A computer simulation developed to study the motion of molecules over a period of time.
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
The study of systems which respond disproportionately (nonlinearly) to initial conditions or perturbing stimuli. Nonlinear systems may exhibit "chaos" which is classically characterized as sensitive dependence on initial conditions. Chaotic systems, while distinguished from more ordered periodic systems, are not random. When their behavior over time is appropriately displayed (in "phase space"), constraints are evident which are described by "strange attractors". Phase space representations of chaotic systems, or strange attractors, usually reveal fractal (FRACTALS) self-similarity across time scales. Natural, including biological, systems often display nonlinear dynamics and chaos.
Computer-based representation of physical systems and phenomena such as chemical processes.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The 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).
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)
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)
The continuous remodeling of MITOCHONDRIA shape by fission and fusion in response to physiological conditions.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
Elements of limited time intervals, contributing to particular results or situations.
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.
Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The characteristic three-dimensional shape of a molecule.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
The 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.
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.
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.
Slender, cylindrical filaments found in the cytoskeleton of plant and animal cells. They are composed of the protein TUBULIN and are influenced by TUBULIN MODULATORS.
The rate dynamics in chemical or physical systems.
Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.
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.
The motion of fluids, especially noncompressible liquids, under the influence of internal and external forces.
Filamentous proteins that are the main constituent of the thin filaments of muscle fibers. The filaments (known also as filamentous or F-actin) can be dissociated into their globular subunits; each subunit is composed of a single polypeptide 375 amino acids long. This is known as globular or G-actin. In conjunction with MYOSINS, actin is responsible for the contraction and relaxation of muscle.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
The tendency of a gas or solute to pass from a point of higher pressure or concentration to a point of lower pressure or concentration and to distribute itself throughout the available space. Diffusion, especially FACILITATED DIFFUSION, is a major mechanism of BIOLOGICAL TRANSPORT.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The physical characteristics and processes of biological systems.
A method used to study the lateral movement of MEMBRANE PROTEINS and LIPIDS. A small area of a cell membrane is bleached by laser light and the amount of time necessary for unbleached fluorescent marker-tagged proteins to diffuse back into the bleached site is a measurement of the cell membrane's fluidity. The diffusion coefficient of a protein or lipid in the membrane can be calculated from the data. (From Segen, Current Med Talk, 1995).
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.
The accumulation of an electric charge on a object
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.
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)
Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye.
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
Theoretical representations that simulate the behavior or activity of the neurological system, processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
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)
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.
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.
Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The network of filaments, tubules, and interconnecting filamentous bridges which give shape, structure, and organization to the cytoplasm.
Number of individuals in a population relative to space.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Recording serial images of a process at regular intervals spaced out over a longer period of time than the time in which the recordings will be played back.
Fibers composed of MICROFILAMENT PROTEINS, which are predominately ACTIN. They are the smallest of the cytoskeletal filaments.
Divisions of the year according to some regularly recurrent phenomena usually astronomical or climatic. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The act, process, or result of passing from one place or position to another. It differs from LOCOMOTION in that locomotion is restricted to the passing of the whole body from one place to another, while movement encompasses both locomotion but also a change of the position of the whole body or any of its parts. Movement may be used with reference to humans, vertebrate and invertebrate animals, and microorganisms. Differentiate also from MOTOR ACTIVITY, movement associated with behavior.
The properties, processes, and behavior of biological systems under the action of mechanical forces.
The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)
A microtubule subunit protein found in large quantities in mammalian brain. It has also been isolated from SPERM FLAGELLUM; CILIA; and other sources. Structurally, the protein is a dimer with a molecular weight of approximately 120,000 and a sedimentation coefficient of 5.8S. It binds to COLCHICINE; VINCRISTINE; and VINBLASTINE.
The thermodynamic interaction between a substance and WATER.
Proteins which are involved in the phenomenon of light emission in living systems. Included are the "enzymatic" and "non-enzymatic" types of system with or without the presence of oxygen or co-factors.
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)
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The relationships of groups of organisms as reflected by their genetic makeup.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.
A dynamic actin-rich extension of the surface of an animal cell used for locomotion or prehension of food.
A light microscopic technique in which only a small spot is illuminated and observed at a time. An image is constructed through point-by-point scanning of the field in this manner. Light sources may be conventional or laser, and fluorescence or transmitted observations are possible.
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.
A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Microscopy in which television cameras are used to brighten magnified images that are otherwise too dark to be seen with the naked eye. It is used frequently in TELEPATHOLOGY.
Monomeric subunits of primarily globular ACTIN and found in the cytoplasmic matrix of almost all cells. They are often associated with microtubules and may play a role in cytoskeletal function and/or mediate movement of the cell or the organelles within the cell.
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.
The scattering of NEUTRONS by matter, especially crystals, with accompanying variation in intensity due to interference effects. It is useful in CRYSTALLOGRAPHY and POWDER DIFFRACTION.
The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.
Measurement of the intensity and quality of fluorescence.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
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.
A synthetic phospholipid used in liposomes and lipid bilayers for the study of biological membranes.
The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
Motion of an object in which either one or more points on a line are fixed. It is also the motion of a particle about a fixed point. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
High molecular weight proteins found in the MICROTUBULES of the cytoskeletal system. Under certain conditions they are required for TUBULIN assembly into the microtubules and stabilize the assembled microtubules.
A meshlike structure composed of interconnecting nerve cells that are separated at the synaptic junction or joined to one another by cytoplasmic processes. In invertebrates, for example, the nerve net allows nerve impulses to spread over a wide area of the net because synapses can pass information in any direction.
A family of low MOLECULAR WEIGHT actin-binding proteins found throughout eukaryotes. They remodel the actin CYTOSKELETON by severing ACTIN FILAMENTS and increasing the rate of monomer dissociation.
The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)
Theoretical construct used in applied mathematics to analyze certain situations in which there is an interplay between parties that may have similar, opposed, or mixed interests. In a typical game, decision-making "players," who each have their own goals, try to gain advantage over the other parties by anticipating each other's decisions; the game is finally resolved as a consequence of the players' decisions.
Patterns (real or mathematical) which look similar at different scales, for example the network of airways in the lung which shows similar branching patterns at progressively higher magnifications. Natural fractals are self-similar across a finite range of scales while mathematical fractals are the same across an infinite range. Many natural, including biological, structures are fractal (or fractal-like). Fractals are related to "chaos" (see NONLINEAR DYNAMICS) in that chaotic processes can produce fractal structures in nature, and appropriate representations of chaotic processes usually reveal self-similarity over time.
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.
The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM of a cell.
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.
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.
Theoretical representations that simulate the behavior or activity of the cardiovascular system, processes, or phenomena; includes the use of mathematical equations, computers and other electronic equipment.
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).
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.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
A 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.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
The longterm manifestations of WEATHER. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.
Resistance and recovery from distortion of shape.
Woody, usually tall, perennial higher plants (Angiosperms, Gymnosperms, and some Pterophyta) having usually a main stem and numerous branches.
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)
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.
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.
Abrupt changes in the membrane potential that sweep along the CELL MEMBRANE of excitable cells in response to excitation stimuli.
The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
A purely physical condition which exists within any material because of strain or deformation by external forces or by non-uniform thermal expansion; expressed quantitatively in units of force per unit area.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
Sequential operating programs and data which instruct the functioning of a digital computer.
Proteins found in any species of bacterium.
The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
A mechanism of communication with a physiological system for homeostasis, adaptation, etc. Physiological feedback is mediated through extensive feedback mechanisms that use physiological cues as feedback loop signals to control other systems.
The motion of phospholipid molecules within the lipid bilayer, dependent on the classes of phospholipids present, their fatty acid composition and degree of unsaturation of the acyl chains, the cholesterol concentration, and temperature.
A microtubule structure that forms during CELL DIVISION. It consists of two SPINDLE POLES, and sets of MICROTUBULES that may include the astral microtubules, the polar microtubules, and the kinetochore microtubules.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
The variety of all native living organisms and their various forms and interrelationships.
Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.
The relationship between an invertebrate and another organism (the host), one of which lives at the expense of the other. Traditionally excluded from definition of parasites are pathogenic BACTERIA; FUNGI; VIRUSES; and PLANTS; though they may live parasitically.
Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The sequence of transfers of matter and energy from organism to organism in the form of FOOD. Food chains intertwine locally into a food web because most organisms consume more than one type of animal or plant. PLANTS, which convert SOLAR ENERGY to food by PHOTOSYNTHESIS, are the primary food source. In a predator chain, a plant-eating animal is eaten by a larger animal. In a parasite chain, a smaller organism consumes part of a larger host and may itself be parasitized by smaller organisms. In a saprophytic chain, microorganisms live on dead organic matter.
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.
Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.
Genotypic differences observed among individuals in a population.
Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.
Synthetic phospholipid used in liposomes and lipid bilayers to study biological membranes. It is also a major constituent of PULMONARY SURFACTANTS.
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.
Polymers synthesized by living organisms. They play a role in the formation of macromolecular structures and are synthesized via the covalent linkage of biological molecules, especially AMINO ACIDS; NUCLEOTIDES; and CARBOHYDRATES.
A type of CELL NUCLEUS division by means of which the two daughter nuclei normally receive identical complements of the number of CHROMOSOMES of the somatic cells of the species.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
Conformational transitions of the shape of a protein to various unfolded states.
Established cell cultures that have the potential to propagate indefinitely.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
The study of the deformation and flow of matter, usually liquids or fluids, and of the plastic flow of solids. The concept covers consistency, dilatancy, liquefaction, resistance to flow, shearing, thixotrophy, and VISCOSITY.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
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.
Molecules which contain an atom or a group of atoms exhibiting an unpaired electron spin that can be detected by electron spin resonance spectroscopy and can be bonded to another molecule. (McGraw-Hill Dictionary of Chemical and Technical Terms, 4th ed)
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
The resistance that a gaseous or liquid system offers to flow when it is subjected to shear stress. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Reduced (protonated) form of THIAZOLES. They can be oxidized to THIAZOLIDINEDIONES.
A technique of inputting two-dimensional images into a computer and then enhancing or analyzing the imagery into a form that is more useful to the human observer.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Characteristics or attributes of the outer boundaries of objects, including molecules.
Chemical reaction in which monomeric components are combined to form POLYMERS (e.g., POLYMETHYLMETHACRYLATE).
The process by which two molecules of the same chemical composition form a condensation product or polymer.
The measurement of frequency or oscillation changes.
A physical property showing different values in relation to the direction in or along which the measurement is made. The physical property may be with regard to thermal or electric conductivity or light refraction. In crystallography, it describes crystals whose index of refraction varies with the direction of the incident light. It is also called acolotropy and colotropy. The opposite of anisotropy is isotropy wherein the same values characterize the object when measured along axes in all directions.
A change of a substance from one form or state to another.
Investigative technique commonly used during ELECTROENCEPHALOGRAPHY in which a series of bright light flashes or visual patterns are used to elicit brain activity.
That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The property of 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.
The isotopic compound of hydrogen of mass 2 (deuterium) with oxygen. (From Grant & Hackh's Chemical Dictionary, 5th ed) It is used to study mechanisms and rates of chemical or nuclear reactions, as well as biological processes.
Instinctual behavior pattern in which food is obtained by killing and consuming other species.
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.
Signal transduction mechanisms whereby calcium mobilization (from outside the cell or from intracellular storage pools) to the cytoplasm is triggered by external stimuli. Calcium signals are often seen to propagate as waves, oscillations, spikes, sparks, or puffs. The calcium acts as an intracellular messenger by activating calcium-responsive proteins.
Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Light-induced change in a chromophore, resulting in the loss of its absorption of light of a particular wave length. The photon energy causes a conformational change in the photoreceptor proteins affecting PHOTOTRANSDUCTION. This occurs naturally in the retina (ADAPTATION, OCULAR) on long exposure to bright light. Photobleaching presents problems when occurring in PHOTODYNAMIC THERAPY, and in FLUORESCENCE MICROSCOPY. On the other hand, this phenomenon is exploited in the technique, FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING, allowing measurement of the movements of proteins and LIPIDS in the CELL MEMBRANE.
Macromolecular complexes formed from the association of defined protein subunits.
The time from the onset of a stimulus until a response is observed.
The physiological mechanisms that govern the rhythmic occurrence of certain biochemical, physiological, and behavioral phenomena.
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.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.
An anchoring junction of the cell to a non-cellular substrate. It is composed of a specialized area of the plasma membrane where bundles of the ACTIN CYTOSKELETON terminate and attach to the transmembrane linkers, INTEGRINS, which in turn attach through their extracellular domains to EXTRACELLULAR MATRIX PROTEINS.
Proteins that are involved in or cause CELL MOVEMENT such as the rotary structures (flagellar motor) or the structures whose movement is directed along cytoskeletal filaments (MYOSIN; KINESIN; and DYNEIN motor families).
A microtubule-associated mechanical adenosine triphosphatase, that uses the energy of ATP hydrolysis to move organelles along microtubules toward the plus end of the microtubule. The protein is found in squid axoplasm, optic lobes, and in bovine brain. Bovine kinesin is a heterotetramer composed of two heavy (120 kDa) and two light (62 kDa) chains. EC 3.6.1.-.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Orientation of intracellular structures especially with respect to the apical and basolateral domains of the plasma membrane. Polarized cells must direct proteins from the Golgi apparatus to the appropriate domain since tight junctions prevent proteins from diffusing between the two domains.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
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)
A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
The ceasing of existence of a species or taxonomic groups of organisms.
Derivatives of phosphatidic acids in which the phosphoric acid is bound in ester linkage to a choline moiety. Complete hydrolysis yields 1 mole of glycerol, phosphoric acid and choline and 2 moles of fatty acids.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Free-floating minute organisms that are photosynthetic. The term is non-taxonomic and refers to a lifestyle (energy utilization and motility), rather than a particular type of organism. Most, but not all, are unicellular algae. Important groups include DIATOMS; DINOFLAGELLATES; CYANOBACTERIA; CHLOROPHYTA; HAPTOPHYTA; CRYPTOMONADS; and silicoflagellates.
