linked by α‐helix pistoning within the βI domain to swing of the hybrid domain away from the integrin α‐subunit (Fig 1A). Although the affinities of these states have not yet been measured, previous studies have correlated integrin adhesiveness and high affinity for ligand with the EO conformation (Takagi et al, 2002, 2003; ...
RCSB PDB - 4NVL: Predicting protein conformational response in prospective ligand discovery.
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
DPD simulation of protein conformations: From α-helices to β-structures<...
TY - JOUR. T1 - DPD simulation of protein conformations. T2 - From α-helices to β-structures. AU - Vishnyakov, Aleksey. AU - Talaga, David S.. AU - Neimark, Alexander V.. PY - 2012/11/1. Y1 - 2012/11/1. N2 - We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. ...
Publisher: American Chemical Society / Subject: Molecular Structure and Protein Conformation - Linus Pauling - Profiles in...
DECI 11th Call - PRACE Research Infrastructure
The present study on the ATP-lid of HSP90, a pharmaceutically relevant oncology target is aimed at shedding light on the differences in conformational plasticity in the presence or absence of known fragments and small molecules. Unbiased, atomistic simulations in the upper microsecond range in explicit solvent will be used to generate a large number of conformational ensembles which will serve as a basis to address the conformational preferences in terms of the induced fit or the conformational selection concept. We expect to get useful atomistic insights for designing ligands which are able to "freeze" HSP90 in a particular conformation and therefore have a higher binding affinity and residence time. The project addresses the two extremes which underlie protein-ligand interactions, namely induced fit (1) and conformational selection (2). While in the former, binding is obtained by a specific structural change, the later selects the adequate protein conformation from the unbound ensemble. The ...
How is Energy Transferred Across the Cellular System? | MBInfo
When in a complex, a protein has bonds that mediate protein-protein interactions as well as those that maintain its own conformation. Upon force application, the dissociation of bonds between proteins in the complex competes with the dissociation of bonds within the protein, with the latter instance being favored as this allows the complex as a whole to maintain tension. This has been demonstrated using actin, filamin and a-actinin .. A change in conformation can be explained as a transition between two energy minima that are separated by a high energy state that slows down the transition . Applied force favors this transition by lowering the energy requirement and altering the energy minima i.e. stabilizing the new conformation  (see figure below). Thus conformational changes are therefore dependent on force sensing, in terms of both the magnitude and duration of the detected force ,. The conformational changes pass the signal onto neighboring molecules by exposing catalytic ...
Questions about Conformations and Energy Profiles
Another example of the initial conformer affecting systematic results can be found by inspecting an 8 member carbon chain: "C1-C2-C3-C4-C5-C6-C7-C8". For illustrative purposes consider the central "C4-C5" bond as we rotate it 360 degrees; from -180 to 180 degrees. If one starts in the all trans conformation, we find that as we rotate the "C4-C5" bond the final conformation of 360 degrees is identical to the initial at 0 degrees. However, if the initial conformation had a number of kinks in it, we might discover that at the 120 degree mark, the C1 and C8 ran into each other. To relieve this steric problem the other dihedral angles, will relax, likely changing by more than 100 degrees and falling into new energy wells. As we continue the coordinate driving of the central C4-C5 angle to trans (180), we might find that the final conformation is not the same as the initial conformation because these other dihedrals have changed ...
Obstructing conformational shifts in active proteins keeps therapeutic guarantee biologically. of - Role of adrenergic...
Obstructing conformational shifts in active proteins keeps therapeutic guarantee biologically. of taxol in vitro and in a xenograft style of lung tumor. Also the expected mode of actions of the energetic peptides was experimentally confirmed. Both peptides destined to their mother or father protein and their natural activity was abolished in the current presence of the peptides related towards the counterpart helices. These data demonstrate a uncharacterized way for rational style of proteins antagonists previously. displays the experimentally-derived get in touch with map of HIV-1 gp41 as extracted from PDB 1ENV. The helix-helix relationships can be recognized with a peak in the total value from the Fourier transform of the get in touch with map when used on the amount by rows (or individually by columns) from the relevant 21 × 21 operating submatrix. Fig. 1illustrates the Fourier transform related to the amount of rows representing the discussion between two 21-mer sections focused around ...
iomolecules can play a significant role in the formation of nanostructured hard tissues in living organisms. These materials are formed with a degree of control that cannot yet be exerted in synthetic laboratories. To mimic these natural biomineralisation strategies, we must identify the mechanisms at work at the biomolecule-mineral interface. We will investigate, via a coupling of theory and experiment, two aspects of this interface. One aspect is how the surface can manipulate the conformation of the adsorbing biomolecule. Conformationally-labile biomolecules such as intrinsically-disordered proteins (IDPs) can change conformation upon exposure to external stimuli. Mineral surfaces provide such a stimulus that can induce folding and thus confer function(s) (such as polymorph stabilisation) related to this new conformation. Another aspect is how the adsorption of biomolecules influences the growth/stability of different crystal faces. Harnessing the ability of biomolecules to modify the growth ...
Protein Conformation (Topic) - Rensselaer Libraries
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FCC Reveals Crucial Piece of TV Channel Repacking Method | TvTechnology
RCSB PDB - 1P1U: Crystal structure of the GluR2 ligand-binding core (S1S2J) L650T mutant in complex with AMPA ...
Increase in Affinity for ATP and change in E1-E2 Conformational Equilibrium after mutations to the phosphorylation site (Asp369...
The Role of Conformational Flexibility in Proteins' Search for their Recognition Sites
A model for the bent conformation responsible for the r | Open-i
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Help! How can I look at the conformational changes in proteins?
Please be VERY careful with this particular assay for conformational change. Not only can a protease sensitive site be uncovered by a structural change, but also a ligand-less protein CAN be more breathe-able with respect to its liganded strucuture which can have a more solid protease protected structure. Typsin can be very sneakey if given the chance. This happened to us. Turns out that by X-ray analysis and by NMR analysis, what was previously thought of as a structural change on ligand binding was actually a firming up of the fold of the protein. No residues actually changed position to any great extend. The protease protection is probably a red herring in this case. There are very well documented examples of protease protection revealing gross structural changes. Just...PLEASE BE CAREFUL with the interpretation of this assay ...
Purdue e-Pubs - Society of Engineering Science 51st Annual Technical Meeting: Microtubule-driven conformational changes in...
The influence of the range of the involved geometric and material parameters, such as the available area for conformational changes, the bilayer thickness, the interaction energy between transmembrane domains and lipids, is largely explored. Bounds on the available conformations experienced by the transmebrane domains are also provided.
H CHOP780101 D Normalized frequency of beta-turn (Chou-Fasman, 1978a) R LIT:2004003a PMID:354496 A Chou, P.Y. and Fasman, G.D. T Empirical predictions of protein conformation J Ann. Rev. Biochem. 47, 251-276 (1978) C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946 CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921 ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897 QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891 LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885 ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878 PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827 QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803 QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837 SUEM840101 -0.845 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47 0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50 // H CHOP780201 D Normalized frequency of alpha-helix (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of ...
Conformation change upon formation of large i - Unspecified - BNID 107914
The formation of complexes that have large interfaces is seen to involve large changes in conformation in those cases where native structures are available. These changes are generally described in publications reporting the X-ray structure of the complexes. They are summarised in Table 2 for the 20 complexes that have B,2000 Å^2. B=interface ...
Evolving L-Systems to Capture Protein Structure Native Conformations | SpringerLink
How many words make out of Conformational | Find all Anagrams
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enzymes - General Biology Discussion
The structure of a molecule dictates its function. If you were to consider NAs, for example, they wouldnt be good enzymes since you only have a limited number of NA types as well as conformation. Which part of the NA would a reactant bind to? Same questions for CHOs and lipids. The way proteins are structured, you have so many conformations (recall 4 levels of structure) possible depending on composition. Variability in conformation among different protein molecules is important since conformation is critical in being able to bind with the reactants to enable catalysis of a reaction ...
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Characterisation, classification and conformational variabilit...
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Functional proteins that do not have unique, stable, folded, three-dimensional native structures or that possess non-ordered regions under physiological conditions. They are characterized by extraordinary structural flexibility and plasticity, which enable them to adopt different conformations in response to different stimuli or different interactions ...
Towards a Spherical Coordinate System Metric for Quantitative Comparison of Protein 3D Structures
conformational analysis - oi
ETIS - Highly sensitive conformational switching of ethane-bridged mono-zinc bis-porphyrin as an application tool for rapid...
Electrostatic energy calculation on the pH-induced conformational change of influenza virus hemagglutinin<...
TY - JOUR. T1 - Electrostatic energy calculation on the pH-induced conformational change of influenza virus hemagglutinin. AU - Ho, Sup Choi. AU - Huh, June. AU - Won, Ho Jo. PY - 2006. Y1 - 2006. N2 - The pH-induced conformational change of influenza virus hemagglutinin (HA) has been investigated by calculating the change of electrostatic energy of the fragment of HA2 upon pH change. The average charge and electrostatic free energy are calculated as a function of pH for the fusion peptide (residues 1-20 of HA2) and the polypeptide of residues 54-77 of HA2 by using the finite difference Poisson-Boltzmann method. It is found that as pH decreases from 8 to 5, the electrostatic free energy of the fusogenic state is lowered by ∼2 kcal/mol and the fusogenic state is less ionized compared to that of the native state for both polypeptides. For the fusion peptide at the fusogenic state, most of ionizable residues are neutral at acidic pH except Glu-11. For the polypeptide of residues 54-77 at the ...
Efficient algorithms to explore conformation spaces of flexible protein loops<...
TY - GEN. T1 - Efficient algorithms to explore conformation spaces of flexible protein loops. AU - Dhanik, A.. AU - Yao, P.. AU - Marz, N.. AU - Propper, R.. AU - Kou, C.. AU - Liu, Guanfeng. AU - Van Den Bedem, H.. AU - Latombe, J. C.. PY - 2007. Y1 - 2007. N2 - Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples conformations broadly distributed over this space, while the "deformation sampling" algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.. AB - Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples ...
Protein-peptide molecular docking with large-scale conformational changes | Laboratory of Theory of Biopolymers
Conformational characterisation of peptide-1 at 10°C i | Open-i
Conformational changes and loose packing promote E. coli Tryptophanase cold lability | BMC Structural Biology | Full Text
where TE-PLPclose is the holo tetrameric active Trpase at 25°C in a close conformation; TE-PLPopen is the holo tetrameric enzyme in the open conformation at 2°C; TE... PLP is the non-covalently bound complex in an open conformation and TE is the apo enzyme in an open conformation at 2°C. Step 4 is the dissociation of the tetrameric form to dimers, TE to DE.. Cooling (step 1) weakens the hydrophobic interactions resulting in a conformational change and a corresponding modified solvation. The change from the closed to an open conformation is associated with a reduction in the tight packing of the tetramer and is enhanced by the point mutations. This conformational change is further supported by the present high pressure studies showing that increasing hydrostatic pressure has the same effect as decreasing temperature in affecting the conformational equilibrium.. The conformational change at low temperatures results in breaking the covalent aldimine bond between residue Lys270 (E. coli ...
Designing Conformational Control of Human Tissue Transglutaminase for Applications in Huntington's Disease Research -...
Human type II transglutaminase (TG2) is an enzyme that exists in two dramatically different conformational states, each with a unique activity. In the open, extended form, the transglutaminase active site is exposed, allowing TG2 to catalyze formation of an isopeptide bond between the sidechain of a peptide-bound glutamine and a primary amine. Upon GTP binding to a separate GTPase active site, TG2 adopts a heavily favored and compact closed conformation, which obstructs the glutaminase active site, and only allows GTPase activity. TG2 has been linked to Huntingtons disease, as well as to many other cellular processes, both physiological and pathological. However, TG2s two conformational states, each with its own activity, have made it difficult to elucidate how this enzyme functions in disease progression. In addition, because TG2 heavily prefers the closed state, attempts to screen for inhibitors that may bind the transglutanimase site exposed in the open conformation, and attempts to obtain ...
Stress Sensor Triggers Conformational Response of the Integral Membrane Protein Microsomal Glutathione Transferase 1 †
"Developing Hybrid Approaches to Predict pKa Values of Ionizable Groups" by Shawn Witham, Kemper Talley et al.
Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups, which ionization is expected to cause conformational changes, termed
An Efficient Null Model for Conformational Fluctuations in Proteins - DTU Orbit
Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a ...
Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychrophilic phosphoglycerate...
en] The cold-active phosphoglycerate kinase from the Antarctic bacterium Pseudomonas sp. TACII18 exhibits two distinct stability domains in the free, open conformation. It is shown that these stability domains do not match the structural N- and C-domains as the heat-stable domain corresponds to about 80 residues of the C-domain, including the nucleotide binding site, whereas the remaining of the protein contributes to the main heat-labile domain. This was demonstrated by spectroscopic and microcalorimetric analyses of the native enzyme, of its mutants, and of the isolated recombinant structural domains. It is proposed that the heat-stable domain provides a compact structure improving the binding affinity of the nucleotide, therefore increasing the catalytic efficiency at low temperatures. Upon substrate binding, the enzyme adopts a uniformly more stable closed conformation. Substrate-induced stability changes suggest that the free energy of ligand binding is converted into an increased ...
