SIMULATION OF ALPHA-HELIX COIL TRANSITIONS IN SIMPLIFIED POLYVALINE -EQUILIBRIUM PROPERTIES AND BROWNIAN DYNAMICS

A quantitative understanding of helix-coil dynamics will help explain their role in protein folding and in folded proteins. As a contributio n to the understanding, the equilibrium and dynamical aspects of the h elix-coil transition in polyvaline have been studied by computer simul ation using a simplified model of the polypeptide chain. Each amino ac id residue is treated as a single quasiparticle in an effective potent ial that approximates the potential of mean force in solution. The equ ilibrium properties examined include the helix-coil transition and its dependence on chain position and well depth at the coil-helix interfa ce. A stochastic simulation of the Brownian motion of the chain in its solvent surroundings has been used to investigate dynamical propertie s. Time histories of the dihedral angles have been used to study the b ehavior of the helical structure. Auto and cross-correlation functions have been calculated from the time histories and from the state (heli x or coil) functions of the residues with relaxation times of tens to hundreds of picoseconds. Helix-coil rate constants of tens of ns-1 wer e found for both directions of the transition. (C) 1993 John Wiley & S ons, Inc.