Cofilin 1 is a member of the cofilin family of proteins that is expressed in non-muscle CELLS. It has ACTIN depolymerization activity that is dependent on HYDROGEN-ION CONCENTRATION.
A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.
Condition of having pores or open spaces. This often refers to bones, bone implants, or bone cements, but can refer to the porous state of any solid substance.
A continuing periodic change in displacement with respect to a fixed reference. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
An 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.
Theoretical representations that simulate the behavior or activity of immune system, processes, or phenomena. They include the use of mathematical equations, computers, and other electrical equipment.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.
A 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.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The subfamily of myosin proteins that are commonly found in muscle fibers. Myosin II is also involved a diverse array of cellular functions including cell division, transport within the GOLGI APPARATUS, and maintaining MICROVILLI structure.
The protection, preservation, restoration, and rational use of all resources in the total environment.
A member of the actin depolymerizing factors. Its depolymerizing activity is independent of HYDROGEN-ION CONCENTRATION.
The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)
Water particles that fall from the ATMOSPHERE.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Palmer, Arthur G. (2007). Protein NMR Spectroscopy. Elsevier Academic Press. ISBN 978-0121644918. Bernstein, M.A.; King, K.F.; ... citing CODATA-recommended values) Levitt, M.H. (2008). Spin Dynamics. John Wiley & Sons Ltd. ISBN 978-0470511176. ...
Proteins can be isotopically labeled by cultivating them in a medium containing nitrogen-15 as the only source of nitrogen. In ... doi:10.1351/pac197437010225 M H Levitt (2008). Spin Dynamics. John Wiley & Sons Ltd. ISBN 978-0470511176. Arthur G Palmer (2007 ... 15N NMR is also extremely valuable in protein NMR investigations. Most notably, the introduction of three-dimensional ... Protein NMR Spectroscopy. Elsevier Academic Press. ISBN 978-0121644918. Stone, Nicholas J (2005). "Table of nuclear magnetic ...
Cysteine-rich motor neuron 1 protein is a protein that in humans is encoded by the CRIM1 gene. Motor neurons are among the ... Developmental Dynamics. 219 (4): 582-7. doi:10.1002/1097-0177(2000)9999:9999<::AID-DVDY1072>3.0.CO;2-I. PMID 11084657. v t e. ... Kolle G, Georgas K, Holmes GP, Little MH, Yamada T (Feb 2000). "CRIM1, a novel gene encoding a cysteine-rich repeat protein, is ... Protein Science. 13 (10): 2819-24. doi:10.1110/ps.04682504. PMC 2286551. PMID 15340161. Wilkinson L, Kolle G, Wen D, Piper M, ...
... is a protein that in humans is encoded by the C21orf91 gene. EURL is a structural protein ... Developmental Dynamics. 227 (3): 409-15. doi:10.1002/dvdy.10310. PMID 12815627. S2CID 40129186. "Tissue expression of C21orf91 ... among them is a protein that influences neural development. This protein-coding region helps to code for neural development in ... Scientists are currently working on a hypothesis that the dosage of the EURL protein is directly correlated to neural ...
Gene and Protein Evolution. Genome Dynamics. 3 (3rd ed.). Basel: S. Karger. p. 166. doi:10.1159/000107610. ISBN 978-3-8055-8341 ...
Gene and Protein Evolution. Genome Dynamics. 3. pp. 30-47. doi:10.1159/000107602. ISBN 978-3-8055-8340-4. PMID 18753783. ... It is correct to say that a set of simultaneous mutations that form a complex protein structure is so unlikely as to be ... The needle's base has ten elements in common with the flagellum, but it is missing forty of the proteins that make a flagellum ... In contrast to Behe's claims, many proteins can be deleted or mutated and the flagellum still works, even though sometimes at ...
"tubulin in Protein sequences". EMBL-EBI. Heald R, Nogales E (January 2002). "Microtubule dynamics". Journal of Cell Science. ... as well as the bacterial protein TubZ, the archaeal protein CetZ, and the FtsZ protein family widespread in Bacteria and ... Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member ... Tubulin is characterized by the evolutionarily conserved Tubulin/FtsZ family, GTPase protein domain. This GTPase protein domain ...
Mustard D; Ritchie DW (August 2005). "Docking essential dynamics eigenstructures". Proteins. 60 (2): 269-274. CiteSeerX 10.1. ... In the case of protein docking, the search space consists of all possible orientations of the protein with respect to the ... that will bind well at the active site of the protein. Compared to the all-atom molecular dynamics approaches, these methods ... In this approach, proteins are typically held rigid, and the ligand is allowed to freely explore their conformational space. ...
Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies". Proteins. 77 (4): 760-77. ... structural changes that accompany partial dehydration and protein action". Proteins. 71 (1): 241-249. doi:10.1002/prot.21695. ... doi:10.1093/protein/5.5.399. PMID 1518787. Srinivasan, Bharath (27 September 2020). "Words of advice: teaching enzyme kinetics ... Nagendra, H.G.; Sukumar, N.; Vijayan, M. (1 August 1998). "Role of water in plasticity, stability, and action of proteins: The ...
... possibly by competing with Arp2/3 protein. Alpha catenin exhibits significant protein dynamics. The amino acid sequence of ... It has been reported that the actin binding proteins vinculin and alpha-actinin can bind to alpha-catenin. It has been ... Nagafuchi A, Takeichi M, Tsukita S (May 1991). "The 102 kd cadherin-associated protein: similarity to vinculin and ... Alpha-catenin functions as the primary protein link between cadherins and the actin cytoskeleton. ...
Examples of these models can be found in the Protein Data Bank. Computational techniques like Molecular Dynamics simulations ... 3D encyclopedia of proteins and other molecules. Protein structure prediction Banaszak LJ (2000). Foundations of Structural ... The first tertiary protein structure, that of Myoglobin, was published in 1958 by John Kendrew. During this time, modeling of ... See protein folding. A third approach that structural biologists take to understanding structure is bioinformatics to look for ...
"A consensus view of protein dynamics". PNAS. 104 (3): 796-801. doi:10.1073/pnas.0605534104. PMC 1783393. PMID 17215349. Zhou Y ... Care must be taken if the molecule possesses globally defined dynamics, such as about a hinge or pivot, because these motions ...
He published articles in NMR crystallography, structural biology, protein dynamics, dynamic nuclear polarization (DNP) enhanced ... "Direct observation of hierarchical protein dynamics" (PDF). Science. 348 (6234): 578-81. Bibcode:2015Sci...348..578L. doi: ... "Polarization Transfer over the Water Protein Interface in Solid Proteins". Angew. Chem. 47 (31): 5851-5854. doi:10.1002/anie. ... "Waking proteins up from deep sleep to study their motions". Phys.org. 30 April 2015. Retrieved 1 January 2016. Blaise, Benjamin ...
"Entrez Gene: NOL7 nucleolar protein 7, 27kDa". Andersen JS, Lam YW, Leung AK, et al. (2005). "Nucleolar proteome dynamics". ... Nucleolar protein 7 is a protein that in humans is encoded by the NOL7 gene. GRCh38: Ensembl release 89: ENSG00000225921 - ...
Intrinsically disordered proteins Protein dynamics Perdigão, Nelson. "Dark Proteome Database: Studies on Dark Proteins." Dark ... Dark protein regions are dark due to originating from unusual organisms with no sufficient close relatives in current protein ... Dark proteins are not applicable to the structure-function paradigm the all proteins follow. They are predominately consisted ... and signaling via protein networks. These processes are commonly executed intracellularly, however, dark proteins are over- ...
... a portrait of protein kinase dynamics". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1697 (1-2): 259-69. doi: ... The group has subsequently published a number of papers on the dynamics and mechanism of PKA, or cyclic AMP-dependent protein ... She is known for her research on protein kinases, particularly protein kinase A. She was elected to the Institute of Medicine ... Taylor's research group has focused on the structure and function of protein kinases, particularly protein kinase A, since ...
Her laboratory focuses on work in molecular dynamics simulations of proteins and other biomolecules. Daggett is well known for ... A Comprehensive Database of Protein Dynamics". Structure. 18 (4): 423. doi:10.1016/j.str.2010.01.012. PMC 2892689. PMID ... Doerr, Alison (2010). "A database of dynamics". Nature Methods. 7 (6): 426. doi:10.1038/nmeth0610-426. Van Der Kamp, M. W.; ... large-scale simulations of protein folding, especially unfolding, and native state dynamics through her "dynameomics" project. ...
"Simultaneous determination of protein structure and dynamics". Nature. 433 (7022): 128-32. Bibcode:2005Natur.433..128L. doi: ... He edited computational programs able to predict essential characteristics of protein folding and protein aggregation. In a ... Knowles TP, Vendruscolo M, Dobson CM (June 2014). "The amyloid state and its association with protein misfolding diseases". ... Vendruscolo provided contributions in the field of protein folding, misfolding and aggregation. He introduced the approach of ...
The hydration layer around a protein has been found to have dynamics distinct from the bulk water to a distance of 1 nm. The ... This interaction of the protein surface with the surrounding water is often referred to as protein hydration and is fundamental ... "Mapping hydration dynamics around a protein surface". Proceedings of the National Academy of Sciences. 104 (47): 18461-18466. ... A dehydron is a backbone hydrogen bond in a protein that is incompletely shielded from water attack and has a propensity to ...
Multi-protein assemblies in signaling • Catalysis and regulation. 41: 73-82. doi:10.1016/j.sbi.2016.05.019. PMID 27336183. Dang ... Syrén PO, Henche S, Eichler A, Nestl BM, Hauer B (December 2016). "Squalene-hopene cyclases-evolution, dynamics and catalytic ... For instance, the radical SAM protein HpnH adds an adenosine group to diploptene, forming the extended C35 hopanoid ... Researchers indicate this could be due to direct regulation of transport proteins by hopanoids or indirectly by altering ...
Nunn KL, Forney LJ (September 2016). "Unraveling the dynamics of the human vaginal microbiome". The Yale Journal of Biology and ... Probiotics and Antimicrobial Proteins. 4 (4): 217-226. doi:10.1007/s12602-012-9117-8. PMID 26782181. ...
Protein domain dynamics plays key roles in a multitude of molecular recognition and cell signalling processes. Protein domains ... "Accurate and efficient description of protein vibrational dynamics " comparing molecular dynamics and gaussian models". ... Another model for protein dynamics based on elastic mass-and-spring networks is the Anisotropic Network Model. The Gaussian ... Bahar, I.; Atilgan, A. R.; Demirel, M. C.; Erman, B. (1998). "Vibrational dynamics of proteins: Significance of slow and fast ...
"Capping protein regulators fine-tune actin assembly dynamics". Nature Reviews Molecular Cell Biology. 15 (10): 677-689. doi: ... The activity regulation of this protein can be done by other regulatory proteins that bind to the actin filaments blocking the ... as seen with other capping proteins, such as Gelsolin. A modest reduction in cardiac CapZ protein protects hearts against acute ... CapZ, also known as CAPZ, CAZ1 and CAPPA1, is a capping protein that caps the barbed end of actin filaments in muscle cells. ...
Y. Sugita & Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters. 314 ... Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic ... Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field. 3D molecular graphics Automatic ... "Molecular-dynamics study of atomic motions in water". Physical Review B. 31 (5): 2643-2648. Bibcode:1985PhRvB..31.2643T. doi: ...
Jouvenet N, Zhadina M, Bieniasz PD, Simon SM (April 2011). "Dynamics of ESCRT protein recruitment during retroviral assembly". ... Vta1 is a dimeric protein containing one VSL domain (so named because it is found in the proteins Vps4, SBP1, and LIP5), which ... A summary table of all of these proteins is provided below. In yeast, the following complexes/accessory proteins exist as ... The process is initiated by viral Gag proteins, the major structural proteins of retroviral coats, which interact with TSG101 ...
Phys., 7, 3910 Y. Sugita & Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical ... this is usually known as replica-exchange molecular dynamics or REMD. Essentially, one runs N copies of the system, randomly ... Sugita and Okamoto formulated a molecular dynamics version of parallel tempering: ...
2001). "Clasps are CLIP-115 and -170 associating proteins involved in the regional regulation of microtubule dynamics in motile ... Cytoplasmic linker associated protein 2, also known as CLASP2, is a protein which in humans is encoded by the CLASP2 gene. ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ... X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (3): 169-76 ...
Jouvenet N, Zhadina M, Bieniasz PD, Simon SM (April 2011). "Dynamics of ESCRT protein recruitment during retroviral assembly". ... Bieniasz PD, Grdina TA, Bogerd HP, Cullen BR (December 1998). "Recruitment of a protein complex containing Tat and cyclin T1 to ... Subsequently, another inhibitor of HIV-1 replication was discovered in his lab, Mx2, a cellular protein shown to inhibit post- ... Bieniasz showed that the retroviral protein Gag assembles at the plasma membrane, recruiting the viral genome by hijacking a ...
"Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters. 314 (1-2): 141-151. Bibcode:1999CPL ... Short for Car-Parrinello Molecular Dynamics, this core performs ab-initio quantum mechanical molecular dynamics. Unlike ... Short for Assisted Model Building with Energy Refinement, AMBER is a family of force fields for molecular dynamics, as well as ... In 2009, the Pande Group was working on a complementary new technique called Normal Mode Langevin Dynamics which had the ...
Daggett, V.; Levitt, M. (1993). "Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations". Journal of ... Levitt, M. (1976). "A simplified representation of protein conformations for rapid simulation of protein folding". Journal of ... 1987-present Levitt was one of the first researchers to conduct molecular dynamics simulations of DNA and proteins and ... where he criticised molecular dynamics for inability to refine protein structures. He has also worked on simplified ...