Compugen Announces New Drug Discovery Platform to Predict Peptides that Block Disease-Associated Conformations of Proteins -...
Tel Aviv, Israel - March 18, 2008 - Compugen Ltd. (NASDAQ: CGEN) announced today the development and validation of its Blockers of Disease-Associated Conformation (DAC Blockers) platform, a new discovery platform for the identification of peptides that block proteins from adopting their disease-associated conformations. To date, two of the predicted therapeutic peptide candidates from the pilot validation run of the platform have shown initial experimental verification, one with anti-inflammatory and the other with anti-cancer activities.. The newly developed DAC Blockers platform has been designed to identify segments in proteins of interest that, if introduced therapeutically as synthetic peptides, would block specific conformational changes of such proteins, and thereby prevent them from adopting disease-associated conformations and related activities. A key capability of the platform is that it enables the proteome-wide search for such conformational change blocking peptides in human, viral ...
Automated combined assignment of NOESY spectra and three-dimensional protein structure determination | SpringerLink
Insights into the structure and function of the aggregate-reactivating molecular chaperone CLPB
ClpB is a bacterial heat-shock protein that disaggregates and reactivates strongly aggregated proteins in cooperation with the DnaK chaperone system. ClpB contains two ATP-binding AAA+ modules, a linker coiled-coil domain, and a highly mobile N-terminal domain. It forms ring-shaped hexamers in a nucleotide-dependent manner. The unique aggregation reversing chaperone activity of ClpB involves ATP-dependent translocation of substrates through the central channel in the ClpB ring. The initial events of aggregate recognition and the events preceding the translocation step are poorly understood. In addition to the full-length ClpB95, a truncated isoform ClpB80, that is missing the whole N-terminal domain, is also produced in vivo. Various aspects of the structure and function of ClpB were addressed in this work. The thermodynamic stability of ClpB in its monomeric and oligomeric forms, as well as the nucleotide-induced conformational changes in ClpB were investigated by fluorescence spectroscopy. ...
Chiwook Park - Interdisciplinary Life Science - PULSe - Purdue University
Proteins are dynamic molecules. Even under native conditions, they do not adopt a single static conformation. Rather, they access many different conformations in their native state ensemble. This native state ensemble includes small fluctuations around the native conformation, partially unfolded forms, and even globally unfolded forms. The distribution of these conformations and the kinetic barriers between the conformational states define the conformational energy landscapes of proteins. My research interest is investigating conformational energy landscapes of proteins and deciphering the relationship between the energetics of proteins and their biochemical functions, such as catalysis, signal transduction, and ligand binding. We use proteolysis as a major tool to probe protein structures and dynamics as well as conventional spectroscopic methods. We also use proteomics extensively for investigating energy landscapes of proteins on a system level.. Investigation of conformational energy ...
PDB-1e1r: BOVINE MITOCHONDRIAL F1-ATPASE INHIBITED BY MG2+ADP AND ALUMINIUM... - Yorodumi
Details: INITIAL REFINEMENT CARRIED OUT WITH TNT AND XPLOR RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. THE POSITIONS OF SIDE CHAIN ATOMS WITH TEMPERATURE FACTORS GREATER THAN 75 IS UNCERTAIN. THE MAIN CHAIN CONFORMATION IS ALSO UNCERTAIN FOR REGIONS WITH TEMPERATURE FACTORS ABOVE 60. SOLVENT MOLECULES HAVE BEEN USED TO MODEL SOME FEATURES IN THE ELECTRON DENSITY THAT ARE PROBABLY DUE TO THE "MISSING" REGIONS OF THE GAMMA SUBUNIT (CHAIN G) THE PEPTIDE BOND BETWEEN ASP 269 AND ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION. RESIDUAL FEATURES IN THE ELECTRON DENSITY MAP SUGGEST THAT THERE IS SOME CONFORMATIONAL DISORDER IN ASP 270 IN CHAINS A, B, AND C. CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE ...
Abstract: Biomolecular assemblies exhibit "emergent behavior" in both the temporal and spatial domains. As observed in long-timescale molecular dynamics simulations or in 3D models of large-scale biomolecular systems, the behavior that emerges on these scales is not only more than the sum of the (temporal or spatial) parts, but quite different and unexpected. Examples include: (1) slow conformational changes in protein folding and protein-protein binding enabled by fast motion in long molecular dynamics simulations; (2) the interpretation and refinement of intermediate-resolution electron microscopy (EM) structures using multiple or flexible atomic fragments; and (3) the segmentation of the molecular building blocks of living organisms in low-resolution data from EM or tomography. The unifying goal of our efforts is to observe and to take into account functional dynamics in the native environment (solution or vitreous ice) or in silico and then to reconstruct and interpret the 3D shapes of the ...
Analysis of allosteric effect of pathologic variants at the light of local protein conformations - Inserm
Proteins are highly dynamic macromolecules. To analyze their inherent flexibility, computational biologists often use molecular dynamics (MD) simulations. The quantification of protein flexibility is based on various methods such as Root Mean Square Fluctuations (RMSF) that rely on multiple MD snapshots or Normal Mode Analysis (NMA) that rely on a single structure and focus on quantifying large movements. Alternative in silico approaches assess protein motions through the protein residue network or dynamical correlations from MD simulations. An alternative yet powerful approach based on small prototypes or structural alphabets (SAs) can be used. SAs approximate conformations of protein backbones and code the local structures of proteins as one-dimensional sequences. Protein Blocks (PBs) are one of these SAs. Applying PB-based approaches to biological systems such as the DARC protein, the human αIIb β3 integrin and the KISSR1 protein highlighted the major interest of PBs in understanding local
Transient state imaging probes patterns of altered oxygen consumption in cancer cells
Due to their long lifetime, triplet, redox and other transient states of fluorophores are highly sensitive to the micro-environment. Imaging their spatial distribution in biological samples can therefore help answer interesting questions about the metabolism, molecular interactions and dynamics in living cells. However, as these states are at best weakly luminescent, they have up to now only been used to a limited extent in life sciences. In Transient State (TRAST) imaging, the characteristic build up of transient states is instead monitored via fluorescence, as the excitation is modulated. When the illumination pulse width is step-wise increased, transient states are progressively populated. The resulting depletion of the singlet excited state can be monitored via time-averaged fluorescence. This fluorescence decay is characteristic for the transient state kinetics of the fluorophore in a given environment. Traditional fluorescence parameters can only be influenced within the lifetime of the ...
Conformational characterization of oligomeric intermediates and aggregates in β-lactoglobulin heat aggregation - Carrotta -...
The present work is one of the first characterizations of multimeric intermediates in protein aggregation, and offers direct information about the assembly process. The results of the Ellman assay confirm that the dimer is linked by a disulfide bond, as previously proposed (Manderson et al. 1998; Bauer et al. 2000). Formation of the dimer therefore requires at least unfolding of the proteins main helix (Qi et al. 1997), which protects the free cysteine from the solvent in the native structure. We have previously shown that the Blg oligomers are productive intermediates in aggregation: assembly of aggregates coincides with consumption of oligomers, and purified oligomers at high concentration aggregate very rapidly (Bauer et al. 2000). The molten globule character of the oligomers observed here is perfectly in line with previous studies on other proteins (Booth et al. 1997; Kayed et al. 1999; McParland et al. 2000; Rochet and Lansbury 2000), demonstrating that aggregation is accelerated by ...
Equine conformation - Wikipedia
Equine conformation evaluates the degree of correctness of a horses bone structure, musculature, and its body proportions in relation to each other. Undesirable conformation can limit the ability to perform a specific task. Although there are several universal "faults," a horses conformation is usually judged by what its intended use may be. Thus "form to function" is one of the first set of traits considered in judging conformation. A horse with poor form for a Grand Prix show jumper could have excellent conformation for a World Champion cutting horse, or to be a champion draft horse. Every horse has good and bad points of its conformation and many horses (including Olympic caliber horses) excel even with conformation faults. The standard of the ideal head varies dramatically from breed to breed based on a mixture of the role the horse is bred for and what breeders, owners and enthusiasts find appealing. Breed standards frequently cite large eyes, a broad forehead and a dry head-to-neck ...
Ch431 Lec 14
Lets look at folding in another way: You might guess a protein would fold to lowest free energy conformation. Problem: is there time? (Levinthals Paradox, formulated by Cyrus Levinthal in 1968) Stryer calculation (very conservative): Assume 100 aa residue protein with 3 possible conformations/residue; then get 3100or 5 x 1047 possible conformations. If search at a rate of one structure/10-13sec then get (5 x 1047)(10-13)= 5 x 1034 sec or 1.6 x 1027 years to search (and thus to fold protein). This is greater than the age of our Universe (13.7 x 109 yrs). [Rawn calculation (perhaps more realistic): same but assume 10 conformations, then get 1087sec or 3 x 1080 yrs!]. Obviously from these calculations not searching all possible conformations (or we have the process wrong!), so cannot say protein achieves the lowest global free energy, but rather a local free energy minima. (Like a valley in mountain range: a local energy minima, but not lowest [Marianas trench].) [sketch - note represents ...
Language: English / Publisher: American Chemical Society / Subject: Molecular Structure and Molecular Conformation - Linus...
You searched for: Language English Remove constraint Language: English Publisher American Chemical Society Remove constraint Publisher: American Chemical Society Subject Molecular Structure Remove constraint Subject: Molecular Structure Subject Molecular Conformation Remove constraint Subject: Molecular Conformation ...
Identifying multiple active conformations in the G protein-coupled receptor activation landscape using computational methods -...
G protein-coupled receptors (GPCRs) are membrane proteins critical in cellular signaling, making them important targets for therapeutics. The activation of GPCRs is central to their function, requiring multiple conformations of the GPCRs in their activation landscape. To enable rational design of GPCR-targeting drugs, it is essential to obtain the ensemble of atomistic structures of GPCRs along their activation pathways. This is most challenging for structure determination experiments, making it valuable to develop reliable computational structure prediction methods. In particular, since the active-state conformations are higher in energy (less stable) than inactive-state conformations, they are difficult to stabilize. In addition, the computational methods are generally biased toward lowest energy structures by design and miss these high energy but functionally important conformations. To address this problem, we have developed a computationally efficient ActiveGEnSeMBLE method that ...
Probing large-scale conformational changes and other coupled processes in RNA polymerase, lac repressor, and IHF - DNA...
Solute effects arise from PREFERENTIAL INTERACTIONS (Timasheff): Solute and water compete for the biopolymer surface Preferential Accumulation of Solute: Solute-Biopolymer interactions more favorable than interactions of both species with water Local concentration of solute higher than bulk Preferential Exclusion of Solute (Preferential Hydration) Local concentration of solute lower than bulk To describe solute distribution: Schellman 1:1 solute: water competitive binding model Our solute partitioning model; partition coefficient K p K p = m 3 loc /m 3 bulk If K p > 1, solute is accumulated; if K p < 1, solute is excluded
Divalent cations regulate the folding and activation status of integrins during their intracellular trafficking | Journal of...
Monoclonal antibodies have become essential tools to study the structure and function of integrins because they recognise distinct conformational states of the receptors (Mould, 1996). Many of these antibodies have been used to study changes in the ligand-binding affinity of integrins on the cell surface (Humphries, 2000); however, in this study, we used their specificities to report defined conformational states during β1-integrin biosynthesis. In particular, we noted that two conformation-specific antibodies, 8E3 and 9EG7, which have been shown to recognise the unbent form of β1-integrins, also react with monomeric β1-integrin subunits. 9EG7 was of particular interest because it seems to recognise an epitope that requires the formation of a disulphide and once this disulphide is formed, the epitope is not lost even after denaturation. The epitope has been mapped previously to within a cysteine-rich stretch (residues 495-602) at the back of the β1-integrin knee region (Bazzoni et al., ...
Automating the Determination of 3d Protein Structure 3.2 Databases 3.3 New Method of Determining Structural Similarity 4...
The creation of an automated method for determining 3D protein structure would be invaluable to the eld of biology and presents an interesting challenge to computer science. Unfortunately , given the current level of protein knowledge, a completely automated solution method is not yet feasible; therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the rst step toward designing a program to determine protein conformation automatically. The properties of a protein are largely determined by its three-dimensional structure Voet and Voet 1990]. This statement would seem to simplify the process of understanding proteins and
Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis | The EMBO Journal
PINK1‐mediated phosphorylation of Ub at Ser65 has dramatic consequences for Ub structure, and key processes in the Ub system, namely Ub attachment and removal.. It could be expected that phosphorylation of Ub would change its surface properties due to the addition of a negative charge. The obtained high‐resolution crystal structure and solution studies agree that the majority of phosphoUb is structurally similar to wt Ub. To our amazement, NMR studies showed a second, minor conformation of phosphoUb, which is in slow exchange with the major conformation. Strikingly, the minor conformation shows distinct hydrogen bonding patterns and long‐range NOEs for its C‐terminal β5‐strand, which can only be structurally satisfied when this strand is shifted by two residues. Our phosphoUbretraCT model explains numerous observations and is structurally feasible due to the existence of four Leu‐Xaa repeats in the β5‐strand that would allow a shift of two residues without significantly ...
