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Conformation protein

Averbukh I Sh, Blumenfeld L A, Kovarsky V A and Perelman N F 1986 A model of the mechanism of enzyme action in terms of protein conformational relaxation Blochim. Blophys. Acta. 873 290-6... [Pg.2848]

M. Levitt and Shneior Lifson. Refinement of protein conformation using a macromolecular energy minimization procedure. J. Mol. Biol., 46 269-279, 1969. [Pg.93]

Gibson K D and H A Scheraga 1987. Revised Algorithms for the Build-up PrcKedure for Predi Protein Conformations by Energy Minimization. Journal of Computational Chemistry 8 826-83-... [Pg.575]

Levitt M 1976. A Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. Journal of Molecular Biology 104 59-107. [Pg.576]

Levitt M1992. Accurate Modeling of Protein Conformation by Automatic Segment Matching. Journal of Molecular Biology 226 507-533. [Pg.576]

Molecular dynamics simulations of proteins often begin with a known structure (such as an X-ray diffraction structure) that you want to maintain during equilibration. Since the solvent may contain high energy hot spots, equilibration of the protein and solvent at the same time can change the protein conformation. To avoid this, select only the water molecules and run a molecular dynamics equilibration. This relaxes the water while fixing the protein structure. Then deselect the water and equilibrate the whole system. [Pg.75]

JM Troyer, EE Cohen. Protein conformational landscapes Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23 97-110, 1995. [Pg.90]

MJ Sippl, S Weitckus. Detection of native-like models for ammo acid sequences of unknown thi ee-dimensional stiaicture in a data base of known protein conformations. Proteins 13 258-271, 1992. [Pg.303]

M Levitt. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226 507-533, 1992. [Pg.305]

TF Flavel, ME Snow. A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 217 1-7, 1991. [Pg.305]

W Braun, N. Go. Calculation of protein conformations by proton—proton distance constraints A new efficient algorithm. J Mol Biol 186 611-626, 1985. [Pg.305]

EE Cohen, ID Kuntz. Tertiary stiaicture prediction. In CD Easman, ed. Prediction of Protein Structure and the Principles of Protein Conformation. New York Plenum Press, 1989, pp 647-705. [Pg.305]

M Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104 59-107, 1976. [Pg.308]

M Vasquez, ElA Scheraga. Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. J Biomol Struct Dyn 5 705-755, 1988. [Pg.309]

Fasman, G.D. Protein conformational prediction. Trends Biochem. Sci. 14 295-299, 1989. [Pg.371]

Several different kinds of noncovalent interactions are of vital importance in protein structure. Hydrogen bonds, hydrophobic interactions, electrostatic bonds, and van der Waals forces are all noncovalent in nature, yet are extremely important influences on protein conformations. The stabilization free energies afforded by each of these interactions may be highly dependent on the local environment within the protein, but certain generalizations can still be made. [Pg.159]

The factors accounting for the stabilization of protein conformation are shown in... [Pg.13]

Thermodynamically it would be expected that a ligand may not have identical affinity for both receptor conformations. This was an assumption in early formulations of conformational selection. For example, differential affinity for protein conformations was proposed for oxygen binding to hemoglobin [17] and for choline derivatives and nicotinic receptors [18]. Furthermore, assume that these conformations exist in an equilibrium defined by an allosteric constant L (defined as [Ra]/[R-i]) and that a ligand [A] has affinity for both conformations defined by equilibrium association constants Ka and aKa, respectively, for the inactive and active states ... [Pg.14]

Linderstrom-Lang, A., and Schellman, P. (1959). Protein conformation. Enzymes 1 443-471. [Pg.20]

Ikura M, Ames JB (2006) Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily two ways to promote multifunctionality. Proc Natl Acad Sci USA 103 1159-1164... [Pg.295]

A basic concept in receptor pharmacology is the idea of orthosteric and allosteric interaction. Orthosteric interaction occurs when two molecules compete for a single binding domain on the receptor. With allosteric interactions two molecules each have their own binding domain on the receptor and the two interact through effects on the protein (conformational change). Tims, with orthosteric interactions only one molecule may occupy the receptor at any one instant whereas with allosteric interactions both molecules can bind to the receptor at the same time. There are implications for... [Pg.452]