Anderson, Charles H.; Eliasmith, Chris (2004). Neural Engineering: Computation, Representation, and Dynamics in Neurobiological ... proteins, and chemical coupling to network oscillations, columnar and topographic architecture, and learning and memory. ... Eliasmith, Chris; Anderson, Charles H. (2003). Neural engineering: Representation, computation, and dynamics in neurobiological ... Gerstner, W.; Kistler, W.; Naud, R.; Paninski, L. (2014). Neuronal Dynamics. Cambridge, UK: Cambridge University Press. ISBN ...
Trophic dynamics[edit]. The trophic level concept was introduced in a historical landmark paper on trophic dynamics in 1942 by ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... 2004). "Detritus, trophic dynamics and biodiversity". Ecology Letters. 7 (7): 584-600. doi:10.1111/j.1461-0248.2004.00606.x.. ... The basis of trophic dynamics is the transfer of energy from one part of the ecosystem to another.[13][16] The trophic dynamic ...
The protein balance at time of dormancy is also maintained by lower levels of protein breakdown during the winter time. At ... mitochondrial dynamics and functions). Moreover, HMB is cheap (~30- 50 US dollars per month at 3 g per day) and may prevent ... Furthermore, 1 gram of nitrogen is roughly equivalent to 6 gram of protein, and 1 gram of protein is roughly equivalent to 4 ... Muscle atrophy occurs by a change in the normal balance between protein synthesis and protein degradation. During atrophy, ...
protein binding. •extracellular matrix constituent conferring elasticity. •extracellular matrix binding. Componente celular. • ... 2009). «Human tropoelastin sequence: dynamics of polypeptide coded by exon 6 in solution». Biopolymers. 91 (11): 943-52. PMID ... Rosenbloom J (1984). «Elastin: relation of protein and gene structure to disease». Lab. Invest. 51 (6): 605-23. PMID 6150137. ... 2010). «Functional consequences of homocysteinylation of the elastic fiber proteins fibrillin-1 and tropoelastin». J. Biol. ...
... which code for proteins with antiviral properties.[51] EBOV's V24 protein blocks the production of these antiviral proteins by ... "Transmission dynamics and control of Ebola virus disease (EVD): a review". BMC Med. 12 (1): 196. doi:10.1186/s12916-014-0196-0 ... which are then translated into structural and nonstructural proteins. The most abundant protein produced is the nucleoprotein, ... EBOV replication overwhelms protein synthesis of infected cells and the host immune defences. The GP forms a trimeric complex, ...
Protein targeting and importEdit. See also: Protein targeting. The movement of so many chloroplast genes to the nucleus means ... Sakamoto W, Takami T (June 2018). "Chloroplast DNA Dynamics: Copy Number, Quality Control and Degradation". Plant & Cell ... A protein kinase drifting around on the outer chloroplast membrane can use ATP to add a phosphate group to the Toc34 protein, ... Protein synthesisEdit. See also: Transcription and translation. Protein synthesis within chloroplasts relies on an RNA ...
A hexavalent (OspA) protein subunit-based vaccine candidate VLA15 was granted fast track designation by the U.S. Food and Drug ... "Spatial dynamics of lyme disease: a review" (PDF). EcoHealth. 5 (2): 167-95. CiteSeerX 10.1.1.580.8928. doi:10.1007/s10393-008 ... Within the tick midgut, the Borrelia's outer surface protein A (OspA) binds to the tick receptor for OspA, known as TROSPA. ... A recombinant vaccine against Lyme disease, based on the outer surface protein A (ospA) of B. burgdorferi, was developed by ...
The balance between potassium and sodium is maintained by ion transporter proteins in the cell membrane.[231] The cell membrane ... in a molecular dynamics (MD) simulation study". Biophys. Chem. 120 (1): 1-9. doi:10.1016/j.bpc.2005.10.002. PMID 16253415.. ...
In fluid dynamics, an incompressible fluid's velocity must increase as it passes through a constriction in accord with the ... Protein skimmers (filtration devices for saltwater aquaria). *In automated pool cleaners that use pressure-side water flow to ...
S. frugiperda cells (Sf9 and Sf21 cell lines) are commonly used in biomedical research for the purpose of recombinant protein ... "Population dynamics and occurrence of Spodoptera frugiperda host strains in southern Florida". Ecological Entomology. 29 (5): ... This protein was found to significantly decrease fall armyworm larva growth.[12] ...
and interstitial protein osmotic pressure (. π. i. {\displaystyle \pi _{i}}. ), and two absorptive forces, plasma protein ... Derangedphysiology.com: Starling's Principle of Transvascular Fluid Dynamics [1]. Retrieved from "https://en.wikipedia.org/w/ ... Thus, the difference in protein concentration would produce a flow of fluid into the vessel at the venous end equivalent to 28 ... Albumin and other proteins in the interstitial spaces return to the circulation via lymph. ...
signalni put G-protein spregnutog receptora. • hemosensorno ponašanje. • detekcija hemijskog stimulusa koji učestvuje u ... Olsen JV, Blagoev B, Gnad F, et al. (2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks ... Receptor ukusa tip 2 član 19 je protein koji je kod ljudi kodiran TAS2R19 genom.[1] ...
protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ... "Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules". Proceedings of the National Academy of ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2[10] and RAD52. ... Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, ...
Salman D, Okuda LH, Ueno A, Dautu G, et al «Evaluation of novel oocyst wall protein candidates of Toxoplasma gondii» (en anglès ... Simon A, Bigras Poulin M, Rousseau AN, Dubey JP, Ogden NH «Spatiotemporal dynamics of Toxoplasma gondii infection in Canadian ... Chronic Toxoplasma infection is associated with distinct alterations in the synaptic protein composition» (en anglès). J ...
... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... "Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break". Current Biology. 14 (19): ... 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 ...
This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell. Fatty acid synthase ... Wang Q, Matsui T, Domitrovic T, Zheng Y, Doerschuk PC, Johnson JE (March 2013). "Dynamics in cryo EM reconstructions visualized ... 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 ...
Dynamics of mechanical properties of a nucleic acid double helix such as bending and twisting can also be studied using NMR. ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics ... Robinson, B.H.; Drobny, G.P. (1995). "[19] Site-specific dynamics in DNA: Theory and experiment". Nuclear Magnetic Resonance ...
A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy. ... the adenovirus E1A proteins bind to the retinoblastoma gene product". Nature. 334 (6178): 124-9. Bibcode:1988Natur.334..124W. ... a highly conserved protein complex that recognizes and binds to specific DNA sequences, marking starting points for replication ...
FT protein movement contributes to long distance signalling in floral induction of Arabidopsis. Science. 2007, 316 (5827): 1030 ... 6.0 6.1 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1692983 The shoot apical meristem: the dynamics of a stable ... Movement Protein of Tobacco Mosaic Virus Modifies Plasmodesmatal Size Exclusion Limit Science 20 October 1989: Vol. 246. no. ... Not just another hole in the wall: understanding intercellular protein trafficking. Genes Dev. January 2005, 19 (2): 189-95. ...
Quantum dynamics. *Quantum electronics. *Quantum error correction. *Quantum imaging. *Quantum information. *Quantum key ...
Two mature PDHA proteins come together with two PDHB proteins to form a heterotetrameric E1 subunit. Crystal Structures allowed ... 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635-48. doi:10.1016/ ... Click on genes, proteins and metabolites below to link to respective articles. [§ 1] ... 2001). "Activation and mitochondrial translocation of protein kinase Cdelta are necessary for insulin stimulation of pyruvate ...
... identified a protein that later became known as superoxide dismutase as an indophenol oxidase by protein analysis of starch ... "Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase". Acta Crystallogr. B. 47 ( ... SOD1 is an extremely stable protein. In the holo form (both copper and zinc bound) the melting point is , 90 °C. In the apo ... However, in the chronic stage, SOD does not seem to be sufficient and tends to decrease due to the destruction of proteins from ...
This method is especially useful in cell-to-cell propagation of infectious cytosolic protein aggregates. In one study, protein ... However, most of this fluid returns into the capillary at the venous end, creating capillary fluid dynamics. Two opposing ... Research at the cell level can deliver proteins, ions, or specific small molecules into the intercellular cleft as a means of ... The cleft contains gap junctions, tight junctions, desmosomes, and adheren proteins, all of which help to propagate and/or ...
In particular, the energetics and dynamics of such systems and processes are of interest to physical chemists. Important areas ... Neurochemistry is the study of neurochemicals; including transmitters, peptides, proteins, lipids, sugars, and nucleic acids; ...
இதனால் புரதத் தொகுப்புக்கு (protein synthesis) க்கு முன்னான டி.என்.ஏ படியெடுத்தலில் (transcription) சட்டக மாற்றம் (frame shift ... "Evolutionary dynamics of the human ABO gene". Human Genetics 124 (2): 123-135. doi:10.1007/s00439-008-0530-8. பப்மெட்:18629539 ...
They serve as protein and starch storage units serving as a nutrient source for newly developed plants. ... "Lattice population dynamics for plants with dispersing seeds and Vegetative propagation". Researches on Population Ecology. 36 ...
R. L. Wysong (1976). "5: Origin of Proteins". The Creation-evolution Controversy (implications, Methodology and Survey of ... complexity of biological systems and organisms might result as much from self-organization and far-from-equilibrium dynamics as ... for their studies of the structures of hemoglobin and globular proteins.[269] ... awarded the 2001 Nobel Prize in Physiology or Medicine along with Leland Hartwell and Tim Hunt for their discoveries of protein ...
Two examples of adaptor proteins are AP180[3] and epsin.[4][5][6] AP180 is used in synaptic vesicle formation. It recruits ... Role of the Clathrin Terminal Domain in Regulating Coated Pit Dynamics Revealed by Small Molecule Inhibition,Cell, Volume 146, ... Clathrin is a protein that plays a major role in the formation of coated vesicles. Clathrin was first isolated and named by ... Coat-proteins, like clathrin, are used to build small vesicles in order to transport molecules within cells. The endocytosis ...
The protein degradation processEdit. Ribbon diagram of ubiquitin, the highly conserved protein that serves as a molecular tag ... "Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome". Nature. 565 (7737): 49-55. doi:10.1038/s41586-018- ... 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 ...
"Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms" (PDF). 》Mol Biosyst》 5 ... Hunter T (January 1995). "Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling". 》Cell》 ... Protein structure and function》. London: New Science. 27쪽. ISBN 978-1405119221. .. ... Anfinsen CB (July 1973). "Principles that govern the folding of protein chains". 》Science》 181 (4096): 223-30. Bibcode:1973Sci ...
... The United States and China emerge top players, ... Pea Protein Ingredients Alter Production Dynamics as Global Demand Escalates. News provided by ... Whole Yellow Peas and Pea Protein Ingredients: A Close Supply and Value Chain Relationship is part of the Food and Agriculture ... Recent analysis from Frost & Sullivan, Whole Yellow Peas and Pea Protein Ingredients: A Close Supply and Value Chain ...
Protein localization and dynamics within a bacterial organelle. H. Velocity Hughes, Edgar Huitema, Sean Pritchard, Kenneth C. ... Protein localization and dynamics within a bacterial organelle. H. Velocity Hughes, Edgar Huitema, Sean Pritchard, Kenneth C. ... Protein localization and dynamics within a bacterial organelle. H. Velocity Hughes, Edgar Huitema, Sean Pritchard, Kenneth C. ... protein mobility. Mechanisms exist in prokaryotic and eukaryotic cells to direct specialized proteins to distinct subcellular ...
The Society provides video resources to students and teachers. Videos of the National Lectures at the BPS Annual Meeting can be used to help plan a syllabus.
The dynamics of protein phosphorylation in bacterial chemotaxis.. Borkovich KA1, Simon MI. ... The systems dynamics depends on the relative distribution of CheA among these three forms at any time. ... The pathway includes ligand binding receptors, and the CheA, CheY, CheW, and CheZ proteins. We showed previously that ...
... are widely used tools to visualize proteins and study their intracellular distribution. One feature of working with GFP ... FLIP can be used to study the dynamics of different pools of a protein or can show how a protein diffuses, or is transported ... Revealing protein dynamics by photobleaching techniques Methods Mol Biol. 2004;284:287-306. doi: 10.1385/1-59259-816-1:287. ... Green fluorescent proteins (GFPs) are widely used tools to visualize proteins and study their intracellular distribution. One ...
Alzheimers Disease »Dysfunctional protein dynamics »NMR spectroscopy »Parkinsons disease »Science TV »nerve cell »nerve cells ... Further reports about: , Alzheimers Disease , Dysfunctional protein dynamics , NMR spectroscopy , Parkinsons disease , ... Dysfunctional protein dynamics behind neurological disease?. 13.10.2009. Researchers at Lund University, Sweden, have taken a ... The research team headed by Mikael Akke at the Center for Molecular Protein Science of Lund University used NMR spectroscopy to ...
Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles. In: Marsh J. (eds) Protein Complex Assembly. Methods ... The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software ... Small-angle X-ray scattering (SAXS) Protein-protein docking Conformational heterogeneity Multi-state models Conformational ... Jimenez-Garcia B, Pons C, Svergun DI, Bernado P, Fernandez-Recio J (2015) pyDockSAXS: protein-protein complex structure by SAXS ...
Direct observation of hierarchical protein dynamics. By Józef R. Lewandowski, Meghan E. Halse, Martin Blackledge, Lyndon Emsley ... Direct observation of hierarchical protein dynamics. By Józef R. Lewandowski, Meghan E. Halse, Martin Blackledge, Lyndon Emsley ... One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. ... The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow ...
Albert-Ludwigs-Universität »ERC »Hsp90 »Nano »Nanoparticles »gold nanoparticles »individual proteins »movements »proteins » ... The function of proteins - the molecular tools of the cell - is governed by the interplay of their structure and dynamics. ... Dynamics of individual proteins. 09.10.2018. New measurement method allows researchers to precisely follow the movement of ... Conformational dynamics of a single protein monitored for 24 hours at video rate. In: Nano Letters. DOI: 10.1021/acs.nanolett. ...