The Single Best Strategy To Use For Rule One Protein
Discovering the tertiary framework of the protein, or even the quaternary structure of its complexes, can offer significant clues about how the protein performs its function. Frequent experimental methods of composition dedication consist of X-ray crystallography and NMR spectroscopy, equally of which can produce facts at atomic resolution. Our site Even so, NMR experiments can deliver information from which a subset of distances among pairs of atoms may be approximated, and the ultimate achievable conformations for a protein are determined by solving a length geometry issue. Twin polarisation interferometry can be a quantitative analytical approach for measuring the overall protein conformation and conformational modifications due to interactions or other stimulus ...
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor
Background: Techniques for inferring the functions of the protein by comparing their shape similarity have been receiving a lot of attention. Proteins are functional units and their shape flexibility occupies an essential role in various biological processes. Several shape descriptors have demonstrated the capability of protein shape comparison by treating them as rigid bodies. But this may give rise to an incorrect comparison of flexible protein shapes. Results: We introduce an efficient approach for comparing flexible protein shapes by adapting a local diameter (LD) descriptor. The LD descriptor, developed recently to handle skeleton based shape deformations , is adapted in this work to capture the invariant properties of shape deformations caused by the motion of the protein backbone. Every sampled point on the protein surface is assigned a value measuring the diameter of the 3D shape in the neighborhood of that point. The LD descriptor is built in the form of a one dimensional histogram ...
Analysing the microenvironment of 2-p-toluidinylnaphthalene-6-sulfonate (TNS) in solvents and in different conformational...
Characterization of different conformational states of proteins is essential to understand their stability and activity. Biophysical techniques aid in analysing these conformational states and molecular fluorescence is one of the most reliable and quickly accessible methods. Apart from the intrinsic fluoresc
"Analysis of Structural Stability of Human Prosecretory Mitogenic Lacri" by Anna P. Desmarais and Casey Q. Ramirez Cortes
Purpose: Lacritin is a human tear glycoprotein that has high thermal stability. When cleaved, lacritin has antimicrobial activity resulting from the C-terminus amphipathic alpha helical region. The alpha helices contain three salt bridges; ionic bonds between neighboring oppositely charged amino acids. The purpose of this research was to investigate the hypothesis that the salt bridges within the alpha helices contribute to the high thermal stability. Methods: To determine the role of salt bridges in the thermal stability of lacritin, point mutants were prepared for each salt bridge by site directed mutagenesis that replaced the oppositely charged amino acids with serine. The point mutants were expressed in E. coli and purified. Western blot analysis confirmed the identity of lacritin proteins. Circular dichroism (CD) was used to study conformational changes in the secondary structure of these mutants compared to unaltered lacritin along with two controls, bovine serum albumin (BSA) and lysozyme.
A Porphyrin Terminated Molecular Tweezer for Conformational Restriction of Flexible Molecules in Solution.
Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy.. Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also ...
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data | BMC Structural Biology | Full Text
Protein NMR is the method of choice for determining protein structures at the atomic level in solution. In addition, NMR experiments allow characterization of protein dynamics at a wide range of time scales [1-7]. Dynamical studies of the past decade led to the emerging paradigm that the so-called native structure of a protein can be better viewed as a number of more or less similar conformers interconverting on different time scales. Functional interactions perturb this state by shifting the equilibrium towards active conformations that are present but are low-populated in the apo state. The most extreme examples of this kind of behavior are provided by intrinsically disordered proteins (IDPs) that adopt a plethora of diverse conformations in their free state but, at least some of them, might become fully or partially well ordered upon partner molecule binding [8, 9].. IDPs can not be described with single-conformer models but only with conformational ensembles capturing the diversity of ...
Conformational fluctuations affect protein alignment in dilute liquid crystal media - Danish National Research Database-Den...
The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions of each member to the residual dipolar coupling signals. We find that molecular fluctuations can affect the alignment and discover a resulting emphasis of certain conformations. However, the internal fluctuations are largely uncorrelated with those of the alignment, implying that proteins have liquidlike molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method ...
Different conformations of nascent polypeptides during translocation across the ER membrane | BMC Molecular and Cell Biology |...
In eukaryotic cells, proteins are translocated across the ER membrane through a continuous ribosome-translocon channel. It is unclear to what extent proteins can fold already within the ribosome-translocon channel, and previous studies suggest that only a limited degree of folding (such as the formation of isolated α-helices) may be possible within the ribosome. We have previously shown that the conformation of nascent polypeptide chains in transit through the ribosome-translocon complex can be probed by measuring the number of residues required to span the distance between the ribosomal P-site and the lumenally disposed active site of the oligosaccharyl transferase enzyme (J. Biol. Chem 271: 6241-6244).Using this approach, we now show that model segments composed of residues with strong helix-forming properties in water (Ala, Leu) have a more compact conformation in the ribosome-translocon channel than model segments composed of residues with weak helix-forming potential (Val, Pro). The main
Different conformations of nascent polypeptides during translocation across the ER membrane
Background. In eukaryotic cells, proteins are translocated across the ER membrane through a continuous ribosome-translocon channel. It is unclear to what extent proteins can fold already within the ribosome-translocon channel, and previous studies suggest that only a limited degree of folding (such as the formation of isolated α-helices) may be possible within the ribosome.. Results. We have previously shown that the conformation of nascent polypeptide chains in transit through the ribosome-translocon complex can be probed by measuring the number of residues required to span the distance between the ribosomal P-site and the lumenally disposed active site of the oligosaccharyl transferase enzyme (J. Biol. Chem 271: 6241-6244).Using this approach, we now show that model segments composed of residues with strong helix-forming properties in water (Ala, Leu) have a more compact conformation in the ribosome-translocon channel than model segments composed of residues with weak helix-forming potential ...
Shape-shifting serpins--advantages of a mobile mechanism
Serpins use an extraordinary mechanism of protease inhibition that depends on a rapid and marked conformational change and causes destruction of the covalently linked protease. Serpins thus provide stoichiometric, irreversible inhibition, and their dependence on conformational change is exploited fo …
From fluctuations to function: The role of dynamics in gene expression and biomolecular function | Duke Chemistry
Link for Professor Gonzalez. Abstract: Over the past two decades, stunning breakthroughs in the field of structural biology have continued to produce groundbreaking high-resolution structures of large, multi-component biomolecular machines. Comparative analyses of these static structures reveals the remarkable conformational flexibility of these machines and hints at the significant structural rearrangements that evidently accompany their functional cycles. Unfortunately, the experimental observation and characterization of these conformational dynamics is severely impeded by the size and complexity of biomolecular machines, severely limiting our understanding of the contributions that dynamics make to their functions. Using a combination of molecular genetic-, biochemical-, and single-molecule biophysical approaches, my research group aims to overcome these challenges and elucidate the precise roles that the conformational dynamics of biomolecular machines play in driving and controlling their ...
Entropy in the Coil-to-Globule Transition of Macromolecules
The coil to globule transition is a fundamental phenomenon in the physics of macro-molecules by reason of the multiplicity of arrangements of their conformation. Such conformational freedom is the main source of entropy in the molecule and is the main opponent to the transition towards the compact state, since a system tends to the state of maximum entropy. This phenomenon is captured by very simple models, such as the ensemble of Interacting Self avoiding Walks on the lattice. This model shows that the coil to globule transition belongs to the universality class of continuous transition called Θ point. Starting from a critical inspection of the definition of the interacting walks model, we introduce a refinement aiming to represent more precisely the entropy sourced from the local fluctuations of the molecule around its equilibrium conformations; this contribution is absent in the standard model which includes only the entropy generated by the multiplicity of the global conformations. Through ...
Annals of Laboratory Medicine
Some residues of the C, G, and H helices of Hb are a part of the α1β1 contact area. Most of these contacts are weak, non-covalent bonds, such as Van der Waals interactions and hydrogen bonds, although the latter have a less prominent role in α1β1 contact. These contacts form a rigid dimer, so that during Hb oxygenation and deoxygenation, movement in this area is extremely limited . Therefore, any constitutional variation could give rise to structural modifications that can cause Hb precipitation in erythropoietic progenitors depending on the location of the residue within the helix, its participation in Hb functionality, and the characteristics of the residue. This, in turn, may cause ineffective erythropoiesis or hemolytic anemia. An example of these behaviors is Hb variants at position G19. Position 19 of the G helix of the globin β chain is occupied by residue 118, a histidine. This residue is located externally in the three-dimensional protein structure and interacts with two ...
Protein structure ensembles from mathematical models - Bioinformatics Centre - University of Copenhagen
Understanding the 3D molecular structure of proteins is of enormous importance in science, medicine and biotechnology. When determining the 3D structure of a protein using biophysical methods, it is often assumed that a protein molecule has a single, specific shape. Yet in reality, many proteins adopt a number of radically different conformations, that can interchange dynamically. Such a set of conformations is called an ensemble. It is precisely the ensemble aspect of protein structure that plays a major role in important diseases such as Parkinsons, type II diabetes or Alzheimers. Currently, there are few methods that can handle such ensembles, and the available methods are suboptimal, ad hoc and heuristic.. We have developed a statistically rigorous and computationally efficient method to determine the structure of protein ensembles (Olsson et al., J. Magn. Reson., 2010; Olsson et al., PLoS ONE, 2013), based on previous methods developed at the Bioinformatics center, targeting both NMR and ...
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling - Authorea
A technique for identifying folding patterns of proteins using mass spectrometry that is potentially faster and requires less sample than X-ray crystallographic or NMR methods has been developed by B.W. Gibson and I.D. Kuntz. They believe the time needed to determine the fold family of a protein can be reduced to one week and that less than 10mg of protein may be required to elucidate macromolecular interactions, and multiple conformational states, and to contribute to the design of protein mimetics ...
Motomasa Tanaka, Protein Conformation Diseases | RIKEN Center for Brain Science (RIKEN CBS)
Label-free optical detection of single enzyme-reactant reactions and associated conformational changes | Science Advances
Enzymes fulfill a plethora of metabolic functions in all living organisms. In many cases, enzymatic activity is closely connected to changes in the enzymes conformation often involving the transition through multiple substates. One of the most important and, perhaps, most studied enzymes is DNA polymerase, which is present in all cells and responsible for replicating genetic information. Outside of the actual metabolisms, it is used for important biological applications, such as polymerase chain reaction (PCR) and DNA sequencing. The enzymatic activity of DNA polymerase involves multiple steps, such as the binding of primer-hybridized template DNA, insertion of a deoxynucleoside triphosphate (dNTP), and incorporation of dNTP, thereby extending the strand by 1 nucleotide (nt). Each step of such a catalytic process is accompanied by conformational changes of the DNA polymerase. These transitions, together with the corresponding reaction pathways, have an intrinsically transient nature and have ...
Difference between revisions of "User:Gevorg" - OpenWetWare
In many computational approaches to protein structure, the flexibility of amino-acid sidechains is represented via a finite set of rigid rotational isomers, known as rotamers. This representation is structurally justified (i.e. there is indeed a small set of conformations, which describe most of the flexibility of sidechains in proteins) and simplifies many of the aspects of the calculations. However, potential energies of protein conformations calculated using this so-called rotamer approximation are not necessarily in good agreement with the "true" potential energies due to the sensitivity of some energy terms to precise atomic location (see the schematic diagram below, where RCE and NCE represent the rotamer-based and true energy landscapes). The idea behind this study was to elucidate the extent to which this is a problem for such applications as computation protein design and structure prediction and to test the variety of simple "hacks" that are used in the field to address this problem ...
Bio 1A Lect 2 Quiz - Bio 1A Lect 2 Quiz 50 adenine aldose alpha alpha-helix amino Amino acids antiparallel beta beta-pleated...
The Curious Wavefunction: Modeling magic methyls
And indeed, thats what they find. Most of the cases they look at concern potency gains coming from putting methyls at the ortho position of a biaryl ring. Organic chemists are quite familiar with the steric, planarity-disrupting effects of ortho substituents on biaryl rings; in fact its a tried and tested strategy to improve solubility by disrupting crystal packing effects. It turns out that the bound structures of the molecules present a twisted, non-planar conformation. In the absence of methyls, the rings would prefer to stay almost coplanar (or at least less non-planar) in the unbound conformation. But putting methyl groups on twists the rings in the unbound conformation into a form thats similar to the bound one; basically theres more overlap between the solution and bound conformations in case of the methylated versions compared to the non-methylated ones. Consequently, the protein has to expend less energy to turn an already similar conformation into its bound counterpart. This ...
List of protein structure prediction software Chou PY, Fasman GD (1974). "Prediction of protein conformation". Biochemistry. 13 ... Chou PY, Fasman GD (1978). "Empirical predictions of protein conformation". Annu Rev Biochem. 47: 251-276. doi:10.1146/annurev. ... doi:10.1093/protein/11.5.345. PMID 9681866. Chen H, Gu F, Huang Z (2006). "Improved Chou-Fasman method for protein secondary ... Kyngas J, Valjakka J (1998). "Unreliability of the Chou-Fasman parameters in predicting protein secondary structure". Protein ...
