CONFORMATIONAL TRANSITION OF AN ALPHA-HELIX STUDIED BY MOLECULAR-DYNAMICS

Molecular dynamics simulations were performed on a 20-residue polyalan ine helix and a spontaneous transition from a kinked to a straight con formation was observed. The kinetics of the transition was analyzed wi thin the framework of the Kramers model for chemical reactions and wit hin a random walk model. The Kramers model which is based on diffusion along a one-dimensional reaction pathway and the crossing of an energ y barrier was found to be inadequate. Instead, a random walk model bas ed on diffusion in the high-dimensional phase space of the system was found to be compatible with the data. The high dimensionality of the p hase space permits the system to circumvent high energy barriers and d iffuse rapidly at about constant energy, but decelerates the reaction since in the labyrinth of pathways the transition state is reached rar ely.