Quaternary dynamics and plasticity underlie small heat shock protein chaperone function. Florian Stengel, Andrew J. Baldwin, ... Quaternary dynamics and plasticity underlie small heat shock protein chaperone function. Florian Stengel, Andrew J. Baldwin, ... Quaternary dynamics and plasticity underlie small heat shock protein chaperone function Message Subject (Your Name) has sent ... Quaternary dynamics and plasticity underlie small heat shock protein chaperone function. Florian Stengel, Andrew J. Baldwin, ...
... making it feasible to identify a panel of blood proteins for monitoring different aspects of muscle protein dynamics. The ... Proteome dynamics in rat gastrocnemius muscle. (A) Heatmap of FSRs (% day-1) of 75 proteins in rat muscle measured in n = 3 ... Circulating protein synthesis rates reveal skeletal muscle proteome dynamics. Mahalakshmi Shankaran,1 Chelsea L. King,1 Thomas ... 25 proteins from the contralateral limb, 122 ± 26 proteins from the vehicle-treated muscle, and 109 ± 20 proteins from the ...
... and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across ... Names are listed in the order they appear on the scatter plots for each class of proteins. Data represent mean ± SD, n. = 3-4/ ... Heatmap of FSRs (% day-1) of 75 proteins in rat muscle measured in n. = 3 rats per group after denervation and clenbuterol ... FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human ...
Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and ... Computational Methods for Prediction of Membrane Protein Structure and Dynamics. * Front Matter Pages 165-165 ... The first section details the procedures used for measurements of structure and dynamics of membrane proteins. While the second ... spectroscopy mass spectrometry membrane receptors nuclear magnetic resonance spectroscopy protein structure protein-protein ...
Vertical axis: turnover rate (k) (d−1). (b) Correlations between protein turnover rates and protein abundance. Protein turnover ... A large dataset of protein dynamics in the mammalian heart proteome.. Lau E1,2, Cao Q1,2,3, Ng DC1,2, Bleakley BJ1,2, Dincer TU ... Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and ... Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding ...
Source at Brookhaven Lab to develop a technique that pinpoints the location and motion of water molecules bound to proteins. ... So, in order to find water thats tightly bound to a protein, the team chemically activated protein waters with an x-ray beam, ... Temperature-dependent Radiolysis Reveals Dynamics of Bound Protein Waters. April 18, 2013 ... They then wash out the system and take a measurement of the mass of the protein. A shift in mass tells them where the water is ...
Keywords: 4D-QSAR; Molecular dynamics; PK inhibitors; X-ray crystallographic data; docking; free energy calculations; protein ... That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on ... Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have ... Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been ...
Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. Detailed dynamics ... of 13C relaxation to probe the dynamics of protein side chains is detailed mainly for the dynamics of non-deuterated proteins ... Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural ... Keywords: 13C relaxation; 13C relaxation of methine; Carr-Purcell-Meiboom-Gill (CPMG); HSQC; IFABP; INEPT; NMR; NOEs; Protein ...
... fluctuation spectroscopy data to directly measure the oligomerization state and dynamics of fluorescently tagged proteins in ... Altered dynamics of a lipid raft associated protein in a kidney model of Fabry disease. Mol. Genet. Metab. 111, 184-192 (2014). ... Monomer dimer dynamics and distribution of GPI-anchored uPAR are determined by cell surface protein assemblies. J. Cell Biol. ... Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. *Francesco Cutrale ORCID: orcid ...
Membrane dynamics, as well as protein-protein and protein-membrane interactions are particularly addressed. In addition, it ... Membrane dynamics, as well as protein-protein and protein-membrane interactions are particularly addressed. In addition, it ... However, it is also induced under stress conditions, remodeling the eukaryotic cell by regulating energy, protein and lipid ... However, it is also induced under stress conditions, remodeling the eukaryotic cell by regulating energy, protein and lipid ...
... Chen-Wei Jiang,1 Ai- ... Our nonadiabatic molecular dynamics simulation method was named semiclassical electron-radiation-ion dynamics (SERID), which ... "Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: Evidence for cis-trans isomerism," ... Y. Dou, Y. Lei, A. Li et al., "Detailed dynamics of the photodissociation of cyclobutane," The Journal of Physical Chemistry A ...
High-resolution microscopic analysis has precisely revealed the control of microtubule dynamics by individual microtubule- ... associated proteins (MAPs) in vitro. Furthermore, transfection of MAP cDNA into fibroblasts and subsequent analysis using ... Microtubule organization and dynamics dependent on microtubule-associated proteins Curr Opin Cell Biol. 1994 Feb;6(1):74-81. ... microscopic analysis has precisely revealed the control of microtubule dynamics by individual microtubule-associated proteins ( ...
Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence. By Hohjai Lee, Yuan-Chung Cheng, Graham R. ... Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence. By Hohjai Lee, Yuan-Chung Cheng, Graham R. ... Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence Message Subject. (Your Name) has forwarded a ... The result is a map showing the dephasing dynamics of the ,g 〉 〈H, coherence along the t1 axis and the dynamics of the ,B 〉 〈H ...
This band is a superposition of a large number of low frequency modes of the protein and the expected shift in frequency of ... Small changes in the dynamics can be treated classically with many changes being required to give observed cooperative free ... This thesis explores the possible uses of dynamical fluctuations in protein structure for ligand binding and catalysis. ... predictions of this model are tested using laser Raman spectroscopy of solid samples to study low frequency modes in proteins ...
3] D.H. de Jong, C.A. Lopez, S.J. Marrink. Molecular view on protein sorting into liquid-ordered membrane domains mediated by ... The MD group uses large scale simulations to probe the lateral partitioning and self-assembly of proteins. Together with our ... Lipid-anchor driven partitioning of Hedgehog proteins into the liquid-ordered domain of a model membrane. The four different ... Cell membranes are comprised of a heterogeneous mixture of lipids and proteins. The heterogeneity of biological membranes plays ...
In order to develop a complementation system, NanoLuc® Luciferase is divided into two subunits - a larger protein domain and a ... Reversible interaction dynamics of proteins in living cells.. Measuring PPIs Using Bioluminescence Imaging. With the help of ... Using NanoBiT® Technology to Study the Dynamics of Protein Interactions in Live Cells. *Download PDF Copy ... After Protein-Protein Interactions. Evaluating the NanoBiT® PPI Assay Using Two Model Systems. In this article, two PPI model ...
In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods ... Protein Dynamics: Methods and Protocols describes the most common and powerful methods used to characterize protein dynamics. ... In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods ... Protein Structural Dynamics Revealed by Site-Directed Spin Labeling and Multifrequency EPR ...
... Now playing at a supercomputer near you: proteins in action. June 29, 2005 ... In each case, the simulations furthered their understanding of protein dynamics and helped guide real-world experiments. They ... Home » News & Publications » News » Science News » Protein Dynamics Hit the Big Screen ... Mutant forms of these proteins can trigger cancer. Theyve also simulated the conformational and energy changes that proteins ...
Promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface ... independently of the mitochondrial fission FIS1 and MFF proteins. Regulates DNM1L GTPase activity and DNM1L oligomerization. ... Mitochondrial outer membrane protein which regulates mitochondrial fission. ... Mitochondrial dynamics protein MID51Add BLAST. 463. Amino acid modifications. Feature key. Position(s). DescriptionActions. ...
Dynamics of protein-DNA interactions in a Mu transpososome. Download Alternative Title: Dynamics of protein-Deoxyribonucleic ... Dynamics of protein-DNA interactions in a Mu transpososome. Research and Teaching Output of the MIT Community. ... Transposition is mediated by a protein, the transposase, encoded by the transposon. DNA sequence signals at the two ends of the ...
... with a special emphasis on how lipids regulate the structure and function of their effector proteins. In the final session, we ... serve primarily as a passive barrier and a host for membrane proteins, an idea many standard biochemistry textbooks have ... and directly monitor lipid dynamics and lipid-mediated cellular activities with high spatiotemporal resolution. These exciting ... advances in chemical biology and molecular imaging technologies have allowed researchers to identify new lipid-binding proteins ...
  • In Membrane Protein Structure Predictions Methods: Methods and Protocols, expert researcher in the field detail the advances in both experimental and computational approaches of the structure, dynamics and interactions of membrane proteins dividing the volume into two sections. (springer.com)
  • Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. (ingentaconnect.com)
  • Membrane dynamics, as well as protein-protein and protein-membrane interactions are particularly addressed. (frontiersin.org)
  • When interactions occur between the two target proteins, SmBiT and LgBiT are brought close together, enabling structural complementation to produce an extremely bright, luminescent enzyme. (news-medical.net)
  • By using the parts of the NanoBiT™ PPI Starter Systems, protein-protein interactions can be tracked in real time in living cells. (news-medical.net)
  • This demonstrates the fast signal changes in response to varying intracellular [cAMP] levels and also shows that reversible dynamics of protein interactions in living cells can be tracked using the NanoBiT™ PPI Assay. (news-medical.net)
  • With the help of the bright signal produced by the NanoBiT ® PPI Assay, interactions between proteins can be observed in each cell using bioluminescence imaging. (news-medical.net)
  • NMR spectroscopy will be employed for accessing the structures, dynamics of the "excited state" protein conformations and protein-protein interactions. (weizmann.ac.il)
  • The project aims to characterize substrate binding, membrane-receptor interactions, and the conformational response to phosphorylation of protein tyrosine kinases to elucidate recognition and regulation of signaling pathways in the cell. (weizmann.ac.il)
  • This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). (springer.com)
  • We cover areas such as protein dynamics, protein folding dynamics, DNA dynamics, DNA-protein interactions and dynamics in single living cells. (tifr.res.in)
  • However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. (mdpi.com)
  • Interactions between proteins are also often required to be weak, for example in signaling pathways where efficiency and reversibility of information transfer are of key importance. (frontiersin.org)
  • To investigate the Ca2+-dependency of CaM binding NOS, nuclear magnetic resonance (NMR) studies were performed at various free Ca2+ concentrations to determine the structure and dynamics of NOS and CaM interactions at physiological Ca2+ concentrations. (uwaterloo.ca)
  • Attaching fluorescent molecules to protein surfaces, however, enables direct imaging of dynamic biomolecular interactions using light, which could be improved, say A*STAR researchers, with predictive modeling of fluorescence lifetimes. (phys.org)
  • This suggests that the metal binding region might be involved in intermolecular protein-protein interactions which may constitule the eariy stages in formation of aggregates. (diva-portal.org)
  • The study showed persistent dimer interactions and high catalytic activity at GdmCllevels where the holo-protein according to CD measurements is fully unfolded. (diva-portal.org)
  • Here, we provide detailed instructions for using this method to study protein complexes, protein-protein interactions, and the dynamics of protein abundance and posttranslational modifications. (sciencemag.org)
  • We also found that 4EGI-1 normalized the phenotypes of enhanced metabotropic glutamate receptor (mGluR)-mediated long-term depression (LTD), enhanced Rac1-p21-activated kinase (PAK)-cofilin signaling, altered actin dynamics, and dysregulated CYFIP1/eIF4E and CYFIP1/Rac1 interactions in FXS mice. (sciencemag.org)
  • The PhD candidate will employ advanced experimental and computational methods to determine structure and interactions of key proteins of biopharmaceutical interest, and further develop them using cutting-edge MS equipment available at the Astbury Centre, and our expertise in bioinformatics. (findaphd.com)
  • Recent studies have suggested that AVP signal transduction may involve dynamic protein-protein interactions, ultimately leading to the phosphorylation and inhibition of delayed rectifier potassium channels (Kv1.2). (jaoa.org)
  • Following these treatments, protein-protein interactions were examined by immunoprecipitation of PYK2 and by Western blot analysis to identify proteins that become associated with PYK2 during the time course of the treatments. (jaoa.org)
  • Additional new evidence of protein-protein interactions was observed in AVP treated A7r5 cells where an unknown protein band was visible on a Ponceau red stain of a Western blot membrane. (jaoa.org)
  • It is frequently found that proteins find and recognize their specific targets quickly and efficiently despite the complex nature of protein-DNA interactions in living cells. (rice.edu)
  • Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. (ingentaconnect.com)
  • To furnish a deeper and detailed mechanistic understanding of the photoisomerization reaction of those green fluorescent protein chromophore based molecular switches, semiclassical nonadiabatic molecular dynamics simulations were performed for a molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH, named as 2e in [ 27 ]) in our group. (hindawi.com)
  • The MD group uses large scale simulations to probe the lateral partitioning and self-assembly of proteins. (rug.nl)
  • Although these high-resolution simulations take days to prepare even on a supercomputer, they enable Kuriyan and colleagues to test-drive proteins under a variety of conditions. (nersc.gov)
  • The simulations allow us to push here and there and determine how the protein responds," says Kuriyan, who is also a Howard Hughes Medical Institute investigator and a Chancellor's Professor in UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry. (nersc.gov)
  • So far, Kuriyan and colleagues have used NERSC simulations to learn how certain proteins, called Src tyrosine kinases, transmit signals initiated by growth factor receptors in human cells. (nersc.gov)
  • In each case, the simulations furthered their understanding of protein dynamics and helped guide real-world experiments. (nersc.gov)
  • On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. (springer.com)
  • Sylte, I. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5. (mdpi.com)
  • Lindin I, Wuxiuer Y, Ravna AW, Moens U, Sylte I. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5. (mdpi.com)
  • 2014. "Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5. (mdpi.com)
  • This work shows that a deep-sea protein, 3LEZ, with known in vitro β -lactamase activity, proved stable, substantially in the conformation detected by X-ray diffraction of the crystal, when subjected to molecular-dynamics (MD) simulations under conditions compatible with shallow seas. (wiley.com)
  • We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. (wiley.com)
  • One method uses short MD simulations to enrich structural ensembles of protein switches in the neighborhood of their initial conformations for scoring by contact maps. (utexas.edu)