"Conformation of polypeptides and proteins". Advances in Protein Chemistry. Advances in Protein Chemistry. 23: 283-437. doi: ... Richardson, J.S. (1981). "Anatomy and Taxonomy of Protein Structures". Advances in Protein Chemistry. Advances in Protein ... Richardson, J.S. (1981). "Anatomy and Taxonomy of Protein Structures". Advances in Protein Chemistry. Advances in Protein ... Hovmöller, S.; Zhou, T.; Ohlson, T. (2002). "Conformations of amino acids in proteins". Acta Crystallographica D. 58 (Pt 5): ...
Ramachandran GN, Sasisekharan V (1968). "Conformation of polypeptides and proteins". Adv Protein Chem. Advances in Protein ... Richardson JS (1981). "The anatomy and taxonomy of protein structure". Adv Protein Chem. Advances in Protein Chemistry. 34: 167 ... Protein Common Interface Database Database of similar protein-protein interfaces in crystal structures of homologous proteins ... MMDB Protein Data Bank Structural Classification of Proteins database STING Molecular modelling List of software for molecular ...
Levitt, M. (1976). "A simplified representation of protein conformations for rapid simulation of protein folding". Journal of ... Michael Levitt publications indexed by Google Scholar Levitt, Michael (1972). Conformation analysis of proteins (PhD thesis). ... He has also worked on simplified representations of protein structure for analysing folding and packing, as well as developing ... Xia, Y.; Huang, E. S.; Levitt, M.; Samudrala, R. (2000). "Ab initio construction of protein tertiary structures using a ...
David Chilton Phillips
Sibanda, B.L.; Blundell, T.L.; Thornton, J.M. (1989). "Conformation of β-hairpins in protein structures:: A systematic ... 1968). "Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units". ... Rajashankar KR, Ramakumar S (1996). "Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and ... Hutchinson, E.G.; Thornton, J.M. (1994). "A revised set of potentials for β-turn formation in proteins". Protein Science. 3 (12 ...
Beta bulge loop
Sibanda, BL; Blundell TL; Thornton JM (1989). "Conformation of β-hairpins in protein structures. A systematic classification ... Leader, DP; Milner-White EJ (2009). "Motivated Proteins: A web application for studying small three-dimensional protein motifs ... Chan, EAW; Hutchinson EG (1993). "Identification, classification and analysis of β-bulges in proteins". Protein Science. 2 (10 ... Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins:  and PDBeMotif: . ...
Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. (1989). "Conformation of beta-hairpins in protein structures. A systematic ... Thornton, J. M.; Singh, J; Campbell, S; Blundell, T. L. (1988). "Protein-protein recognition via side-chain interactions". ... Hubbard, Simon Jeremy (1991). Analysis of protein-protein molecular recognition (PhD thesis). University College London. EThOS ... "The Protein Feature Ontology: A tool for the unification of protein feature annotations". Bioinformatics. 24 (23): 2767-2772. ...
"An analysis of side-chain conformation in proteins". International Journal of Peptide and Protein Research. 13 (2): 170-84. ... Banerjee, R.; Das, K.; Ravishankar, R.; Suguna, K.; Surolia, A.; Vijayan, M. (7 June 1996). "Conformation, protein-carbohydrate ... side chain conformation in proteins and additional binding sites in lysozyme. Vijayan has published more than 260 peer reviewed ... "Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: ...
"Roles of electrostatics and conformation in protein-crystal interactions". PLoS ONE. 5 (2): e9330. doi:10.1371/journal.pone. ... Osteopontin is an extracellular structural protein and therefore an organic component of bone. Synonyms for this protein ... bone sialo protein, and alkaline phosphatase. Collagen type I counts for 90% of the protein mass. The inorganic part of bone is ... "Cooperative Unfolding of Compact Conformations of the Intrinsically Disordered Protein Osteopontin". Biochemistry. 52 (31): ...
During illumination with light, these proteins change their conformation. In the process they gain or lose their ability to ... Some fluorescent proteins can be switched on and off by light of appropriate wavelength. They can be used in a RESOLFT-type ... Just as with proteins, also some organic dyes can change their structure upon illumination. The ability to fluoresce of such ... Inducing conformational changes in proteins can be achieved already at much lower switching light intensities as compared to ...
Durussel I, Rhyner JA, Strehler EE, Cox JA (1993). "Cation binding and conformation of human calmodulin-like protein". ... Calmodulin-like protein 3 is a protein that in humans is encoded by the CALML3 gene. GRCh38: Ensembl release 89: ... Rogers MS, Kobayashi T, Pittelkow MR, Strehler EE (2001). "Human calmodulin-like protein is an epithelial-specific protein ... 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ...
Chou, Peter Y.; Fasman, Gerald D. (1974-01-15). "Prediction of protein conformation". Biochemistry. 13 (2): 222-245. doi: ... UPF0575 protein C19orf67 is a protein which in humans (Homo sapiens) is encoded by the C19orf67 gene. Orthologs of C19orf67 are ... Protein Engineering, Design and Selection. 20 (11): 561-567. doi:10.1093/protein/gzm057. ISSN 1741-0126. "Genomatix - NGS Data ... The protein is expressed at low levels throughout the body with the exception of the testis and breast tissue. Where it is ...
The binding typically results in a change of conformation of the target protein. In DNA-ligand binding studies, the ligand can ... The conformation of a receptor protein composes the functional state. Ligands include substrates, inhibitors, activators, and ... In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. ... The etymology stems from ligare, which means 'to bind'. Ligand binding to a receptor protein alters the chemical conformation ...
43 (4) 482-487 (1998) ^ "Toy Model Studies of Soliton Mediated Protein Folding and Conformation Changes" Caspi, S., Ben-Jacob, ... 47, 522-527 (1999). ^ "Conformation changes and folding of proteins mediated by Davidov's soliton". Caspi, S., Ben-Jacob, E., ... Soliton Mediated Protein Folding. Pattern Formation and Self-Organization. In ... "Lethal protein produced in response to competition between sibling bacterial colonies". Be'er, A., Ariel, G., Kalishman, O., ...
"Ubiquitin chain conformation regulates recognition and activity of interacting proteins". Nature. 492 (7428): 266-70. doi: ... "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ... Polyubiquitin-C is a protein encoded by the UBC gene in humans. Polyubiquitin-C is one of the sources of ubiquitin, along with ... Chen L, Dong W, Zou T, Ouyang L, He G, Liu Y, Qi Y (August 2008). "Protein phosphatase 4 negatively regulates LPS cascade by ...
β-Sheets predominate as the secondary level of protein conformation. Recent emergence of oseltamivir and zanamivir resistant ... There are two major proteins on the surface of influenza virus particles. One is the lectin haemagglutinin protein with three ... The first step involves the distortion of the α-sialoside from a 2C5 chair conformation (the lowest-energy form in solution) to ... which allow for secretion of FLAG-tagged proteins and further purification. The enzymatic mechanism of influenza virus ...
Transmissible spongiform encephalopathy
July 2003). "A prion protein epitope selective for the pathologically misfolded conformation". Nature Medicine. 9 (7): 893-9. ... The PRNP gene provides the instructions to make a protein called the prion protein (PrP). Under normal circumstances, this ... which expresses prion proteins that contort by themselves into the disease-causing conformation. Transmission occurs when ... thus being composed solely of protein material. Misshapen prion proteins carry the disease between individuals and cause ...
Sibanda, B.L.; Blundell, T.L.; Thorton, J.M. (1985). "Conformations of Beta-Hairpins in Protein Structures". Nature(London) 316 ... To see this clearly, the Pin1 Domain protein is shown to the left as an example. Proteins that are β-sheet rich, also called WW ... function by adhering to proline-rich and/or phosphorylated peptides to mediate protein-protein interactions. The "WW" refers to ... have used protein NMR to show that beta-hairpins can be formed from isolated short peptides in aqueous solution, suggesting ...
"The conformation of neurotensin bound to its G protein-coupled receptor". Proceedings of the National Academy of Sciences. 100 ... He has used the technology amongst others to study the behavior of bacterial proteins, protein aggregation in Alzheimer's and ... for the analsyis of membrane embedded proteins such as G-protein coupled receptors and ion channels and for the ... permanent dead link] "University of Utrecht Orders Bruker's 527 GHz DNP-NMR System to Study Membrane Proteins". Genetic ...
McLean PJ, Kawamata H, Ribich S, Hyman BT (Mar 2000). "Membrane association and protein conformation of alpha-synuclein in ... The majority form of the protein, and the one most investigated, is the full-length protein of 140 amino acids. Other isoforms ... Certain sections of the alpha-synuclein protein may play a role in the tauopathies. A prion form of the protein alpha-synuclein ... "The precursor protein of non-A beta component of Alzheimer's disease amyloid is a presynaptic protein of the central nervous ...
However, only half of the protein has a defined secondary conformation. The rest of this protein is intrinsically disordered. ... This protein has a length of 421 amino acids, among which, we have to highlight the Glutamine number 58 (Gln or Q), which is ... ATAT1 it is not a modular protein because it only have one domain localized from the first amino acid to the one hundred and ... The protein's active site contains several conserved residues that could potentially function as general bases in the reaction ...
Hamelryck T, Kent JT, Krogh A (2006). "Sampling Realistic Protein Conformations Using Local Structural Bias". PLoS Comput. Biol ... Applications to protein modeling". J. Mol. Biol. 235 (5): 1501-31. doi:10.1006/jmbi.1994.1104. PMID 8107089. Krogh A, Mian IS, ... Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001). "Predicting transmembrane protein topology with a hidden Markov model: ... Winther O, Krogh A (2004). "Teaching computers to fold proteins". Phys. Rev. E. 70 (3): 030903. doi:10.1103/PhysRevE.70.030903 ...
Familial amyloid neuropathy
Kelly JW (February 1996). "Alternative conformations of amyloidogenic proteins govern their behavior". Curr. Opin. Struct. Biol ... These proteins include: transthyretin (ATTR, the most commonly implicated protein), apolipoprotein A1, and gelsolin. Due to the ... Ghoshdastider U, Popp D, Burtnick LD, Robinson RC (2013). "The expanding superfamily of gelsolin homology domain proteins". ... The aggregation of one precursor protein leads to peripheral neuropathy and/or autonomic nervous system dysfunction. ...
... is a signal transducing protein; thus, the balance between conformations regulates protein activity. ADK has a ... shows the conformations of ADK when binding with ATP or AMP. The study shows that there are three relevant conformations or ... conformations amongst those that are sampled by ADK. These 'closed' conformations are hypothesized to help with removal of ... Sub-cellular localization of the ADK enzymes is done by including a targeting sequence in the protein. Each isoform also has ...
Thus the protein cannot achieve native conformation and is degraded by proteosome. Addition of such inhibitor causes ... Hsp90 client proteins, activates the apoptosis-associated doublestranded RNA-dependent protein kinase, PKR and promotes an ... proteins but it was a question of debate if 17 AAG affected the genes for client proteins or it inhibited cytosolic proteins. ... p23 also has chaperone activity on its own and is able to inhibit aggregation of denatured proteins in the absence of ATP. The ...
Vauquelin G, Van Liefde I (2005). "G protein-coupled receptors: a count of 1001 conformations". Fundamental & clinical ... The fact that receptor conformation (state) would affect binding affinity of a ligand was used to explain a mechanism of ... The original Ternary complex model was used to describe ligand, receptor, and G-protein interactions. It uses equilibrium ... Bridges TM, Lindsley CW (July 2008). "G-Protein-Coupled Receptors: From Classical Modes of Modulation to Allosteric Mechanisms ...
Sedimentation Velocity Analysis of Heterogeneous Protein-Protein Interactions: Lamm Equation Modeling and Sedimentation ... and conformation. Samples are centrifuged with a high-density solution such as sucrose, caesium chloride, or iodixanol. The ... By 1900, it had been generally accepted that proteins were composed of amino acids; however, whether proteins were colloids or ... Howlett, G.J., Minton, A.P., Rivas, G. Analytical Ultracentrifugation for the Study of Protein Association and Assembly. ...
ER Translocon complex. Many protein complexes are involved in protein synthesis. The actual production takes place in the ... Move these two large substrates into their proper locations and conformations.. *Activate the Asn amide nitrogen atom for the ... Sec61 is the protein-conducting channel and the OST adds sugar moieties to the nascent protein. ... Oligosaccharyltransferase or OST (EC 188.8.131.52) is a membrane protein complex that transfers a 14-sugar oligosaccharide from ...
The term alpha-1 refers to the protein's behavior on protein electrophoresis. On electrophoresis, the protein component of the ... Elliott PR, Abrahams JP, Lomas DA (January 1998). "Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation". ... which could confer this protein particular protein-cell recognition properties. The single cysteine residue of A1AT in position ... As protein electrophoresis is imprecise, the A1AT phenotype is analysed by isoelectric focusing (IEF) in the pH range 4.5-5.5, ...
GABAA receptor positive allosteric modulator
Fig 2. Schematic diagram of a GABAA receptor protein ((α1)2(β2)2(γ2)) which illustrates the five combined subunits that form ... weak modulators of GABAA receptor function because the flexible side chains in these analogues do not have the conformations ... The synaptic anchoring protein Gephyrin is indirectly linked to the GABAA receptors. ... molecules that increase the activity of the GABAA receptor protein in the vertebrate central nervous system. ...
