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Helix–coil transitions in a simple polypeptide model
Author(s) -
McCammon J. A.,
Northrup S. H.,
Karplus M.,
Levy R. M.
Publication year - 1980
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1980.360191108
Subject(s) - chemistry , helix (gastropod) , brownian dynamics , residue (chemistry) , electromagnetic coil , chain (unit) , polypeptide chain , alpha helix , brownian motion , thermodynamics , chemical physics , molecular dynamics , solvent , crystallography , statistical physics , computational chemistry , physics , amino acid , quantum mechanics , organic chemistry , ecology , biochemistry , circular dichroism , snail , biology
A simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix–coil transition. The equilibrium properties examined include helix–coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix–coil transition rates.