Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides

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Title: Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides
Alternative Title: Monte Carlo study of cooperativity in homopolypeptides
Author: Kolinski, Andrzej ; Skolnick, Jeffrey
Abstract: A discretized model of globular proteins is employed in a Monte Carlo study of the helix-coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal structures to be represented at the level of 1 A resolution. Furthermore, the Monte Carlo dynamic scheme is capable of moving elements of assembled secondary and supersecondary structure. The potentials of mean force for the interactions are constructed from the statistics of a set of high resolution x-ray structures of nonhomologous proteins. The cooperativity of formation of ordered structures is found to be larger when the major contributions to the conformational energy of the low temperature states come from hydrogen bonds and short range conformational propensities. The secondary structure seen in the folded state is the result of an interplay between the short and long range interactions. Compactness itself, driven by long range, nonspecific interactions, seems to be insufficient to generate any appreciable secondary structure. A detailed examination of the dynamics of highly helical model proteins demonstrates that all elements of secondary structure are mobile in the present algorithm, and thus the folding pathways do not depend on the use of a lattice approximation. Possible applications of the present model to the prediction of protein 3D structures are briefly discussed.
Description: ©1992 American Institute of Physics The electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/9412/1 DOI:10.1063/1.463317
Type: Article
URI: http://hdl.handle.net/1853/26937
ISSN: 0021-9606
Citation: Journal of Chemical Physics, 1992:97: 9412-9426
Date: 1992-12-15
Contributor: Scripps Research Institute. Dept. of Molecular Biology
Publisher: Georgia Institute of Technology
American Institute of Physics
Subject: Proteins
Molecular models
Monte Carlo method
Polypeptides
Lattice gas
Resolution
Coupling
Conformational changes
Randomness
Globular clusters

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