Receptor binding, as well as membrane fusion, are catalyzed by the protein E, which changes its conformation at low pH, causing ... and forms a complex with protein E. The immature particles are processed in the Golgi apparatus by the host protein furin, ... At first, an immature form of the virus particle is produced inside the ER, whose M-protein is not yet cleaved to its mature ... Host proteases cut this polyprotein into three structural (C, prM, E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, ...
This process increases transcription of certain genes, notably CYP1A1, followed by increased CYP1A1 protein production. ... Absolute configuration and conformation". Proceedings of the National Academy of Sciences. Retrieved January 3, 2006.. ... "Basal and inducible CYP1 mRNA quantitation and protein localization throughout the mouse gastrointestinal tract". Free Radic ...
... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around ... Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a ... The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins ...
Single particle analysis
This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell. Fatty acid synthase ... However, a micrograph often contains particles in multiple different orientations and/or conformations, and so to get more ... Proteins in vitreous ice usually adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic ... Important information on protein synthesis, ligand binding and RNA interaction can be obtained using this novel technique at ...
Nuclear magnetic resonance spectroscopy of nucleic acids
NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... and sugar pucker conformations. The presence or absence of imino proton resonances, or of coupling between 15N atoms across a ... Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller ... Nucleic acids also tend to have resonances distributed over a smaller range than proteins, making the spectra potentially more ...
Ligands connect to specific receptor proteins based on the shape of the active site of the protein. ... Change in the receptor conformation such that binding of the agonist does not activate the receptor. This is seen with ion ... and can be a protein or peptide (short protein), or another small molecule such as a neurotransmitter, hormone, pharmaceutical ... In biochemistry and pharmacology, a receptor is a protein molecule that receives chemical signals from outside a cell. When ...
فهرست یهودیان برنده جایزه نوبل - ویکیپدیا، دانشنامهٔ آزاد
"for their studies of the structures of globular proteins" ۱۹۷۲ ویلیام اشتین United States "for his work on ribonuclease ... especially concerning the connection between the amino acid sequence and the biologically active conformation" ... "for their discovery of جی پروتئینs and the role of these proteins in ورارسانی پیام in cells" ... "for their interpretation of the رمز ژنتیکی and its function in protein synthesis" ...
I. Isolation and characterization of the protein-glycogen complex". Journal of Biological Chemistry. 245 (24): 6642-6648. PMID ... There is also an alternative proposed mechanism involving a positively charged oxygen in a half-chair conformation. ... First, the catalytic sites are relatively buried, 15Å from the surface of the protein and from the subunit interface. This ... The glycogen phosphorylase monomer is a large protein, composed of 842 amino acids with a mass of 97.434 kDa in muscle cells. ...
Հեպարին - Վիքիպեդիա՝ ազատ հանրագիտարան
Fractionation of proteins by heparin chromatography։ Methods Mol Biol։ Methods in Molecular Biology™ 424։ 2008։ էջեր 213-21։ ... N.M.R. and molecular-modelling studies of the solution conformation of heparin»։ Biochem. J. 293 (Pt 3): 849-858։ հունվարի 1, ... B. Mulloy, M.J. Forster։ «N.M.R. and molecular-modeling studies of the solution conformation of heparin» ... Gatti G., Casu B., Hamer G. K., Perlin A. S. (1979)։ «Studies on the Conformation of Heparin by1H and13C NMR Spectroscopy»։ ...
The hydroxyl group also forces the ribose into the C3'-endo sugar conformation unlike the C2'-endo conformation of the ... DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA ... where a nucleotide-based molecule is needed to synthesize protein, and a peptide-based (protein) molecule is needed to make ... The ability to catalyse the formation of peptide bonds between amino acids to produce short peptides or longer proteins. This ...
The protein degradation processEdit. Ribbon diagram of ubiquitin, the highly conserved protein that serves as a molecular tag ... Three distinct conformational states of the 26S proteasome. The conformations are hypothesized to be responsible for ... Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks ... Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ...
Innate immune system
This leads to antiviral protein production, such as protein kinase R, which inhibits viral protein synthesis, or the 2′,5′- ... When the cytoplasmic receptors MDA5 and RIG-I recognize a virus the conformation between the caspase-recruitment domain (CARD) ... "Resistance" (R) proteins, encoded by R genes, are widely present in plants and detect pathogens. These proteins contain domains ... The cascade is composed of many plasma proteins, synthesized in the liver, primarily by hepatocytes. The proteins work together ...
Beta-amiloide, a enciclopedia libre
"The Alzheimer's Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide". PLoS ONE 5 (3): e9505. Bibcode:2010PLoSO... ... "The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study". J. Mol. Biol. 368 ... Shinkai Y, Yoshimura M, Ito Y, Odaka A, Suzuki N, Yanagisawa K, Ihara Y (September 1995). "Amyloid beta-proteins 1-40 and 1-42( ... Zou K, Gong JS, Yanagisawa K, Michikawa M (June 2002). "A novel function of monomeric amyloid beta-protein serving as an ...
Immunoglobulin-binding protein - Proteins such as protein A, protein G, and protein L that are capable of binding to antibodies ... Antigen specificity is due primarily to the side-chain conformations of the antigen. It is measurable and need not be linear or ... An autoantigen is usually a normal protein or protein complex (and sometimes DNA or RNA) that is recognized by the immune ... Lipids and nucleic acids are antigenic only when combined with proteins and polysaccharides. Non-microbial non ...
Wiskott-Aldrich syndrome protein
In the absence of CDC42 and PIP2, N-WASp is in an inactive, locked conformation. Cooperative binding of both CDC42 and PIP2 ... protein binding. • identical protein binding. • actin binding. • protein kinase binding. • small GTPase binding. • Rac GTPase ... "The Wiskott-Aldrich syndrome protein-interacting protein (WIP) binds to the adaptor protein Nck". The Journal of Biological ... The Wiskott-Aldrich Syndrome protein (WASp) is a 502-amino acid protein expressed in cells of the hematopoietic system. In the ...
"Cellular prion protein conformation and function". Proc. Natl. Acad. Sci. U.S.A. 108 (42): 17308-13. Bibcode:2011PNAS.. ... ATP-dependent protein binding. • metal ion binding. • tubulin binding. • protein binding. • identical protein binding. • copper ... PRNP (prion protein) is the human gene encoding for the major prion protein PrP (proetase-resistant-protein, Pr for prion, and ... negative regulation of protein processing. • protein destabilization. • activation of protein kinase activity. • calcium- ...
نوبل انعام برائے کیمیا وصول کنندگان کی فہرست - آزاد دائرۃ المعارف، ویکیپیڈیا
"for their contributions to the development of the concept of conformation and its application in chemistry" ... "for their preparation of enzymes and virus proteins in a pure form" ... "for his work on the structure of proteins, especially that of insulin" ... "for the discovery and development of the green fluorescent protein, GFP" ...
டி. என். ஏ. - தமிழ் விக்கிப்பீடியா
Contributions of protein-protein and protein-membrane interactions toward complex formation". The Journal of Biological ... Factor Xa inhibitors generally bind in an L-shaped conformation, where one group of the ligand occupies the anionic S1 pocket ... The affinity of this protein for factor Xa is increased 1000-fold by the presence of protein Z, while it does not require ... protein binding. • serine-type peptidase activity. • serine-type endopeptidase activity. • phospholipid binding. • hydrolase ...
The shape into which a protein naturally folds is known as its native conformation. Although many proteins can fold ... Main article: Protein domain. Many proteins are composed of several protein domains, i.e. segments of a protein that fold into ... globular proteins, fibrous proteins, and membrane proteins. Almost all globular proteins are soluble and many are enzymes. ... Protein purification. Main article: Protein purification. To perform in vitro analysis, a protein must be purified away from ...
The ACTH receptor is a seven-membrane-spanning G protein-coupled receptor. Upon ligand binding, the receptor undergoes ... conformation changes that stimulate the enzyme adenylyl cyclase, which leads to an increase in intracellular cAMP and ... and their associated electron transfer proteins. This effect is observed over several hours. ... subsequent activation of protein kinase A. ACTH influences steroid hormone secretion by both rapid short-term mechanisms that ...
This is how the protein checks for the recognition site as it allows the DNA duplex to follow the shape of the protein. In ... the repressor changes conformation and falls off the operator. RNAP is then able to bind to the promoter and begin ... The lacI gene synthesizes LacI repressor protein. The LacI repressor protein represses lacZYA by binding to the operator ... lacZYA transcribes the proteins needed for lactose breakdown. lacI synthesizes the repressor of the lacZYA gene. The gene ...
வேதியியலுக்கான நோபல் பரிசு பெற்றவர்கள் - தமிழ் விக்கிப்பீடியா
"for their contributions to the development of the concept of conformation and its application in chemistry" ... "for their preparation of enzymes and virus proteins in a pure form" ... "for his work on the structure of proteins, especially that of insulin" ... especially concerning the connection between the amino acid sequence and the biologically active conformation" ...
Evolving L-Systems to Capture Protein Structure Native Conformations | SpringerLink
In this state, proteins show repeated substructures like alpha helices and beta sheet ... A protein is a linear chain of amino acids that folds into a unique functional structure, called its native state. ... Unger, I., Moult, J.: Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications. ... Patton, A., Punch, W., Goodman, E.: A Standard GA approach to native protein conformation prediction. In: Proceedings of the ...
Protein Conformation (Topic) - Rensselaer Libraries
Context of Protein Conformation Focus of. * Protein Conformation * Protein Conformation -- Congresses * Protein Conformation ... Protein Conformation The Resource Protein Conformation Label Protein Conformation. 43 Items that are about the Topic Protein ... Protein Conformation,/a,,/span, - ,span property=offers typeOf=Offer,,span property=offeredBy typeof=Library ll:Library ... Protein Conformation,/a,,/span, - ,span property=offers typeOf=Offer,,span property=offeredBy typeof=Library ll:Library ...
NMR paper Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR. - BioNMR
Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR. Related Articles Effects of ... NMR paper] Insights into conformation and dynamics of protein GB1 during folding and unfolding b Insights into conformation and ... Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR.. Related Articles Effects of ... Related Articles Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR. J Mol Biol. 2004 ...
DPD simulation of protein conformations: From α-helices to β-structures<...
DPD simulation of protein conformations: From α-helices to β-structures. Journal of Physical Chemistry Letters. 2012 Nov 1;3(21 ... DPD simulation of protein conformations: From α-helices to β-structures. Aleksey Vishnyakov, David S. Talaga, Alexander V. ... DPD simulation of protein conformations : From α-helices to β-structures. / Vishnyakov, Aleksey; Talaga, David S.; Neimark, ... Vishnyakov, A., Talaga, D. S., & Neimark, A. V. (2012). DPD simulation of protein conformations: From α-helices to β-structures ...
Conformation change upon formation of large i - Unspecified - BNID 107914
Conformation change upon formation of large interfaces (of proteins). Range. Table - link ... Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol. 1999 Feb 5 285(5):2177- ... Researchers performed an analysis of the atomic structure of the recognition sites seen in 75 protein-protein complexes of ... The formation of complexes that have large interfaces is seen to involve large changes in conformation in those cases where ...
Conformationally-labile biomolecules such as intrinsically-disordered proteins (IDPs) can change conformation upon exposure to ... One aspect is how the surface can manipulate the conformation of the adsorbing biomolecule. ... related to this new conformation. Another aspect is how the adsorption of biomolecules influences the growth/stability of ... the search for conserved calcite-binding domains in eggshell proteins. Our overarching goal here is the adaptation, development ...
Protein Conformation | Life Sciences | Subjects | Wiley
Derek J. Chadwick and Kate Widdows are editors for Protein Conformation and other scientific titles. ... protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and ... Comparative Analysis of Protein Three-Dimensional Structures and an Approach to the Inverse Folding Problem (T. Blundell). ... How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry ...
Stabilization Energies of Protein Conformation | SpringerLink
The study of protein stability is currently undergoing a dramatic change. Early work, especially after Kauzmann (1959), ... In: Fasman G.D. (eds) Prediction of Protein Structure and the Principles of Protein Conformation. Springer, Boston, MA. * DOI ... Prediction of Protein Structure and the Principles of Protein Conformation pp 161-192 , Cite as ... Amino Acid Substitution Cross Link Protein Stability Stabilization Energy Protein Conformation These keywords were added by ...
Protein - Conformation of proteins in interfaces | Britannica.com
Conformation of proteins in interfaces: Like many other substances with both hydrophilic and hydrophobic groups, soluble ... Proteins, when forming an interfacial film, are present as a monomolecular layer-i.e., a layer one molecule in height. Although ... Within the interface, proteins spread, forming thin films. Measurements of the surface tension, or interfacial tension, of such ... proteins tend to migrate into the interface between air and water or oil and water; the term oil here means a hydrophobic ...
Influence of proline residues on protein conformation. - PubMed - NCBI
Influence of proline residues on protein conformation.. MacArthur MW1, Thornton JM. ... an analysis has been made of all proline residues and their local conformations extracted from the Brookhaven Protein Data bank ... the influence of proline on the conformation of the preceding residue and the conformations of various proline patterns (Pro- ... We have considered the conformation of the proline itself, the relative occurrence of cis and trans peptides preceding proline ...