  • Applying adapted sampling schemes to both native-centric models and to three well-studied example proteins shows that experimental results and behaviour observed in detailed all-atom simulations can be better explained in the profile-based model than in the Go-model. (tu-darmstadt.de)
  • Based on our previous comprehensive study (Jahandideh and Zhi, 2013), three missense mutations, from two different functional groups, i.e. disease- related mutations, and protective mutations, were selected and extensive molecular dynamics simulations of these three mutants performed to compare their dynamics and conformations to those of the wildtype HuPrP. (omicsonline.org)
  • In conclusion, the simulations of dimeric forms suggest that the dominant-negative effect of protective mutation (E219K) is due to the incompatible structures and dynamics of allelic variants during conversion process. (omicsonline.org)
  • qsar from qsar.org Subject: [QSAR] Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Hi all, Here's an interesting topic I'd like your thoughts on - please pass along to your colleagues. (bio.net)
  • Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Molecular dynamics simulation provides a potentially powerful tool for understanding the behavior of proteins at an atomic level of detail, but its relevance to drug design has been limited in part by the computational demands of such simulations. (bio.net)
  • 100 times the length of the longest such simulations previously published - revealing pharmaceutically relevant aspects of protein dynamics that were previously inaccessible to both computational and experimental study. (bio.net)
  • SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. (springer.com)
  • Here we probe the architecture and dynamics of complexes formed between an oligomeric sHSP and client by employing unique mass spectrometry strategies. (pnas.org)
  • Here we capitalize on these unique advantages to study the complexes formed between pea HSP18.1 and a model client protein, firefly luciferase (Luc). (pnas.org)
  • Molecular Dynamics of Protein Kinase-Inhibitor Complexes: A Valid. (ingentaconnect.com)
  • mTOR exists as part of at least two complexes: complex 1 (mTORC1) is sensitive to nutrient abundance and is made-up of mTOR along with the subunits Raptor, mLST8 (also known as G protein beta subunit-like) and PRAS40. (frontiersin.org)
  • Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis. (sciencemag.org)
  • Highly efficient solar energy harvesting and trapping in photosynthesis relies on sophisticated molecular machinery built from pigment-protein complexes ( 1 , 2 ). (sciencemag.org)
  • 660 fs) quantum coherences between excitonic states play an important role in the dynamics of energy transfer in photosynthetic complexes-i.e., the energy transfer is described by wavelike coherent motion instead of incoherent hopping ( 4 ). (sciencemag.org)
  • In other words, the protein environment protects electronic coherences and plays a role in the optimization of excitation energy transfer in photosynthetic complexes. (sciencemag.org)
  • Using interdisciplinary approaches, the Liu Lab aims to explore the molecular mechanism underlying the self-assembly, dynamics and regulation of biological membranes and macromolecular protein complexes. (news-medical.net)
  • Domain motions are important for: ABC transporters catalysis cellular locomotion and motor proteins formation of protein complexes ion channels mechanoreceptors and mechanotransduction regulatory activity transport of metabolites across cell membranes[citation needed] One of the largest observed domain motions is the 'swivelling' mechanism in pyruvate phosphate dikinase. (wikipedia.org)
  • The results illustrate that structures of CaM-NOS complexes determined at saturating Ca2+ concentrations cannot provide a complete picture because the differences in intramolecular dynamics become visible only at physiological Ca2+ levels. (uwaterloo.ca)
  • 15N relaxation and H/D exchange experiments also allowed for the analysis of the structural dynamics occurring in these complexes. (uwaterloo.ca)
  • NMR spectroscopy is an efficient method for studying the dynamics and structures of protein-protein and protein-peptide complexes. (uwaterloo.ca)
  • The larger diatom Coscinodiscus radiatus showed generally similar responses but had a smaller allocation of PSII complexes relative to total protein content, with nearly equal stiochiometries of PsbA and PsbD subunits. (plantphysiol.org)
  • More recently, the activation pathway of different GPCR complexes have been investigated using molecular dynamics (MD), where the solvent and membrane environment is taken into account [ 8 - 11 ]. (pubmedcentralcanada.ca)
  • In our work, we employ photoinduced electron transfer (PET) combined with fluorescence correlation spectroscopy (FCS) for studying the conformational dynamics of one specific class of IDPs: phenylalanine-glycine rich protein domains (FG repeats) which are dominant building blocks within the pore of nuclear pore complexes. (spie.org)
  • Nuclear pore complexes are large protein assemblies that cross the nuclear envelope and form selective barrier, which regulate bidirectional exchange between nucleus and cytoplasm. (spie.org)
  • Thus, loss of FMRP increased the abundance of eIF4G-bound eIF4E, CYFIP1-Rac1 complexes, and inactivated cofilin, thereby impairing the actin polymerization dynamics necessary for synaptic plasticity and learning. (sciencemag.org)
  • These patches cause two or several protein molecules to stick together, thereby forming the cornerstone of the larger structures that are believed to underlie ALS. (innovations-report.com)
  • In future, it might be possible to test whether individual molecules display memory, or whether proteins with an identical chemical structure might behave differently over long periods of time. (innovations-report.com)
  • All of the molecules in our bodies function in water, but until now, we haven't had a lot of experimental techniques to understand what water is doing or where it is binding to the interior surfaces of proteins. (bnl.gov)
  • A team of scientists from Case Western Reserve University used the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory to develop a technique that pinpoints the location and motion of water molecules bound to proteins. (bnl.gov)
  • A commonly used approach for studying protein aggregates in cells is number and brightness (N&B), a fluorescence microscopy method that is capable of measuring the apparent average number of molecules and their oligomerization (brightness) in each pixel from a series of fluorescence microscopy images. (nature.com)
  • Scientists from Berkeley Lab and UC Berkeley are using one the world's most powerful computers to simulate how protein molecules move, rotate, and fold as they carry out life's most fundamental tasks.Although they only approximate real-life phenomena, the increasingly realistic movies are becoming useful complements to real-world experiments in helping scientists determine how proteins function. (nersc.gov)
  • Proteins are very complex molecules with thousands of atoms, but they don't come with a user's manual," says John Kuriyan of Berkeley Lab's Physical Biosciences Division. (nersc.gov)
  • While theirs was a seminal paper in the lipid field, the authors did make one unfortunate mistake: depicting lipids as bland molecules that serve primarily as a passive barrier and a host for membrane proteins, an idea many standard biochemistry textbooks have adopted. (asbmb.org)
  • This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. (springer.com)
  • In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. (springer.com)
  • A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. (springer.com)
  • With the state-of-the-art laser technology available today one can observe dynamics of molecules in ultrafast timescales with high sensitivity and selectivity. (tifr.res.in)
  • In addition, recent attempts at therapeutic targeting of IDPs by small molecules, noting in particular that IDPs represent a potentially important source of new drug targets in light of their central role in protein-protein interaction networks, are also reviewed. (dovepress.com)
  • By doing so, the membrane is a rather complex system on its own, consisting mainly of lipid molecules and membrane proteins. (pubmedcentralcanada.ca)
  • Transmembrane proteins can function on both sides of the membrane or transport molecules across it. (pubmedcentralcanada.ca)
  • Cell-surface receptors are transmembrane proteins that bind water-soluble signal molecules in the extracellular space and generate different intracellular signals. (pubmedcentralcanada.ca)
  • Endothelial adhesion molecules, such as E-selectin or ICAM-1, are connected to the actin cytoskeleton via actin-binding proteins (ABPs). (jimmunol.org)
  • During inflammation, the endothelium actively contributes to leukocyte extravasation by expression of adhesion molecules, release of cytokines, presentation of chemokines, and by accommodating leukocyte crawling on its apical surface and transmigration across its cell body or intercellular contacts by "customized" actin dynamics controlling endothelial cell (EC) functionality. (jimmunol.org)
  • Non-Brownian Phase Space Dynamics of Molecules, the Nature of Their Vibrational States, and Non-RRKM Kinetics ( David M. Leitner, Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki, Akira Shojiguchi, and Mikito Toda ). (wiley.com)
  • These components can be related to the dynamics of the molecules that make up the fluid, and thus microrheology has the potential to reveal new information about the microscopic properties of complex materials. (gla.ac.uk)
  • Determining how proteins interact with other molecules is key in understanding most biological process, development of novel therapeutics and biotechnology. (findaphd.com)
  • Researchers at Lund University, Sweden, have taken a snapshot of proteins changing shape, sticking together and creating structures that are believed to trigger deadly processes in the nervous system. (innovations-report.com)
  • Chacon P, Moran F, Diaz JF, Pantos E, Andreu JM (1998) Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. (springer.com)
  • JPK Instruments, a world-leading manufacturer of nanoanalytic instrumentation for research in life sciences and soft matter, reports on the use of their NanoWizard ® ULTRA Speed AFM system at the University of Liverpool in the group of Dr Luning Liu of the Institute of Integrative Biology to study biological membrane structures and protein dynamics. (news-medical.net)
  • The Group applies the JPK ULTRA Speed AFM to study biological membrane structures and protein dynamics. (news-medical.net)
  • Proteins are generally thought to adopt unique structures determined by their amino acid sequences. (wikipedia.org)
  • Portions of protein structures often deviate from the equilibrium state. (wikipedia.org)
  • Many residues are in close spatial proximity in protein structures. (wikipedia.org)
  • Domain motions can be inferred by comparing different structures of a protein (as in Database of Molecular Motions), or they can be directly observed using spectra measured by neutron spin echo spectroscopy. (wikipedia.org)
  • Associated with complex structures are the 'dynamics' of these macromolecules which make the biological world. (tifr.res.in)
  • The classical view holds that proteins fold into essentially unique three-dimensional structures before becoming biologically active. (dovepress.com)
  • Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). (portlandpress.com)
  • The structural biology of proteins and nucleic acids has undergone many revolutions in the past few decades, and there are now multiple techniques, including both solution and solid-state NMR in addition to X-ray crystallography and cryoEM to determine accurate three-dimensional structures of these biomolecules. (portlandpress.com)
  • The diverse functions of proteins are closely related to their dynamics and structures. (utexas.edu)
  • In this dissertation I discuss the dynamics of a special class of proteins through studies of their sequences and structures. (utexas.edu)
  • These proteins are "switches," which are made of highly similar sequences that fold to dramatically different structures. (utexas.edu)
  • To identify protein switches, we developed methods that assign switch sequences to structures with high accuracy. (utexas.edu)
  • Both methods were first tested against a series of experimentally engineered proteins in a switching system and then applied to examine a large number of computationally sampled protein switches for a particular pair of structures in sequence space. (utexas.edu)
  • From the sampled switch sequences we found that making a point mutation near the N- and C-termini of the sequences is more likely to make the proteins switch between structures. (utexas.edu)
  • Conventional fluorophores have large, flexible structures that press against proteins in multiple ways, making it tricky to gage the ruler's length. (phys.org)
  • His research interests include structures, properties and dynamics of clusters and biopolymers. (wiley.com)
  • We know that polypeptide chains fold into complex structures, but how can another protein help to solve this puzzle? (amolf.nl)
  • Yet many protein structures are highly dynamic and heterogeneous, making it difficult to capture their complete conformational behavior and assembly pathways using such high-resolution structural snapshots. (findaphd.com)
  • In comparing two structures, the method partitions a protein into domains of preserved geometry and characterizes the relative movement of domains by effective rotation axes. (illinois.edu)
  • It is important to understand how proteins fold, as folding into wrong structures leads to Alzheimer's disease, Parkinson's disease, type II diabetes, and cancer. (rug.nl)
  • To investigate functions and folding of proteins one needs to know their structures. (rug.nl)
  • We have developed methodologies that allow to resolve proteins structures which are involved in ultrafast interconversions (time scale ~100000 femtoseconds). (rug.nl)
  • Both forms of CaM are able to bind to target proteins. (uwaterloo.ca)
  • CaM also undergoes post translational modifications that play a role in its regulation of target proteins. (uwaterloo.ca)
  • To differentiate between the primary and secondary target proteins of ERα signaling, we measured dynamics of protein expression induced by 17β-estradiol in MCF-7 breast cancer cells. (mcponline.org)
  • The central a-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. (illinois.edu)
  • The dynamics of protein phosphorylation in bacterial chemotaxis. (nih.gov)
  • Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. (ingentaconnect.com)
  • Some of these conformational changes are induced by post-translational modifications in protein structure, such as phosphorylation and methylation. (wikipedia.org)
  • Reversible protein phosphorylation is a key regulatory mechanism of mitotic progression. (mcponline.org)
  • hence, phosphorylation dynamics of kinases hold a wealth of information about phosphorylation networks. (mcponline.org)
  • Here, we investigated the site-specific phosphorylation dynamics of human kinases during mitosis using synchronization of HeLa suspension cells, kinase enrichment, and high resolution mass spectrometry. (mcponline.org)
  • In biological triplicate analyses, we identified 206 protein kinases and more than 900 protein kinase phosphorylation sites, including 61 phosphorylation sites on activation segments, and quantified their relative abundances across three specific mitotic stages. (mcponline.org)
  • Reversible phosphorylation is a ubiquitous posttranslational protein modification that is involved in the regulation of almost all biological processes ( 1 ⇓ - 3 ). (mcponline.org)
  • Regulation of kinases is of particular interest in mitosis as most of the mitotic events are regulated by reversible protein phosphorylation ( 19 ). (mcponline.org)
  • An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. (osti.gov)
  • While the processes that lead to EGFR activation and phosphorylation have been studied in detail, quantitative aspects of the spatiotemporal regulation of EGFR by protein tyrosines phosphatases (PTPs) are not well understood. (upenn.edu)
