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 contribution to the understanding, the equilibrium and dynamical aspects of the helix-coil transition in polyvaline have been studied by computer simulation using a simplified model of the polypeptide chain. Each amino acid residue is treated as a single quasi-particle in an effective potential that approximates the potential of mean force in solution. The equilibrium properties examined include the helix-coil transition and its dependence on chain position and well depth at the coil-helix interface. A stochastic simulation of the Brownian motion of the chain in its solvent surroundings has been used to investigate dynamical properties. Time histories of the dihedral angles have been used to study the behavior of the helical structure. Auto and cross-correlation functions have been calculated from the time histories and from the state (helix or coil) functions of the residues with relaxation times of tens to hundreds of picoseconds. Helix-coil rate constants of tens of ns-1 were found for both directions of the transition.