Protein Conformation and Dynamics | National Heart, Lung, and Blood Institute (NHLBI)
Regulation of protein kinases; controlling activity through activation segment conformation. - PubMed - NCBI
Regulation of protein kinases; controlling activity through activation segment conformation.. Nolen B1, Taylor S, Ghosh G. ... There are currently at least forty-six unique protein kinase crystal structures, twenty-four of which are available in an ... Here we examine these structures using a structural bioinformatics approach to understand how the conformation of the ...
Knowledge-based prediction of protein backbone conformation using a structural alphabet
Predicting the local structure of a protein in terms of protein blocks is the general objective of this work. A new approach, ... This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. ... to scan this database and predict most probable backbone conformations for the protein local structures. Though PB-kPRED uses ... One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. ...
Protein-bound conformation of a specific inhibitor against Candid...: Ingenta Connect
RCSB PDB - 2VVH: IrisFP fluorescent protein in its green form, cis conformation
IrisFP fluorescent protein in its green form, cis conformation. *DOI: 10.2210/pdb2VVH/pdb ... GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP. A, B, C, D. 226. Lobophyllia hemprichii. Mutation(s): 3 ... Like its parent protein EosFP, IrisFP also photoconverts irreversibly to a red-emitting state under violet light because of an ... Photoactivatable fluorescent proteins (FPs) are powerful fluorescent highlighters in live cell imaging and offer perspectives ...
Significance of bound water to local chain conformations in protein crystals | PNAS
Significance of bound water to local chain conformations in protein crystals Message Subject (Your Name) has sent you a message ... Significance of bound water to local chain conformations in protein crystals. C H Robert and P S Ho ... The fractional water occupancy of each was found by comparison of the total number of conformations in the database regardless ... We examine how the polypeptide chain in protein crystal structures exploits the multivalent hydrogen-bonding potential of bound ...
RCSB PDB - 3RRT: Structure of the RSV F protein in the post-fusion conformation
Structure of the RSV F protein in the post-fusion conformation. *DOI: 10.2210/pdb3RRT/pdb ... Here, we present the 2.8-Å crystal structure of the trimeric RSV F ectodomain in its postfusion conformation. The structure ... Mechanistically, these results suggest that 101F and motavizumab can bind to multiple conformations of the fusion glycoprotein ... The structural preservation of neutralizing epitopes in the postfusion state suggests that this conformation can elicit ...
Phosphoinositide-dependent protein kinase 1, a sensor of protein conformation
... is a protein kinase that phosphorylates and activates several other protein kinases from the AGC group (which includes PKA, PKG ... Phosphoinositide-dependent protein kinase 1, a sensor of protein conformation Trends Biochem Sci. 2004 Mar;29(3):136-42. doi: ... Phosphoinositide-dependent protein kinase 1 (PDK1) is a protein kinase that phosphorylates and activates several other protein ... interact with and phosphorylate specific substrate conformations and thus sets PDK1 at the centre of a protein conformation ...
Extracellular Matrix Heparan Sulfate Proteoglycans - Amyloid Proteins: The Beta Sheet Conformation and Disease - Neame - Wiley...
SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations | PNAS
2011) Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins 80(2): ... the crystal conformation for each helix must be in that helixs top 36 conformations. The ranking of the crystal conformation ... We rely on energy ordering the final set of conformations without ligand or G protein and there could be too many nonactive ... SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations. Jenelle K. Bray, ...
PSP - Protein Structure Prediction (protein 3D conformation prediction at rest) | AcronymFinder
... protein 3D conformation prediction at rest). PSP is defined as Protein Structure Prediction (protein 3D conformation prediction ... protein 3D conformation prediction at rest) abbreviated? PSP stands for Protein Structure Prediction ( ... PSP stands for Protein Structure Prediction (protein 3D conformation prediction at rest). ... Protein structure prediction, 2d ed. To that end, this reference sheds light on the methods used for protein structure ...
Protein Conformation | School of Pharmacy | UCSF
Research in my lab focuses on atomic-level mechanisms of protein regulation, protein-ligand interactions, and computer-aided ... I am interested in the structure, function, and evolution of proteins and their assemblies. As Associate Dean of Research, I ... DeGrado receives Protein Societys Stein and Moore Award. Wed Feb 11, 2015 ... The award is given annually by the international society "to recognize eminent leaders in protein science who have made ...
IUCr) Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation
Protein-protein interaction analysis of the halobacterial Che proteins revealed that CheF1 directly interacts with CheY, CheD ... Protein concentration (mg ml−1). 10. 10. Buffer composition of protein solution. 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. ... Proteins from H. salinarum have been expressed recombinantly in E. coli, but primarily as unfolded proteins that rely on the ... In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal ...
Conservation of Topology, But Not Conformation, of the Proteolipid Proteins of the Myelin Sheath | Journal of Neuroscience
... the myelin basic proteins and the proteolipid proteins (DM-20/PLP). The myelin basic proteins are extrinsic membrane proteins ... The proteolipid protein gene products DM-20 and PLP are adhesive intrinsic membrane proteins that make up ≥50% of the protein ... Curiously, changes in protein conformation imparted by the PLP-specific peptide not only confer sensitivity to amino acid ... Conservation of Topology, But Not Conformation, of the Proteolipid Proteins of the Myelin Sheath. Alexander Gow, Alexander ...
Conformation Rules Part 3: News, Common Threads, Debate from San Diego Protein Misfolding Conference | ALZFORUM
Conformation Rules Part 3: News, Common Threads, Debate from San Diego Protein Misfolding Conference. Go to another part. ... Huntingtons Protein Snarls Axonal Traffic 2 Oct 2003. * Conformation Rules Part 1: News, Common Threads, Debate from San Diego ... Conformation Rules Part 2: News, Common Threads, Debate from San Diego Protein Misfolding Conference 17 Dec 2004. ... Conformation Rules Part 2: News, Common Threads, Debate from San Diego Protein Misfolding Conference 17 Dec 2004. ...
An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent...
An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ... An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent ... Driks A, Roels S, Beall B, Moran CP Jr & Losick R (1994) Subcellular localization of proteins involved in the assembly of the ... Ramamurthi KS & Losick R (2008) ATP-driven self-assembly of a morphogenetic protein in Bacillus subtilis. Mol Cell 31: 406-414. ...
DIGITAL.CSIC: Characterizing conformation changes in proteins through the torsional elastic response
Characterizing conformation changes in proteins through the torsional elastic response. Authors: Dos Santos, Helena G.; Klett, ... The relationship between functional conformation changes and thermal dynamics of proteins is investigated with the help of the ... This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, ... than to pairs of conformations with the same ligands. This deep relationship between the thermal dynamics of a protein, ...
Bruker Introduces Novel HDX Solution for Protein Conformation Studies | Bruker
Identifying structural hotspots, understanding drug/protein or protein/protein interactions or determining the structural ... and enable biopharma researchers to gain greater insights into protein conformation and protein interactions more quickly, more ... The information and insights gained following data analysis using the HDExaminer software can be used to probe protein ... biopharmaceutical characterization requires deeper understanding of the conformational structure of biotherapeutic proteins, ...
Molecules | Free Full-Text | Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the...
In an example application we modeled the process of complex assembly between two proteins: Troponin C (TnC) and the N-terminal ... This way our procedure opens up a new possibility for studying mechanisms of protein complex assembly, which may be a ... CABS-dock is a versatile and efficient tool for modeling the structure, dynamics and interactions of protein complexes. The ... a phenomenon that can be modeled only when protein flexibility is properly accounted for. ...
A biphasic change in ribosomal conformation during transneuronal degeneration is altered by inhibition of mitochondrial, but...
Blocking cytoplasmic protein synthesis with cycloheximide had no effect on the biphasic change in Y10B labeling of afferent- ... During this second phase, NM neurons putatively destined to die, based on their failure to synthesize protein, are unlabeled by ... Six hours following afferent deprivation, dying NM neurons demonstrate complete loss of ribosomes and cessation of protein ... A biphasic change in ribosomal conformation during transneuronal degeneration is altered by inhibition of mitochondrial, but ...
Video: Yael Mandel-Gutfreund, "The role of RNA conformation in RNA-protein recognition"
The role of RNA conformation in RNA-protein recognition. ... Advances and Challenges in Protein-RNA: Recognition, Regulation ... The role of RNA conformation in RNA-protein recognition. Yael Mandel-Gutfreund, Video: The role of RNA conformation in RNA- ... Yael Mandel-Gutfreund, The role of RNA conformation in RNA-protein recognition, Advances and Challenges in Protein-RNA: ... Yael Mandel-Gutfreund, Video: The role of RNA conformation in RNA-protein recognition ...
Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors | Science Signaling
Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ... Inverse Agonists: Tools to Reveal Ligand-Specific Conformations of G Protein-Coupled Receptors ...
Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green...
Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green ... Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green ... fluorescent protein Methods Enzymol. 2000;327:472-500. doi: 10.1016/s0076-6879(00)27297-2. ...
Improved Ion Mobility Separation of Protein Conformations in the Gas Phase with SYNAPT G2 HDMS : Waters
... can clearly separate different conformations of equine cytochrome c within minutes, matching that of published work. ... Protein Structure in Vacuo: The Gas Phase Conformations of BPTI and Cytochrome c. Shelimov KB, Clemmer DE, Hudgins RR, Jarrold ... At pH 2.6, the protein is denatured and is therefore expected to produce more open conformations because of the repulsive ... Improved Ion Mobility Separation of Protein Conformations in the Gas Phase with SYNAPT G2 HDMS. Improved Ion Mobility ...
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
The accurate assignment of the secondary structure of proteins from protein atom coordinates underlies the analysis of protein ... Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. ... Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the ... Home » Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and ...