  • To begin to address this, we developed a new compartmentalized mechanistic model of EGFR phosphorylation dynamics and used it to interpret quantitative biochemical measurements to show that EGFR is dephosphorylated at the plasma membrane and in the cell interior with a time scale that is small compared to the time scales for EGFR internalization. (upenn.edu)
  • This effect was mediated by changes in the protein phosphorylation status of occludin via the action of FAK, thereby affecting the endocytic vesicle-mediated protein trafficking events that destabilized the TJ barrier. (popcouncil.org)
  • Green fluorescent proteins (GFPs) are widely used tools to visualize proteins and study their intracellular distribution. (nih.gov)
  • In 2014, the Harvard/Rowland researchers demonstrated the ability of their nanodevice to detect levels of intracellular proteins in living, cultured cells. (eurekalert.org)
  • When there are increasing intracellular cAMP levels, cAMP is bound to the regulatory subunit resulting in dissociation of the protein complex and discharge of catalytic subunits for downstream activity. (news-medical.net)
  • Specific recruitment of different proteins to distinct intracellular membranes is fundamental in the biology of eukaryotic cells, but the molecular basis for specificity is incompletely understood. (europa.eu)
  • This proposal investigates the hypothesis that coincidence detection of proteins and lipids constitutes a major mechanism for specific recruitment of proteins to intracellular membranes in order to control cellular membrane dynamics. (europa.eu)
  • Calmodulin (CaM) is a small, acidic cytosolic calcium binding protein that responds to increases in intracellular Ca2+ concentrations. (uwaterloo.ca)
  • The first part is a study of the intracellular protein human copper zinc superoxide dismutase which has been associated with the fatale disease Amyotrophic lateral Selerosis (ALS). (diva-portal.org)
  • The importance of the sHSPs is evidenced by their almost ubiquitous expression ( 2 ), the presence of multiple sHSP genes in most organisms ( 3 ), and their dramatic up-regulation under stress conditions making them among the most abundant of cellular proteins ( 4 ). (pnas.org)
  • This gene encodes an outer mitochondrial membrane protein that functions in the regulation of mitochondrial morphology. (wikipedia.org)
  • Hongxia Zhao is now continuing studies on regulation of lipid dynamics as an Academy Research Fellow at University of Helsinki. (nanowerk.com)
  • These intrinsically disordered proteins (IDPs) have been found to be highly prevalent in many genomes, including human, and play key roles in central cellular processes, such as regulation of transcription and translation, cell cycle, and cell signaling. (dovepress.com)
  • Ultimately, the new quantitative understanding of EGFR regulation by PTPs developed in this thesis significantly refines our understanding of the dynamics of EGFR-mediated signaling, provides a number of additional testable predictions related to fundamental aspects of EGFR signaling complex nucleation and efficacy of EGFR-targeted therapeutics, and offers a basic quantitative framework for exploring the regulation of other receptor tyrosine kinases by PTPs. (upenn.edu)
  • CYFIP1 shuttles between the FMRP-eIF4E complex and the Rac1-Wave regulatory complex, thereby connecting translational regulation to actin dynamics and dendritic spine morphology, which are dysregulated in FXS model mice that lack FMRP. (sciencemag.org)
  • This resulted in mechanistic insight into the spatio-temporal regulation of HP1 recruitment, chromatin conformational dynamics, templates for similar investigations with 53BP1, and tools for further investigation of nucleosome function in the context of chromatin. (epfl.ch)
  • Names are listed in the order they appear on the scatter plots for each class of proteins. (jci.org)
  • Such considerations are particularly relevant for a highly abundant class of proteins whose physical characteristics are defined by their dynamic nature. (frontiersin.org)
  • Intrinsically disordered proteins (IDP) form a large and functionally important class of proteins that lack an ordered three-dimensional structure. (spie.org)
  • This often necessitates a coarse grained or mesoscopic treatment of the dynamics. (aps.org)
  • Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. (osti.gov)
  • In this paper the first version of a coarse grained model for transmembrane proteins is presented. (pubmedcentralcanada.ca)
  • This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. (pubmedcentralcanada.ca)
  • A severe bottleneck in protein structure prediction is the transition from a coarse-grained to a more detailed structure description and the refinement of structure candidates that are already close to the target structure. (tu-darmstadt.de)
  • MS is an emergent technology for the structural biology of protein assemblies ( 16 ), allowing the interrogation of a wide range of biomolecular systems, including those complicated by polydispersity and dynamics ( 17 , 18 ). (pnas.org)
  • Using them, biologists can gain a better understanding of how incorrectly folded proteins lead to a range of diseases, or how other proteins synthesize adenosine triphosphate (ATP), the fuel that powers many biomolecular motors. (nersc.gov)
  • Summary of the timescales of biomolecular dynamics and the major NMR relaxation techniques. (portlandpress.com)
  • To study the biomolecular dynamics inside of a single living cell Gru. (bio-medicine.org)
  • To study the biomolecular dynamics inside of a single living cell, Gruebele and his team pioneered a hybrid method they've dubbed "Fast Relaxation Imaging," a technique that combines fluorescence microscopy and fast temperature jumps. (bio-medicine.org)
  • Since biomolecular dynamics are predominantly studied in vitro, with the results extrapolated to explain how the same processes would function in a living cell, Gruebele says the new technique has yielded some interesting data that could change standard thinking in the field. (bio-medicine.org)
  • Protein localization mechanisms dictate the functional and structural specialization of cells. (pnas.org)
  • At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their environments. (sciencemag.org)
  • For example, it plays a central role in the folding of linear amino acid chains into functional proteins with a precisely defined structure. (innovations-report.com)
  • With all this functional information, the time is ripe for mechanistic investigation of how lipids perform such diverse regulatory roles, with a special emphasis on how lipids regulate the structure and function of their effector proteins. (asbmb.org)
  • An NIH-funded postdoctoral position is available in the research group of Carol Post at Purdue University ( www.purdue.edu/postlab ) starting immediately to study the functional behavior of protein tyrosine kinases by NMR and other biophysical methods. (weizmann.ac.il)
  • The reduced state displays unprecedented μs-ms conformational dynamics and we propose that this dynamics reflects local and functional unfolding of an α-helix in the active site. (diva-portal.org)
  • Ultrastructural analysis of scrib synapses, in vivo labeling of activity-dependent vesicle recycling, and functional studies using high-frequency stimulation are all consistent with a model by which vesicle dynamics are disrupted in scrib mutants. (jneurosci.org)
  • Actin dynamics and rearrangements of actin filaments are crucial during structural and functional alterations of neurons in response to stress shaping synaptic plasticity and behavior [ 5 ]. (mdpi.com)
  • The recovery stroke is a key step in the functional cycle of muscle motor protein myosin, during which pre-recovery conformation of the protein is changed into the active post-recovery conformation, ready to exersice force. (wiley.com)
  • However, studies over the last several years have provided broad and convincing evidence that some proteins do not adopt a single structure and yet are fully functional. (dovepress.com)
  • In both cases the proton dynamics have important functional consequences. (aps.org)
  • Here, the functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. (osti.gov)
  • Protein Functional Motions: Basic Concepts and Computational Methodologies ( Sotaro Fuchigami, Hiroshi Fujisaki, Yasuhiro Matsunaga, and Akinori Kidera ). (wiley.com)
  • These suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character. (nih.gov)
  • Here, we determine the hierarchy in the protein conformational energy landscape that underlies these motions, based on a series of temperature-dependent magic-angle spinning multinuclear nuclear-magnetic-resonance relaxation measurements in a hydrated nanocrystalline protein. (sciencemag.org)
  • The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow protein side-chain motions, and fast protein backbone motions being activated consecutively. (sciencemag.org)
  • This model shows that changes in either low frequency collective motions or random uncorrelated atomic fluctuations of the protein induced by the binding of a ligand can alter the binding properties of other remote ligand binding sites giving rise to allostery. (bl.uk)
  • Increases in the frequency of vibrational modes and reductions in uncorrelated motions gives rise to positive cooperativity and is equivalent to a stiffening of the protein structure. (bl.uk)
  • On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. (springer.com)
  • Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of Xray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. (archives-ouvertes.fr)
  • 1) To analyze motions in cell motility proteins an algorithm is described to identify and visualize the movements of rigid domains about common hinges in proteins. (illinois.edu)
  • Background: The dynamic motions of many proteins are central to their function. (sciweavers.org)
  • In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. (sciweavers.org)
  • Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. (sciweavers.org)
  • FLIP can be used to study the dynamics of different pools of a protein or can show how a protein diffuses, or is transported through a cell or cellular structure. (nih.gov)
  • Small Heat Shock Proteins (sHSPs) are a diverse family of molecular chaperones that prevent protein aggregation by binding clients destabilized during cellular stress. (pnas.org)
  • This extends the paradigm that intrinsic dynamics are crucial to protein function to include equilibrium fluctuations in quaternary structure, and suggests they are integral to the sHSPs' role in the cellular protein homeostasis network. (pnas.org)
  • HSP18.1 represents the family of class I cytosolic plant sHSPs which accumulate at heat-shock temperatures (≥38 °C) to ≈1% of the total cellular protein ( 19 ). (pnas.org)
  • Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and signaling events that lead to a multitude of biological effects. (springer.com)
  • Protein dimerization and oligomerization are essential to most cellular functions, yet measurement of the size of these oligomers in live cells, especially when their size changes over time and space, remains a challenge. (nature.com)
  • When activated, mTORC1 stimulates cell growth by promoting protein translation and ribosome synthesis, while it inhibits cellular degradation by autophagy ( Chan, 2009 ). (frontiersin.org)
  • Recent advances in chemical biology and molecular imaging technologies have allowed researchers to identify new lipid-binding proteins, specifically manipulate diverse lipid signaling, and directly monitor lipid dynamics and lipid-mediated cellular activities with high spatiotemporal resolution. (asbmb.org)
  • Under the pact, Shamrock will perform structure-activity relationship co-crystallization, synchrotron data collection, and structure determination of an Intra-Cellular Therapies protein target to which inhibitors are bound. (genomeweb.com)
  • In human, 518 protein kinases have been identified in the genome that phosphorylate the majority of cellular proteins and increase the diversity of the proteome by severalfold ( 4 ). (mcponline.org)
  • Consequently, many cellular processes such as endocytosis, migration and morphogenesis rely on proteins that bind directly to membranes and sculpt them into desired shapes. (nanowerk.com)
  • In a new study published in Cell Reports ( 'Membrane-Sculpting BAR Domains Generate Stable Lipid Microdomains' ), Hongxia Zhao working in the Lappalainen laboratory discovered that all BAR domain proteins induce strong clustering of phosphoinositides, which are important lipids involved in regulating protein functions and cellular signalling. (nanowerk.com)
  • These extremely stable protein-lipid scaffolds may contribute to diverse cellular processes by generating lipid phase boundaries at the tips of the BAR domain scaffolds. (nanowerk.com)
  • And, as opposed to the expansive environment of a test tube, there's a lot of cellular furniture for proteins to bump into in living cells. (bio-medicine.org)
  • Proteins are biological macromolecules that are involved in a wide range of cellular processes. (utexas.edu)
  • Thus, it seems logical that actin-binding proteins (ABPs) play a central role in the control of the cellular movements involved in transmigration. (jimmunol.org)
  • The approach also permits multimodal measurements, including fluorescent gel-based analysis of activity in response to varied conditions and treatments, and mass spectrometry-based quantitative identification of labelled proteins. (rsc.org)
  • Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a tag into proteins for relative quantitation by mass spectrometry. (sciencemag.org)
  • Structural proteomics methods which take advantage of recent, cutting-edge mass spectrometry (MS) approaches are coming into their own now as they can map out the conformational space of structurally dynamic, even disordered and unfolded proteins, as well as characterizing heterogeneous assembly pathways, e.g. in amyloid aggregation. (findaphd.com)
  • While the second section contains a survey of the computational methods that have played a critical role in membrane protein structure prediction as well as in providing atomic level insight into the mechanism of the dynamics of membrane receptors. (springer.com)
  • Indeed, colocalization of transmembrane receptors with cytoplasmic signaling components via their interaction with scaffolding proteins has been documented in numerous studies. (jneurosci.org)
  • The largest family of cell surface receptors is formed by the G-protein coupled receptors (GPCRs), which are responsible for most transmembrane signal transduction by hormones and neurotransmitters, as well as for the senses of vision, smell and taste [ 1 - 3 ]. (pubmedcentralcanada.ca)
  • The researchers attached two gold nanoparticles to the protein of interest and observed the distance-dependent interaction of the gold spheres using laser beams. (innovations-report.com)
  • 11 amino acids) has low affinity for LgBiT and hence it was chosen for use in protein:protein interaction (PPI) assays. (news-medical.net)
  • The second model system selected was the interaction between the subunits of protein kinase A (PKA). (news-medical.net)
  • Reversible interaction dynamics of proteins in living cells. (news-medical.net)
  • The research programs encompass an integrated structural biology and biophysics approach to understand protein dynamics, protein recognition and interaction by investigating intermediate protein active conformations (excited state), protein dynamics modulation and the subsequently changes of its activities. (weizmann.ac.il)
  • The project involves biochemistry in terms of protein expression, purification and establishing protein-protein interaction report systems. (weizmann.ac.il)
  • Interaction of MyoVa with ZBP1 was evident by coimmunoprecipitation of endogenous and overexpressed proteins. (jneurosci.org)
  • The interaction between the receptor and its target protein is mediated by a third protein, a trimeric GTP-binding protein (G-protein). (pubmedcentralcanada.ca)