Mosser, D.D., Kotzbauer, P.T., Sarge, K.D., Morimoto, R.I. (1990). In vitro activation of heat shock transcription factor DNA binding by calcium and biochemical conditions that affect protein conformation. Proc. Natl. Acad. Sci. USA 87, 3748-3752. [Pg.458]


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Adsorbed proteins, conformation

Amide Relevant Conformations in Proteins

Anti conformation peptides and proteins

Applications of Hydrogen Exchange to Study Protein Conformations and Dynamics

Calcium-binding protein, helix conformation

Characterization of Protein Conformation in an Oligomer-Specific Fashion

Conformation in proteins

Conformation of membrane proteins

Conformation of protein

Conformation peptides and proteins

Conformation photonic proteins

Conformation unfolded proteins

Conformational Analysis of Proteins Ramachandrans Method

Conformational Change in Native Proteins

Conformational Dynamics in Weakly Structured Regions of Proteins

Conformational analysis protein crystallography

Conformational behaviour protein folding

Conformational change of proteins

Conformational changes in proteins

Conformational changes of the protein

Conformational flexibility, of proteins

Conformational microstates proteins

Conformational protein

Conformational protein

Conformational sampling proteins

Conformational search proteins

Conformational studies proteins

Conformational substates in proteins

Conformations heat shock proteins

Conformations of prion proteins

Conformations proteins, review

Determination of protein conformation

Enzyme protein modification,conformational

Estimations of conformational fractions in a protein

Finding Using Conformationally Constrained Peptides Mimicking Exposed Protein Epitopes

Fluorescence correlation spectroscopy protein conformational studies

Folded proteins, conformational stability

Global conformational changes protein backbone

Haem proteins conformation change

Heme proteins conformation

Iron-sulfur proteins conformational change

Ligand and Protein Conformational Change

Lipid-binding proteins conformational similarity

Measuring Conformational Dynamics of Proteins by Hydrogen Exchange

Native conformation of protein (

Neurologic diseases, protein conformation

Novel Amino Acid-Derived Template Molecules For Protein Epitope Mapping Using Conformationally Constrained Small Peptides

Pheromone binding protein conformational changes

Pleated sheets, protein conformations

Prion protein conformation analysis

Protecting the Native Conformation and Activity of Proteins

Protein , conformational states

Protein , conformational states compact denatured state

Protein , conformational states denaturation

Protein , conformational states dynamic properties

Protein , conformational states local unfolding

Protein , conformational states packing defects

Protein carbohydrate thermodynamics 1/887- conformation

Protein catalytic, conformational

Protein conformation change probing

Protein conformation space

Protein conformational change

Protein conformational change flexibility

Protein conformational changes, monitoring

Protein conformational changes, monitoring techniques

Protein conformational dynamics

Protein conformational entropy

Protein conformational features

Protein engineering, conformational

Protein engineering, conformational variability

Protein folding conformational change

Protein folding conformational unfolding model

Protein folding native conformations

Protein kinase conformational changes

Protein loop conformations

Protein main-chain conformation

Protein structure coil conformation

Protein structure loop conformation

Protein structure random coil conformation

Protein three-dimensional conformation

Protein, analysis conformations

Protein, proteins conformational flexibility

Protein-conformation changes

Protein-inhibitor complexes, conformational

Protein-inhibitor complexes, conformational energies

Protein-ligand conformations

Protein-nucleic acid interactions conformational aspects

Proteins (also conformation

Proteins active conformation

Proteins conformation prediction

Proteins conformation pressure

Proteins conformational analysis

Proteins conformational behavior

Proteins conformational flexibility

Proteins conformational fluctuations

Proteins conformational mobility

Proteins conformational stability

Proteins conformational substates

Proteins fibrous conformations

Proteins globular conformations

Proteins ligand-induced conformational

Proteins solution conformation

Proteins structure and conformation

Rate constants protein conformation changes

Ribosome, protein conformation role

Secondary protein structure coil conformation

Secondary protein structure loop conformation

Secondary protein structures alternative conformations

Sialic acids protein conformation, effect

Side chain conformation tertiary protein structure

Signal peptide protein conformation role

Simultaneous Ligand and Protein Conformational Change

Solvation and Conformation of Proteins

Spectroscopy protein conformation

Template-assembled synthetic protein conformation

The Conformation of Polypeptides and Proteins

Two Types of Protein Conformations Fibrous and Globular

Unfolded proteins backbone conformations

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