Intrinsically-disordered proteinsStructuresHydrogenFunctionalGlobular proteinsAlpha helicesFoldingStructureSimulationAbstractPredictionGlobularStructuresPolypeptidesDynamicsGuanine-nucleotiCharacterizationAffinityStabilizeChanges in proteinsMacromolecularMembrane proteinsMonoclonal antibodiesCoarse-grainedConformational spaceProteolipid proteinsGPCRsSecondary structurePrion proteinMembranesAntigensBackbone conformationsTransitionsPolypeptide chainDifferent conformationsInteractionMoleculeAcidic proteinsReceptorBiologicalInactiveMass spectrometryNeurodegenerative diseasesLigandsTransmembraneAggregatesResidueFluorescent proteinsStability of proteinsFlexibilityCatalysisHelixComplexPeptide chain
- The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments. (montclair.edu)
- Thus the foundations are set for a novel encoding based on L-systems for evolutionary approaches to both the Protein Structure Prediction and Inverse Folding Problems. (springer.com)
- Fraenkel, A.: Complexity of protein folding. (springer.com)
- Mineral surfaces provide such a stimulus that can induce folding and thus confer function(s) (such as polymorph stabilisation) related to this new conformation. (warwick.ac.uk)
- Background: Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. (ebscohost.com)
- abstract = "This study reports on the preparation of riboflavin-loaded whey protein isolate (WPI) microparticles, using desolvation and then spray drying. (monash.edu)
- abstract = "Recent experimental studies of the denatured state and theoretical analyses of the folding landscape suggest that there are a large multiplicity of low-energy, partially folded conformations near the native state. (elsevier.com)
- Is the Subject Area "Protein structure prediction" applicable to this article? (plos.org)
- Among specific topics are the local structure alphabets, integrative protein fold recognition by alignment and machine learning, hybrid methods for protein structure prediction , and the conformational search for the protein native state. (acronymfinder.com)
- et al explain protein structure prediction , Bayesian networks as static models of regulatory pathways, metabolic control theory, dynamic modeling of biological pathways, and gene silencing. (acronymfinder.com)
- This work describes the successes and limitations of various computational methods for protein structure prediction and their assessment, including template-based approaches, structure alignment and indexing, protein features prediction, and de novo methods. (acronymfinder.com)
- To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. (acronymfinder.com)
- Thus the foundations are set for a novel encoding based on L-systems for evolutionary approaches to both the Protein Structure Prediction and Inverse Folding Problems. (springer.com)
- Khimasia, M., Coveney, P.: Protein structure prediction as a hard optimization problem: The genetic algorithm approach. (springer.com)
- As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined. (ebscohost.com)
- This new in silico method relies on the prediction of hidden conformations of the proteins of interest, which is the subject of a scientific paper to be published in the journal Bioinformatics, and is now available online at this link . (cgen.com)
- This is accomplished through in silico prediction based on structures of other proteins that are remotely related to the target proteins of interest. (cgen.com)
- Algorithms, enabling the appropriate weighting of the structural information extracted from the various remote homologous proteins, are a key component of the new method, resulting in the prediction of previously unknown conformations for the target protein. (cgen.com)
- Protein residue-residue contact prediction is important for protein model generation and model evaluation. (biomedcentral.com)
- Here we develop a conformation ensemble approach to improve residue-residue contact prediction. (biomedcentral.com)
- Even after many years of intense attention and development, de novo protein structure prediction remains a difficult and open problem. (biomedcentral.com)
- This paper presents an efficient and novel computational protein prediction methodology called kineto-static compliance method. (asme.org)
- The results show that torques in each joint are minimized to values very close to zero, which demonstrates the method's effectiveness for protein conformation prediction. (asme.org)
- These results suggest that, to fold efficiently and retain robustness to changes in amino acid sequence, proteins may have evolved a native structure situated within a broad basin of low-energy conformations, a feature which could facilitate the prediction of protein structure at low resolution. (elsevier.com)
- The Chou-Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman. (wikipedia.org)
- List of protein structure prediction software Chou PY, Fasman GD (1974). (wikipedia.org)
- Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence-that is, the prediction of its folding and its secondary and tertiary structure from its primary structure. (wikipedia.org)
- Structure prediction is fundamentally different from the inverse problem of protein design. (wikipedia.org)
- Every two years, the performance of current methods is assessed in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). (wikipedia.org)
- A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. (wikipedia.org)
- Although it was once thought that globular protein molecules unfold completely in the interface, it has now been established that many proteins can be recovered from films in the native state. (britannica.com)
- This work constitutes a first step into assessing not only the generality but also the significance of specific water binding in globular proteins. (pnas.org)
- Dill, K.: Theory for the folding and stability of globular proteins. (springer.com)
- It is concluded that the proteins of these membranes are "globular" and that they have considerable helical content. (rupress.org)
- Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein assemblies can be preserved for milliseconds after electrospray ionization. (pubmedcentralcanada.ca)
- In contrast, smaller globular proteins appear to adopt a multitude of gas-phase conformations depending on the condition of the electrospray process and the amount of time that elapses before detection. (pubmedcentralcanada.ca)
- Although this conformational ensemble likely extends beyond that present in solution, the gas-phase conformations of globular proteins offer a window into the nonnative and solvent-free conformational landscape 5 including intermediates along the folding pathway and trapped misfolded species. (pubmedcentralcanada.ca)
- Furthermore, several recent experimental studies suggests that the solution-phase conformers of even small globular proteins can be largely preserved for 30-60 milliseconds following ESI 6 - 10 . (pubmedcentralcanada.ca)
- Thus, sensitive analytical tools are needed for the rapid characterization of conformations of both small globular proteins and large macromolecular complexes in the gas-phase. (pubmedcentralcanada.ca)
- Comparative Analysis of Protein Three-Dimensional Structures and an Approach to the Inverse Folding Problem (T. Blundell). (wiley.com)
- There are currently at least forty-six unique protein kinase crystal structures, twenty-four of which are available in an active state. (nih.gov)
- Here we examine these structures using a structural bioinformatics approach to understand how the conformation of the activation segment controls kinase activity. (nih.gov)
- We examine how the polypeptide chain in protein crystal structures exploits the multivalent hydrogen-bonding potential of bound water molecules. (pnas.org)
- The structure revealed that the 101F and motavizumab epitopes are present in the postfusion state and that their conformations are similar to those observed in the antibody-bound peptide structures. (rcsb.org)
- In this study, two new crystal forms and protein structures of CheY are reported. (iucr.org)
- Secondary structure protein refers to regular repeative sub-structures on the protein backbone. (ebscohost.com)
- Using an alignment of fragment strings for comparing protein structures. (ebscohost.com)
- Motivation: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. (ebscohost.com)
- Physical contacts between proteins have been revealed using experimental approaches that have solved the structures of protein complexes at atomic resolution. (ebscohost.com)
- Background: The total number of known three-dimensional protein structures is rapidly increasing. (ebscohost.com)
- Background Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. (ebscohost.com)
- CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures. (ebscohost.com)
- Crystal structures of the MalFGK 2 -MalE-maltose complex in a so-called "pretranslocation" ("pre-T") state with a partially closed conformation suggest that the formation of this MalE-stabilized intermediate state is a key step leading to the outward-facing catalytic state. (rsc.org)
- Protein structures range in size from tens to several thousand amino acids. (bioscience.ws)
- The alternative structures of the same protein are referred to as different conformational isomers , or simply, conformations, and transitions between them are called conformational changes . (bioscience.ws)
- In addition, the computational methods are generally biased toward lowest energy structures by design and miss these high energy but functionally important conformations. (caltech.edu)
- The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. (dtu.dk)
- SAs approximate conformations of protein backbones and code the local structures of proteins as one-dimensional sequences. (inserm.fr)
- Applying PB-based approaches to biological systems such as the DARC protein, the human αIIb β3 integrin and the KISSR1 protein highlighted the major interest of PBs in understanding local deformations of large protein structures. (inserm.fr)
- Even when there are a series of related crystal structures in differing conformational states, this still does not give the complete picture of all the available protein conformations or indeed any information on the protein energy landscape, so the energy barriers and population states of the observed conformations remain unknown. (cresset-group.com)
- Figure 1: Crystal structures 1sw2 (top right) and 1sw5 (top left) modeled in Flare™ showing the protein movement observed upon ligand binding for the osmoprotection protein ProX . (cresset-group.com)
- Molecular dynamics calculations help to map the energy landscape by solvating the protein with explicit water molecules then adding energy into the system to allow it to move, generating an ensemble of protein structures. (cresset-group.com)
- During this process snapshots of the protein are taken at predefined time steps, calculating a series of protein structures which are likely to be representative of the biologically relevant protein conformations. (cresset-group.com)
- Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations. (semanticscholar.org)
- The unusual BII phosphate conformation detected in B-DNA structures was found sequence dependant and associated to large changes in inter base-pair helical parameters. (jbsdonline.com)
- 0°). We report that high-energy conformations with ϕ ~ 0°, normally expected to occur only as fleeting transition states, are stably trapped in certain highly resolved native protein structures and that an analysis of these residues provides a detailed, experimentally derived map of the bond angle distortions taking place along the transition path. (sciencemag.org)
- Now, state-of-the-art energetics calculations ( 5 ) and the distributions of ϕ,ψ angles seen in high-resolution protein structures ( 6 , 7 ) recapitulate the main features of the original ϕ,ψ plots remarkably well. (sciencemag.org)
- Electron spin relaxation data from five ferric proteins are analyzed in terms of the fractal model of protein structures. (elsevier.com)
- The results lead to a characterization of protein structures by a single parameter, the fractal dimension, d. (elsevier.com)
- To test this idea, 12 ensembles of 500 to 1,000 low- energy structures for 10 small proteins were analyzed by calculating the rms deviation of the Cα coordinates between each conformation and every other conformation in the ensemble. (elsevier.com)
- Shortle, DR , Simons, KT & Baker, D 1998, ' Clustering of low-energy conformations near the native structures of small proteins ', Proceedings of the National Academy of Sciences of the United States of America , vol. 95, no. 19, pp. 11158-11162. (elsevier.com)
- The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. (wikipedia.org)
- The original Chou-Fasman parameters were derived from a very small and non-representative sample of protein structures due to the small number of such structures that were known at the time of their original work. (wikipedia.org)
- The secondary structures are tightly packed in the protein core in a hydrophobic environment. (wikipedia.org)
- Other α helices buried in the protein core or in cellular membranes have a higher and more regular distribution of hydrophobic amino acids, and are highly predictive of such structures. (wikipedia.org)
- These vesicles are complex structures made of proteins encoded by at least 14 genes. (wikipedia.org)
- After two German chemists, Emil Fischer and Franz Hofmeister, independently stated in 1902 that proteins are essentially polypeptides consisting of many amino acids , an attempt was made to classify proteins according to their chemical and physical properties, because the biological function of proteins had not yet been established. (britannica.com)
- Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. (ebscohost.com)
- Proteins are polymers - specifically polypeptides - formed from sequences of amino acids , the monomers of the polymer. (bioscience.ws)
- courtesies of the view Conformation in Fibrous Proteins and Related Synthetic Polypeptides While the racist closed system Frank Cross picks that the copying non-profit g changed sought by vulnerable seasons in 1965, fast CIMOSA( Morris 2000) have that it woods from the terms and the global confirmation of Vorsorgeprinzip, which can be saved as the description or test sense. (fararooy.com)
- Molecular chaperones assist protein folding and also facilitate degradation of misfolded polypeptides by the ubiquitin-proteasome system. (dspacedirect.org)
- The Laboratory of Protein Conformation and Dynamics integrates complementary biophysical and biochemical techniques to understand the molecular mechanisms of amyloid formation. (nih.gov)
- My research is focused on discovering the macromolecular structure and dynamics of proteins-defining conformational states essential for function and understanding transitions between these states. (ucsf.edu)
- The relationship between functional conformation changes and thermal dynamics of proteins is investigated with the help of the torsional network model (TNM), an elastic network model in torsion angle space that we recently introduced. (csic.es)
- We interpret these features as the result of natural selection favoring the intrinsic protein dynamics consistent with functional conformation changes. (csic.es)
- This deep relationship between the thermal dynamics of a protein, represented by its normal modes, and its functional dynamics can reconcile in a unique framework the two models of conformation changes, conformational selection and induced fit. (csic.es)
- The paradigm "structure drives function" had been active for many years until recent evidence suggested that the complex functions of proteins could not be fully explained by a single structure and dynamics played a very important role in deciphering their functions. (iastate.edu)
- This representation has the advantage of representing the dynamics using only a few conformational states, thereby minimizing the potential of over-fitting, while capturing the dynamics of the protein that a single average structure misses. (iastate.edu)
- Understanding protein structure and dynamics is essential for understanding their function. (biomedcentral.com)
- Understanding the connection between protein structure, dynamics and function can contribute substantially to our understanding of cellular processes involving proteins. (biomedcentral.com)
- The question of how the structure and dynamics of proteins relate to their function has challenged scientists for several decades but still remains open. (biomedcentral.com)
- These energy wells are then sampled locally using a finer grid in conformational space to find a locally minimized conformation in each energy well, which can be further relaxed using molecular dynamics (MD) simulations. (caltech.edu)
- Molecular dynamics can be useful for assessing the energetic stability of proteins and identifying available conformations and, therefore, analyzing available binding pockets. (cresset-group.com)
- In order to get the most insight from molecular dynamics it's important to have background understanding of the system of interest and of protein movements in general. (cresset-group.com)
- This is when molecular dynamics can help fill in the missing pieces of the conformational puzzle and protein energy landscape. (cresset-group.com)
- Assessing protein stability: How can molecular dynamics help? (cresset-group.com)
- Analysis of these conformations from a molecular dynamics calculation can enable the assessment of protein movements and the identification of different lower energy conformational states for the system. (cresset-group.com)
- The current fashion for using pure molecular dynamics calculations is to run multiple simulations to generate a collection of energy landscapes for exploring the available conformations. (cresset-group.com)
- This dissertation focuses on the folding dynamics of a bacterial membrane protein, Outer Membrane Protein A (OmpA), using fluorescence and Ultraviolet resonance Raman spectroscopy. (escholarship.org)
- Taking a closer look at these intermediate regions will ultimately help us to fully understand the function and dynamics of PDZK1 as well that of other scaffolding proteins," notes Nelly Hajizadeh, one of the first authors of the study. (cssb-hamburg.de)