  • molecular dynamics, residue correlation studies and residue interaction network (RIN) analyses were conducted, providing a deep insight into the 599th residue and its impact on the overall dynamics of BRAF protein. (rsc.org)
  • Moreover, 31 P solid-state NMR spectroscopy can be used to investigate the interaction of peptides, proteins and drugs with phospholipid head groups [11-14]. (scirp.org)
  • A. Watts, "Solid-State NMR Approaches for Studying the Interaction of Peptides and Proteins with Membranes," Biochim Biophys Acta, Vol. 37, No. 2, 1998, pp. 297-318. (scirp.org)
  • The interaction between Plasmodium vivax Duffy binding protein II (PvDBPII) and human erythrocyte Duffy antigen is necessary for blood stage infections. (ajtmh.org)
  • Plasmodium vivax interaction with the human Duffy blood group glycoprotein: identification of a parasite receptor-like protein. (ajtmh.org)
  • found that through its interaction with the scaffolding protein CYFIP1, FMRP sequesters the translation-initiating factor eIF4E and tempers the CYFIP1-mediated facilitation of Rac1-cofilin signaling. (sciencemag.org)
  • In contrast to folded proteins, the primary sequence of intrinsically disordered proteins (IDPs) does not code for a single, energetically stable fold, but occupies a flatter free-energy surface, spanning a continuum of different conformations. (frontiersin.org)
  • The research team headed by Mikael Akke at the Center for Molecular Protein Science of Lund University used NMR spectroscopy to create a snapshot of the misfolded structure, which had not previously been seen. (innovations-report.com)
  • Using temperature-dependent radiolysis and mass spectroscopy, they are able to identify where water is binding tightly or loosely on the surface of a protein and how it is influencing a protein's function. (bnl.gov)
  • The predictions of this model are tested using laser Raman spectroscopy of solid samples to study low frequency modes in proteins and an allosteric model compound. (bl.uk)
  • There has been a tremendous development in NMR spectroscopy (both hardware and pulse programs) that have enabled detailed studies of protein dynamics. (diva-portal.org)
  • Flexibility can also be observed in very high-resolution electron density maps produced by X-ray crystallography, particularly when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K). Information on the frequency distribution and dynamics of local protein flexibility can be obtained using Raman and optical Kerr-effect spectroscopy in the terahertz frequency domain. (wikipedia.org)
  • The meeting will cover a range of spectroscopic techniques for investigating the dynamics of macromolecules in the sub-picosecond to microsecond time domain, including polarization methods (CD, TRORD), resonance raman, infrared, optical absorption, and 2D spectroscopy methods. (bio.net)
  • Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales. (frontiersin.org)
  • Solid-state NMR spectroscopy is routinely used to determine the structural and dynamic properties of both membrane proteins and peptides in phospholipid bilayers [1-26]. (scirp.org)
  • From the perspective of the perpetuated lipids, 2 H solid-state NMR spectroscopy can be used to probe the effect of embedded proteins on the order and dynamics of the acyl chains of phospholipid bilayers [8-13]. (scirp.org)
  • The secondary structure of 13 C = O site-specific isotopically labeled peptides or proteins inserted into lipid bilayers can be probed utilizing 13C CPMAS solid-state NMR spectroscopy [15-18]. (scirp.org)
  • This simulation of a tyrosine kinase reveals how the protein changes shape. (nersc.gov)
  • Fortunately, over the past few years, rapid increases in computing power and better simulation programs have made it possible to visualize protein dynamics like never before. (nersc.gov)
  • A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. (mdpi.com)
  • Using MD simulation techniques at the atomistic level allows for the exploration of ligand positioning and the initialization of protein activation. (pubmedcentralcanada.ca)
  • We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. (archives-ouvertes.fr)
  • Thus, in this work we studied the dynamics and stability profiles of wild-type human prion protein by Molecular Dynamics (MD) simulation at different solvent temperatures. (scirp.org)
  • Molecular dynamics (MD) simulation techniques have been employed to investigate structure and function relationships in cell motility proteins at atomic resolution. (illinois.edu)
  • A team led by Prof. Dr. Thorsten Hugel from the Institute of Physical Chemistry and the BIOSS Centre for Biological Signalling Studies at the University of Freiburg and Prof. Dr. Carsten Sönnichsen from the Johannes Gutenberg University Mainz have used a new method to record the dynamics of individual proteins in action over 24 hours. (innovations-report.com)
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • The research includes and extends beyond structural characterization to explore the role of conformational dynamics in regulating biological mechanisms. (weizmann.ac.il)
  • Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. (osti.gov)
  • The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. (portlandpress.com)
  • S100 proteins play a crucial role in multiple important biological processes in vertebrate organisms acting predominantly as calcium signal transmitters. (rcsb.org)
  • As a result, the evolutionary dynamics in variable environments has been barely addressed, even though this is considered central to the evolution of complex biological functions. (amolf.nl)
  • Protein search for specific binding sites on DNA is a fundamental biological phenomenon associated with the beginning of most major biological processes. (rice.edu)
  • They've also simulated the conformational and energy changes that proteins involved in DNA replication must undergo in order to rapidly copy DNA strands. (nersc.gov)
  • Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. (jci.org)
  • Here I have studied the conformational dynamics and thermodynamics of three model systems: adenylate kinase (Adk), Peroxiredoxin Q (PrxQ) and the structural protein S16. (diva-portal.org)
  • The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. (mdpi.com)
  • Fluorescence techniques were used to study the motion of protein domains in adenylate kinase, and to characterize the formation of myelin in neuron Schwann cell co-cultures. (illinois.edu)
  • Several likely protein candidates involved in this signaling cascade have been identified, including proline-rich tyrosine kinase 2 (PYK2), which may phosphorylate the Kv1.2 channel protein and protein kinase C (PKC) family members, which may phosphorylate PYK2. (jaoa.org)
  • Here we apply a powerful experimental scheme that integrates genetics with high-throughput localization to discover StpX, an uncharacterized bitopic membrane protein that modulates stalk elongation and is sequestered to the stalk. (pnas.org)
  • Thus, at the submicron scale the localization and the mobility of a protein are precisely regulated in space and time and are important for the correct organization of a subcellular compartment or organelle such as the stalk. (pnas.org)
  • Dissecting the underlying molecular mechanisms for localization is facilitated by the availability of suitable proteins that can be used as molecular probes. (pnas.org)
  • Directed transport of the mRNA binding protein, zipcode binding protein1 (ZBP1), into developing axons is believed to play an important role in mRNA localization and local protein synthesis. (jneurosci.org)
  • its contribution to the trafficking of mRNA binding proteins important for mRNA localization is not well understood. (jneurosci.org)
  • Although asymmetric localization of PCP proteins is central to their function, we understand little about PCP protein localization during convergent extension. (elifesciences.org)
  • Together, these results provide a dynamic and quantitative view of PCP protein localization during convergent extension and suggest a complex and intimate link between the dynamic localization of core PCP proteins, actomyosin assembly, and polarized junction shrinking during cell intercalation in the closing vertebrate neural tube. (elifesciences.org)
  • but less is known about PCP protein localization dynamics during cell intercalation. (elifesciences.org)
  • Gruebele said that in living cells, "You really expect a lot of heterogeneity, that there would be a lot of differences among different areas of the cell, that there might be areas of the cell where the protein might be very stable, and other places where it's very unstable. (bio-medicine.org)
  • The reason for this heterogeneity is that proteins have to thread their way through whatever channel happens to be available, Gruebele said. (bio-medicine.org)
  • Thorough and intuitive, Membrane Protein Structure Predicitons: Methods and Protocols seeks to aid scientists in the further study of membrane protein structure and function. (springer.com)
  • Mitochondrial outer membrane protein which regulates mitochondrial fission. (uniprot.org)
  • How a membrane protein is associated with the lipid membrane reflects the function of the protein. (pubmedcentralcanada.ca)
  • Finally, recent progress in the use of 13C relaxation to probe the dynamics of protein side chains is detailed mainly for the dynamics of non-deuterated proteins on picosecondnanosecond timescales. (ingentaconnect.com)
  • Proteins are however intrinsically dynamic, they can exhibit conformational modes of vastly differing amplitudes, from local bond fluctuations to folding/unfolding transitions, on timescales varying from femtoseconds to days. (frontiersin.org)
  • The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. (portlandpress.com)
  • The method is also well suited to studying aquaporins - proteins embedded in cell membranes that regulate water flow - or ion channels, which transport ions along with water. (bnl.gov)
  • RNA binding proteins not only transport but also regulate translation of mRNAs ( Kiebler and Bassell, 2006 ). (jneurosci.org)
  • This review focuses on recently published evidence that endothelial ABPs, such as cortactin, myosin, or α-actinin, regulate leukocyte extravasation by controlling actin dynamics, biomechanical properties of endothelia, and signaling pathways, such as GTPase activation, during inflammation. (jimmunol.org)
  • This same separation of time scales does, however, allow PTPs to control EGFR association with adapter proteins that regulate downstream signaling. (upenn.edu)
  • The three-dimensional organization of chromatin as well as histone post-translational modifications (PTMs) regulate recruitment of chromatin-associated effector proteins (effectors). (epfl.ch)
  • Cell membranes are comprised of a heterogeneous mixture of lipids and proteins. (rug.nl)
  • Studies by Pekka Lappalainen laboratory at Institute of Biotechnology, University of Helsinki, Finland, now reveal that BAR domain proteins not only bend membranes, but also generate extremely stable lipid microdomains by inhibiting the lateral diffusion of certain lipids nearly completely. (nanowerk.com)
  • It turns out that the protein superoxide dismutase interchanges between its normal structure and a misfolded form. (innovations-report.com)
  • Knowledge of the misfolded protein structure potentially makes possible future efforts to rationally design drugs that prevent the misfolding event and hence the development of ALS. (innovations-report.com)
  • Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. (springer.com)
  • The function of proteins - the molecular tools of the cell - is governed by the interplay of their structure and dynamics. (innovations-report.com)
  • The first section details the procedures used for measurements of structure and dynamics of membrane proteins. (springer.com)
  • The ubiquitous liquid is key to the structure, folding and stability of proteins, but one of the still unanswered questions in the study of the structure and function of proteins and DNA is their exact relationship to their water environment. (bnl.gov)
  • That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. (ingentaconnect.com)
  • Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. (ingentaconnect.com)
  • Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function. (ingentaconnect.com)
  • This thesis explores the possible uses of dynamical fluctuations in protein structure for ligand binding and catalysis. (bl.uk)
  • Postdoc position in NMR protein structure and dynamics, Purdue University U.S.A. (weizmann.ac.il)
  • During the last ten years significant efforts have been invested to understand the structure and dynamics of the actual catalyst (i. e. the enzyme). (diva-portal.org)
  • We also studied the structure and dynamics of the plant enzyme PrxQ in both reduced and oxidized states. (diva-portal.org)
  • Finally, we solved the structure of S16 from Aquifex aeolicus and propose a model suggesting a link between thermostability and structure for a mesophilic and hyperthermophilic protein pair. (diva-portal.org)
  • However, the structure and dynamics of Bm R1 protein is yet to be elucidated. (mdpi.com)
  • Here we study the three dimensional structure and dynamics of Bm R1 protein using comparative modeling, threading and ab initio protein structure prediction. (mdpi.com)
  • Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. (mdpi.com)
  • This thesis is focused on the structure and dynamics of CaM and CaM mutant constructs bound to the target peptides of the NOS CaM-binding domain at saturating and physiological concentrations of Ca2+. (uwaterloo.ca)
  • Therefore, we decided to undertake, using nuclear magnetic resonance methods, a comparative study of the structure and dynamics of native and thionylated human S100A1 in its apo and holo states. (rcsb.org)
  • In this paper, we present the results obtained for both forms of this protein in its holo state and compare them with the previously published structure of native apo-S100. (rcsb.org)
  • The existence of protein switches provides a great challenge to structure prediction algorithms as well as to our understanding of the process of protein structure evolution. (utexas.edu)
  • This is of great practical interest as experimental determination of protein structure is difficult and costly, whereas sequencing is relatively simple and cheap. (tu-darmstadt.de)
  • To this end so-called structural profiles are defined which may act as a link between protein sequence and structure for the task of structure prediction. (tu-darmstadt.de)
  • S. Abu-Baker and G. Lorigan, "Solid-State NMR Spectroscopic Approaches to Investigate Dynamics, Secondary Structure and Topology of Membrane Proteins," Open Journal of Biophysics , Vol. 2 No. 4, 2012, pp. 109-116. (scirp.org)
  • Structure of the HIV spike protein in its closed state, which makes it less detectable to immune system. (scitechdaily.com)
  • In two newly published studies, researchers detail the structure and dynamics of the HIV spike protein, which is used by the virus uses to fuse with and enter cells. (scitechdaily.com)
  • The determination of the structure of this closed configuration of the HIV spike protein and the direct visualization of its fast openings represent a major step forward for drug and vaccine design," Mothes said. (scitechdaily.com)
  • The discovery of IDPs has challenged the traditional paradigm of protein structure which states that protein function depends on a well-defined three-dimensional structure. (spie.org)
  • Due to their high conformational flexibility and the lack of ordered secondary structure, it is challenging to study the flexible structure, dynamics and energetics of these proteins with conventional methods. (spie.org)
  • The structure and function of chaperones like Hsp70 and GroEL has been studied extensively, but traditional methods are not well suited to detect the crucial conformational changes of their client proteins. (amolf.nl)
  • ii) Understand how HP1 binding alters the conformational dynamics of chromatin secondary structure. (epfl.ch)
  • A protein spontaneously folds into the most stable structure with minimum free energy, which is known as protein folding. (rug.nl)
  • Resolving protein structure at different steps of bio-chemical reactions or in a folding process is a great challenge. (rug.nl)
  • Also, solid-state NMR spectroscopic studies can be utilized to ascertain pertinent informa- tion on the backbone and side-chain dynamics of 2 H- and 15 N-labeled proteins, respectively, in phospholipid bilayers [19-26]. (scirp.org)
  • One feature of working with GFP variants, photobleaching, has recently been combined with an older technique known as fluorescence recovery after photobleaching (FRAP) to study protein kinetics in vivo. (nih.gov)
  • Gruebele says that although temperature jumps have been used for some time to study the kinetics of chemical reactions in vitro, that method is limited by what he calls "homogenous kinetics," or an inability to see the dynamics in different areas of the cell. (bio-medicine.org)
  • On the other hand, fluorescence microscopy allows researchers to see inside of cells, but it precludes them from studying cell dynamics and kinetics. (bio-medicine.org)
  • According to Gruebele, the proteins studied in vivo using the new technique were more stable, their thermal denaturation was more gradual and their folding kinetics were slower than the same proteins studied in vitro. (bio-medicine.org)
  • Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. (jci.org)
  • Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. (jci.org)
  • Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. (jci.org)
  • In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. (jci.org)
  • Oxazolone analogs, as well-known intermediates in the synthesis of green fluorescent protein derivatives, have attracted relatively little attention in terms of their photoswitching ability. (hindawi.com)
  • The compound 4EGI-1, which inhibits the formation of eIF4E-mediated translational machinery, reduced protein synthesis and restored a balance with actin dynamics, as well as improved hippocampal synaptic function and dendritic morphology and learning behaviors in FXS model mice. (sciencemag.org)
  • Thus, inhibiting eIF4E-mediated protein synthesis may be therapeutic in FXS patients. (sciencemag.org)
  • They collaborate on method development in structural proteomics and use of such data for computational modelling of structural dynamics. (findaphd.com)
  • The current view of their chaperone action is that they bind unfolding "client" proteins, thereby preventing their irreversible aggregation ( 9 - 12 ). (pnas.org)
  • With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. (pubmedcentralcanada.ca)
  • The mechanism by which mutations in SOD1 causes ALS is still unknown, but it is believed that mutant CuZnSOD proteins misfold followed by aggregation into high molecular species that ultimately lead to the death of motor neurons. (diva-portal.org)
  • Human prion diseases are caused by misfolding or aggregation of the Human Prion Protein (HuPrP). (omicsonline.org)
  • Mechanisms exist in prokaryotic and eukaryotic cells to direct specialized proteins to distinct subcellular sites where they execute topologically constrained functions, for example, morphogenesis ( 1 ). (pnas.org)
  • However, it is also induced under stress conditions, remodeling the eukaryotic cell by regulating energy, protein, and lipid homeostasis. (frontiersin.org)
  • Nanowerk News ) Eukaryotic cells are compartmentalized by membranes, whose shape and dynamics are precisely regulated to maintain their correct functions. (nanowerk.com)
  • One mechanism by which FMRP represses translation is through its association with cytoplasmic FMRP-interacting protein 1 (CYFIP1), which subsequently sequesters and inhibits eukaryotic initiation factor 4E (eIF4E). (sciencemag.org)
  • They are typically composed of multiple protein-binding domains and hence are important in forming a linked network of synaptic constituents and the underlying cytoskeleton. (jneurosci.org)
  • Raw independently influences terminal dendrite elongation through a mechanism that involves modulation of the cytoskeleton, and this pathway is likely to involve the RNA-binding protein Argonaute 1 (AGO1), as raw and AGO1 genetically interact to promote terminal dendrite growth but not adhesion. (biologists.org)
  • When the protein is transferred to a solution with a slightly acidic pH of 5.7, hydrophobic amino acid residues become exposed to the surrounding medium, enabling them to bind the fluorescent probe 8,1-ANS. (diva-portal.org)
  • At this pH-induced open state, Mn2+ and Ca2+ bind to the manganese-stabilizing protein. (diva-portal.org)
  • A model is presented in which the manganese-stabilizing protein undergoes a pH-dependent conformational change that in turn influences its capacity to bind calcium and manganese. (diva-portal.org)
  • With temperature jumps and pressure jumps, you can do those experiments very quickly, but you don't get any imagery that lets you see if proteins fold faster in one region and slower in another," Gruebele said. (bio-medicine.org)
  • They can see what happen when a protein is given just enough energy to teeter on the edge of a conformational change. (nersc.gov)
  • When a ligand binds to the extracellular domain of the GPCR, the receptor undergoes a conformational change that enables the activation of the G-protein [ 4 ]. (pubmedcentralcanada.ca)
  • To study the conformational change of a protein switch with a fixed sequence between two metastable states in conformational space, we proposed a new algorithm, named "Chain Growth", to calculate reaction pathways. (utexas.edu)
  • AFM has been used to investigate the supramolecular architecture of photosynthetic membranes in bacteria and algae, revealing how photosynthetic proteins are organized and interact with each other and how the membranes are synthesized to optimize the photosynthetic efficiency in nature. (news-medical.net)
  • In wild-type synapses, Scrib is tightly colocalized with Dlg, a protein associated with both presynaptic and postsynaptic membranes. (jneurosci.org)
  • BAR proteins can create stable lipid microdomains at cell membranes. (nanowerk.com)
  • T. A. Cross and S. J. Opella, "Solid-State NMR Structural Studies of peptides and Proteins in Membranes," Current Opinion in Structural Biology, Vol. 4, No. 4, 1994, pp. 574-581. (scirp.org)
  • The purpose of antibody protein sequencing is to accurately deduce every single amino acid present in the primary sequence. (news-medical.net)
  • Likewise, internal proton transfer between the chromophore of green fluorescent protein (GFP) and amino acids on the inside of the beta barrel are important both in the ground and excited state. (aps.org)
  • At a neutral pH of 7.2, the hydrophobic amino acid residues that are most likely located inside the beta barrel are "closed" and the protein binds neither Mn2+ nor Ca2+ ions. (diva-portal.org)
  • The human prion protein (hPrP) is a membrane N-linked glycosylphosphatidylinositol-anchored glycoprotein that has 253 amino acids when it is newly synthesized. (scirp.org)
  • Measurement of the global proteomic effects of estradiol by stable isotope labeling by amino acids in cell culture (SILAC) resulted in identification of 103 estrogen-regulated proteins, with only 40 of the corresponding genes having estrogen response elements. (mcponline.org)
  • High-resolution microscopic analysis has precisely revealed the control of microtubule dynamics by individual microtubule-associated proteins (MAPs) in vitro. (nih.gov)
  • Methods: DRR1 domains were cloned and expressed as recombinant proteins to perform in vitro analysis of actin dynamics (binding, bundling, polymerization, and nucleation). (mdpi.com)
  • You have a very simple, very homogenous environment when you study proteins in vitro," he said. (bio-medicine.org)
  • D - F ) Effect of denervation surgery and clenbuterol treatment on the FSRs of myofibril, glycolytic, and mitochondrial proteins. (jci.org)
  • Promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface independently of the mitochondrial fission FIS1 and MFF proteins. (uniprot.org)
  • Mitochondrial elongation factor 2 is a protein that in humans is encoded by the MIEF2 gene. (wikipedia.org)
  • It can directly recruit the fission mediator dynamin-related protein 1 (Drp1) to the mitochondrial surface. (wikipedia.org)
  • Downregulated in renal cell carcinoma 1 (DRR1) protein was characterized as the link between stress, actin dynamics, neuronal function, and cognition. (mdpi.com)
  • Conclusions: DRR1 impacts actin dynamics in several ways with implications for cytoskeletal dynamics in stress physiology and pathophysiology. (mdpi.com)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
  • The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. (sciweavers.org)
  • This occurs through gaps in the pericyte layer that coincide with regions of the BM that contain less extracellular matrix proteins and, therefore, pose a thinner barrier for the transmigrating leukocyte ( 5 , 6 ). (jimmunol.org)
  • P. C. Dave, E. K. Tiburu, K. Damodaran and G. A. Lorigan, "31P and 2H Solid-State NMR Spectroscopic Studies of the Transmembrane Domain of the Membrane-Bound Protein Phospholamban," Biophysical Journal, Vol. 86, 2004, pp. 1564-1573. (scirp.org)
  • Protein dynamics can be characterized by relaxation parameters obtained from traditional 2D HSQC based NMR experiments. (hindawi.com)
  • Detailed dynamics information is crucial for the understanding of protein function and biochemical and biophysical properties, which can be obtained using NMR relaxation techniques. (ingentaconnect.com)
  • In this review, 13C relaxation of methine, methylene and methyl groups with and without 1H decoupling are described briefly for a better understanding of how spin relaxation is associated with motional (dynamics) parameters. (ingentaconnect.com)
  • 22 ] investigated two green fluorescent protein chromophore analogs and proposed a multicoordinate relaxation mechanism. (hindawi.com)
  • Flexibility in folded proteins can be identified by analyzing the spin relaxation of individual atoms in the protein. (wikipedia.org)
  • Furthermore, transfection of MAP cDNA into fibroblasts and subsequent analysis using microinjection of caged fluorescein-labeled tubulin and photoactivation have enabled the function of MAPs in microtubule dynamics to be studied in detail in vivo. (nih.gov)
  • CHAMPAIGN, Ill. A new technique to study protein dynamics in living cells has been created by a team of University of Illinois scientists, and evidence yielded from the new method indicates that an in vivo environment strongly modulates a protein's stability and folding rate, according to research accepted for publication in the journal Nature Methods and posted on the journal's Web site Feb. 28. (bio-medicine.org)
  • We performed a two-color photon echo experiment on a bacterial reaction center that enabled direct visualization of the coherence dynamics in the reaction center. (sciencemag.org)
  • An ideal candidate will have experience in multidimensional NMR, bacterial expression of proteins, ITC and computation. (weizmann.ac.il)
  • In addition, the AFM (located in the Centre for Cell Imaging) is used to explore the assembly dynamics of bacterial microcompartment shell proteins and the formation process of shell facets. (news-medical.net)
  • Moreover, IDPs are overrepresented among proteins implicated in disease, including various cancers and neurodegenerative disorders. (dovepress.com)
  • p>Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors. (uniprot.org)
  • The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. (harvard.edu)
  • Study of how cells perceive and interpret stimuli from their environment and how those signals modify gene expression and the activity of the cell's regulatory proteins. (iric.ca)
  • Diversity and natural selection in Plasmodium vivax Duffy binding protein gene. (ajtmh.org)
  • FXS is caused by silencing of the FMR1 gene, which encodes fragile X mental retardation protein (FMRP), an mRNA-binding protein that represses the translation of its target mRNAs. (sciencemag.org)
  • The number of phase cycling steps in these 3D pulse sequences was restricted to two in order to minimize the time required to perform the dynamics measurements. (hindawi.com)
  • Antibodies targeting specific proteins can be integrated into the probe to give specific measurements of protein levels. (eurekalert.org)
  • Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. (harvard.edu)
  • This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. (sciencemag.org)
  • In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular level fluctuations. (springer.com)
  • on membrane insertion of bacteriophage M13 procoat protein, giving emphasis to structural fluctuations during assocn. (epfl.ch)
  • The stalk is a cylindrical protrusion of all envelope layers (inner membrane, periplasm, outer membrane, and S-layer) at the old cell pole and encloses cytoplasmic material that is free of chromosomal DNA, ribosomes, and most cytoplasmic proteins ( 7 , 8 ). (pnas.org)
  • Above 160 K there was a strong coupling between solvent and protein motion. (sciencemag.org)
  • A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. (aps.org)
  • The other method uses evolutionary profiles and contact maps of the wild-type proteins. (utexas.edu)
  • Plasmodium vivax Duffy binding protein: a modular evolutionary proposal. (ajtmh.org)
  • It therefore follows that the dynamic requirements of a protein are evolutionary constrained. (sciweavers.org)
  • Together with our experimental collaborator Bert Poolman , we aim to unravel the lipid-mediated driving forces underlying protein sorting and clustering, and predict physical mechanisms that could be relevant in real cells. (rug.nl)
  • Due to the bright signal of the NanoBiT ® PPI Assay, fusion proteins are expressed either at or near physiological levels in numerous cases that help reduce experimental artifacts. (news-medical.net)
  • Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. (springer.com)
  • Add the expertise of experimental biologists like Kuriyan, who put real proteins through the wringer to learn how they work, and the Lab has an ideal blend of theory, practical know-how, and computing power to create almost lifelike movies. (nersc.gov)
  • these results are consistent with experimental reports showing that protein mutants in those positions are related to the development of disease. (scirp.org)
  • To study the dynamics of A-beta and tau, we needed a way to trigger the expression of both proteins and a tool to track dynamic changes of protein expression," says lead author Feng Liang, PhD, a research fellow at the Rowland Institute. (eurekalert.org)
  • The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves. (wikipedia.org)
  • In our laboratory we, in collaboration with our biology colleagues, study a variety of systems with an ultimate aim of learning the connection between dynamics and activity. (tifr.res.in)
  • New technique allows study of protein folding, dynamics in li. (bio-medicine.org)
  • CHAMPAIGN Ill. A new technique to study protein dynamics in living c. (bio-medicine.org)
  • We haven't really been able to study dynamics, to see if a chemical reaction like protein folding varies inside of a living cell," he said. (bio-medicine.org)
  • We present a theoretical study of the protein target search dynamics in the presence of semispecific binding sites which are viewed as traps. (rice.edu)
  • In this protocol, we demonstrate the application of eN&B by quantifying receptor clustering dynamics using electron-multiplying charge-coupled device (EMCCD)-based total internal reflection microscopy (TIRF) imaging. (nature.com)
  • Transport of mRNA to distal compartments in neurons, such as growth cones and dendritic spines, ensures local translation of proteins in response to receptor signaling. (jneurosci.org)
  • In other methods, a protein or enzyme is merely separated into two fragments. (news-medical.net)
  • But interesting changes in proteins, such as the rotation of a portion of the ATP-making enzyme, often occur in the microsecond to millisecond time scale - up to nine orders of scale slower than a femtosecond. (nersc.gov)
  • In many cases there exists a strong coupling between enzyme dynamics and function. (diva-portal.org)
  • I will discuss an interesting connection between the proton transfer dynamics in GFP and those in an enzyme, ketosteroid isomerase (KSI), bound to substrate analogs. (aps.org)