- In recent years, biopharmaceutical characterization requires deeper understanding of the conformational structure of biotherapeutic proteins, and how they are affected for example by pH, temperatures or other stress. (bruker.com)
- The Zetasizer Nano is a protein characterization tool. (technologynetworks.com)
- Telling, Glenn C. Characterization of Conformation-dependent Prion Protein Epitopes. (creighton.edu)
- It has been found that the affinity of peptide fragments of the human Pin1 WW domain for Cu(II) ions depends on its conformation. (springer.com)
- Although E2 proteins contact the two half-sites ACCG/CGGT and not the N 4 spacer, the affinity predominantly depends on the spacer base composition: as examples, a sequence containing the ACGT spacer is well-recognized by the bovine PV-E2 protein but makes low affinity target for human PV-E2, whereas the inverse is found for the AAAC spacer. (jbsdonline.com)
- We find that different mutations and ligands stabilize different conformations. (pnas.org)
- The proteolipid protein gene products DM-20 and PLP are adhesive intrinsic membrane proteins that make up ≥50% of the protein in myelin and serve to stabilize compact myelin sheaths at the extracellular surfaces of apposed membrane lamellae. (jneurosci.org)
- In particular, since the active-state conformations are higher in energy (less stable) than inactive-state conformations, they are difficult to stabilize. (caltech.edu)
- We observed that in the presence of Prp8, the population of the high FRET conformation of U2-U6 that is thought to be the active conformation increased indicating that one of the functions of Prp8 would be to stabilize the active site conformation of the spliceosome. (wayne.edu)
- In the absence of the histidine tags, the resulting Cx and Qx proteins, which exhibit lower helicities of 37 and 45%, respectively, stabilize soluble protein·AuNP composites with AuNPs 4.5 nm in diameter for several days without aggregating. (elsevier.com)
Changes in proteins1
- Numerous studies have demonstrated that protein-ligand complexes and even large functional macromolecular protein assemblies can retain their non-covalent bonding in the gas-phase ( 1 - 4 and references therein). (pubmedcentralcanada.ca)
- In the presence of pentameric coiled-coil proteins C and Q, which contain histidine tags and have helicities of 54 and 65%, respectively, templation of AuNP results in precipitation of the protein·AuNP composites with AuNPs 6.5 nm in diameter, creating macromolecular assemblies on the micrometer scale. (elsevier.com)
- By manipulating protein structure via external triggers, such as TFE, we obtain control over the macromolecular conformation and overall physicochemical properties. (elsevier.com)
- In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. (rice.edu)
- Since this dynamic property of proteins is important for their function in healthy and diseased states, a broad view of a protein's conformational space is crucial in many aspects of drug discovery. (cgen.com)
- We present a hierarchical clustering and algebraic topology based method that detects regions of interest in protein conformational space. (biomedcentral.com)
- Characterizing the conformational space of proteins is crucial for understanding the way they perform their function. (biomedcentral.com)
- In this work we use both algebraic topology and dimensionality reduction methods to explore and characterize the conformational space of proteins. (biomedcentral.com)
- In previous work [ 18 , 19 ] we used persistent homology to explore the conformational space of proteins and detect regions of interest that may correspond to local minima, which are hard to detect experimentally due to the relatively short time the protein spends in them. (biomedcentral.com)
- However, various GPCRs differ sufficiently in the tilts of the TMHs that this method need not predict the optimum conformation starting from any other template. (pnas.org)
- This suggests that inverse agonists are not merely "the opposite of agonists," but instead may serve as useful tools to investigate ligand-specific conformations of GPCRs. (sciencemag.org)
- The activation of GPCRs is central to their function, requiring multiple conformations of the GPCRs in their activation landscape. (caltech.edu)
- Many different computational approaches for protein structure comparison apply the secondary structure elements. (ebscohost.com)
- The accurate assignment of the secondary structure of proteins from protein atom coordinates underlies the analysis of protein structure and function. (ebscohost.com)
- We elucidate a strong electrostatic interaction between BSA and the SPIONs, although the secondary structure of the protein is not affected. (icmab.es)
- We demonstrate the fabrication of protein·gold nanoparticle (AuNP) nanocomposites in situ, leading to distinct assemblies dependent upon protein secondary structure. (elsevier.com)
- How good are predictions of protein secondary structure? (wikipedia.org)
- The protein structure can be considered as a sequence of secondary structure elements, such as α helices and β sheets, which together constitute the overall three-dimensional configuration of the protein chain. (wikipedia.org)
- The α helix is the most abundant type of secondary structure in proteins. (wikipedia.org)
- The fundamental event in prion diseases seems to be a conformational change in cellular prion protein (PrP C ) whereby it is converted into the pathologic isoform PrP Sc . (sciencemag.org)
- After several groups determined the genetic sequence of that protein, Prusiner realized that it was a fragment of a normal protein (prion protein or PrP), the function of which is still uncertain, which is found in healthy nerve cells. (encyclopedia.com)
- Significance: Our studies address how denatured conformational epitopes remain functional, provide insights into normal and disease-related prion protein, and expand epitope tagging options. (elsevier.com)
- We also tested for the presence of translocation signals that enable insertion of these proteins into rough endoplasmic reticulum (RER) membranes. (jneurosci.org)
- The general relations between protein conformation and the optical activity of peptide chromophores are outlined and applied to the analysis of the optical rotatory dispersion and circular dichroism of the plasma membranes of human erythrocytes and Ehrlich ascites carcinoma cells. (rupress.org)
- It should then be expected that T-cell recognition of protein antigens in vitro will be independent of protein conformation. (biochemj.org)
- Our results demonstrate that the conformation of antigens in VLPs is of critical importance for optimal stimulation of protective as well as durable immune responses. (umassmed.edu)
- The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. (ebscohost.com)
- In pioneering work, Ramachandran and co-workers ( 4 ) introduced the ϕ and ψ torsion angles to describe protein backbone conformations (see Fig. 1 , A and B), defining some conformations as "allowed" and others as "disallowed" due to collisions between atoms. (sciencemag.org)
- This unanticipated information lays to rest any uncertainty about whether such transitions are possible and how they occur, and in doing so lays a firm foundation for theoretical studies to better understand the transitions between basins that have been little studied but are integrally involved in protein folding and function. (sciencemag.org)
- PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). (ucdenver.edu)
- These findings suggest that the adsorption of acidic proteins to Ca2+-rich crystal faces of biominerals is governed by electrostatics and is facilitated by conformational flexibility of the polypeptide chain. (sparrho.com)
- This application note illustrates that the SYNAPT G2 HDMS System, which provides an orthogonal separation technique with ion mobility mass spectrometry, can clearly separate different conformations of equine cytochrome c within minutes, matching that of published work. (waters.com)
- Biomolecules introduced to a mass spectrometer by electrospray ionization (ESI) exhibit a number of different conformations depending on charge states, eluent pH, and size. (waters.com)
- Understanding the higher order structure of biomolecules is important for the biopharmaceutical industry because different conformations may affect biological activity. (waters.com)
- It is often time-consuming to separate or identify different conformations. (waters.com)
- Different conformations of isobaric biomolecules cannot be separated by mass spectrometric resolution alone. (waters.com)
- This work describes how different conformations of equine cytochrome c can be clearly separated within minutes. (waters.com)
- By selecting a single charge state of biomolecule ions, ions with different conformations can be separated. (waters.com)
- In contrast, the channel had a low conductance (~50 pS) with no detectable ATP permeability when activated by voltage in the absence of K + . The two channel states were associated with different reactivities of the terminal cysteine of Panx1 to thiol reagents, suggesting different conformations. (sciencemag.org)
- Proteins are dynamic entities and can adopt a series of different conformations. (cgen.com)
- Additionally, UVRR was used to monitor changes in trp environmental hydrophobicity, hydrogen bonding, and dihedral torsion angle in different conformations of OmpA. (escholarship.org)
- The various models capture slightly different conformations and contain complementary information which can be pooled together to capture recurrent, and therefore more likely, residue-residue contacts. (biomedcentral.com)
- The PDK1-substrate interaction model describes, at a molecular level, the mechanism used by PDK1 to sense the conformation of its substrates. (nih.gov)
- Fluorinated C3-benzamido substituents induced a shift in the side-chain conformation of R144 to allow for an entropically favored electrostatic interaction between its guanidine group and the 2- O -sulfate of the ligand. (rsc.org)
- Together, RCC1's shape and importin a3's ability to change its conformation drive this selective interaction. (jefferson.edu)
- This specific interaction further rationalizes the kinetics of the phototransduction cascade and provides a general hypothesis to explain the mechanism of interaction of RGS proteins with other G proteins. (caltech.edu)
- Proteins, when forming an interfacial film, are present as a monomolecular layer-i.e., a layer one molecule in height. (britannica.com)
- The application of lateral pressure on a protein film causes it to increase in thickness and finally to form a layer with a height corresponding to the diameter of the native protein molecule. (britannica.com)
- Docking simulations illustrated how the TnC molecule undergoes significant conformational transition on complex formation, a phenomenon that can be modeled only when protein flexibility is properly accounted for. (mdpi.com)
- The importin a3 molecule, or "car," is one of a family of importin proteins that help ferry other proteins across the nuclear membrane where they can alter the course of DNA transcription. (jefferson.edu)
- In our SMD project we are studying the extraction of a non-covalently bound small molecule from a protein, by a user-specified tug, through any of several likely exit routes, and this is followed by batch calculations of the energetics experienced by a molecule moving naturally along such a path, i.e., by diffusion, rather than as the result of an artificial tug. (umn.edu)
- Protein structure is the three-dimensional arrangement of atoms in an amino acid -chain molecule . (bioscience.ws)
- In order to test whether or not Prp8 stabilizes the active-site conformation, we carried out single-molecule fluorescence resonance energy transfer (smFRET) experiments with catalytically important snRNAs U2 and U6 and Prp8. (wayne.edu)
- The data further suggests that PDK1 interacts with its substrates when they are in a particular conformation (inactive). (nih.gov)
- We find that the SuperBiHelix conformational ensemble includes the higher energy conformations associated with the active protein in addition to those associated with the more stable inactive protein. (pnas.org)
- Several novel drugs take advantage of this dynamic nature by binding to a disease-associated protein in its inactive conformation and blocking it from adopting its active form. (cgen.com)
- To address this problem, we have developed a computationally efficient ActiveGEnSeMBLE method that systematically predicts multiple conformations that are likely in the GPCR activation landscape, including multiple active- and inactive-state conformations. (caltech.edu)
- Paul Muchowski tied chaperones into the growing recognition that large protein aggregates may be a lesser culprit in neurodegenerative diseases than early assemblies, however elusive they may be in vivo. (alzforum.org)
- He started out by noting that today's version of the amyloid hypothesis-protein misfolding leads to amyloids, and somewhere along the process the cell dies-applies to many neurodegenerative diseases. (alzforum.org)
- The term was coined in 1982 by Stanley B. Prusiner, a neurologist at the University of California at San Francisco , who proposed that a new type of pathogen consisting solely of protein is responsible for a school of deadly neurodegenerative diseases called Transmissible Spongiform Encephalopathies (TSEs). (encyclopedia.com)
- We earlier reported the BiHelix method for efficiently sampling the (12) 7 = 35 million conformations resulting from 30° rotations about the axis (η) of all seven transmembrane helices (TMHs), showing that the experimental structure is reliably selected as the best conformation from this ensemble. (pnas.org)
- We find that the topologies of DM-20 and PLP are identical, with both proteins possessing four transmembrane domains and N and C termini exposed to the cytoplasm. (jneurosci.org)
- We find that the transmembrane topologies of DM-20 and PLP are identical, with both proteins possessing four transmembrane domains and both N and C termini located within the cytoplasmic compartment. (jneurosci.org)
- ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (~ 13 trillion transmembrane domain conformations) and identifies multiple potential active-state energy wells, using the TM3-TM6 intracellular distance as a surrogate activation coordinate. (caltech.edu)
- These studies resulted in increased stability relative to the full-length protein and suggest the absence of the soluble domain may destabilize the unfolded transmembrane domain. (escholarship.org)
- Alternative in silico approaches assess protein motions through the protein residue network or dynamical correlations from MD simulations. (inserm.fr)
- When operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. (biomedcentral.com)
- Given the importance and applicability of protein contacts, considerable effort has been put forth to develop methods which can predict protein residue-residue contacts. (biomedcentral.com)
- C.d. and fluorescence studies showed that rupture of this disulphide bond changed the protein conformation, which was reflected in partial loss of helical structure and in a greater exposure to the solvent of at least one tryptophan residue. (elsevier.com)
Stability of proteins1
- Conformation analysis using HYDFIT (which globally combines sedimentation and viscosity data), "Conformation Zoning" and Wales-van Holde approaches showed a high degree of flexibility - at least as great as the unconjugated polysaccharides, and very different from the tetanus toxoid (TT) protein used for the conjugation. (hud.ac.uk)
- The quantification of protein flexibility is based on various methods such as Root Mean Square Fluctuations (RMSF) that rely on multiple MD snapshots or Normal Mode Analysis (NMA) that rely on a single structure and focus on quantifying large movements. (inserm.fr)
- Our results confirm the hypothesis that the spacer flexibility determines the affinities for PV-E2 proteins and, moreover, precise the nature of this flexibility: a dramatic intrinsic instability of the non-contacted dinucleotide backbones. (jbsdonline.com)
- The SAXS experiments revealed however, that PDZK1 has a relatively defined L-shaped conformation with only moderate flexibility. (cssb-hamburg.de)
- Glycine takes on a special position, as it has the smallest side chain, only one Hydrogen atom, and therefore can increase the local flexibility in the protein structure. (wikipedia.org)
- Although proteins are essential for splicing, they may not be directly involved in catalysis. (wayne.edu)
- Therefore, it is hypothesized that Prp8 may catalyze splicing either by directly participating in catalysis or by stabilizing the conformation of the catalytically active spliceosome. (wayne.edu)
- In an example application we modeled the process of complex assembly between two proteins: Troponin C (TnC) and the N-terminal helix of Troponin I (TnI N-helix), which occurs in vivo during muscle contraction. (mdpi.com)
- In this paper, we have used PROTOFOLD to predict the final conformation of a small peptide chain segment, an alpha helix, and the Triponin protein chains from a denatured configuration. (asme.org)
- This way our procedure opens up a new possibility for studying mechanisms of protein complex assembly, which may be a supporting tool for rational drug design. (mdpi.com)
- We characterized recombinant Env proteins and virus particles produced in mammalian cells that lack N-acetylglucosaminyltransferase I (GnTI), an enzyme necessary for the conversion of oligomannose N-glycans to complex N-glycans. (iavi.org)
- The spliceosome is a large, RNA-protein complex that catalyzes pre-mRNA splicing during mRNA maturation. (wayne.edu)
- Complex stability and conformation of bound substrate protein. (docphin.com)
- Circular dichroism and fluorescence studies of the complex between DnaK and a thermally unstable mutant of staphylococcal nuclease indicate that the bound substrate protein is significantly unfolded. (docphin.com)
- Only by integrating a range of techniques and collaborating with colleagues, will we be able to fully understand complex proteins like PDZK1," states Löw. (cssb-hamburg.de)
- However, for a folded protein or a protein complex the picture may be more complex, since many bonds allow for substantial freedom and may produce an ensemble of conformations that exchange slow and can get trapped. (grantome.com)