The kinetics of conformational transitions: Effect of variation of bond angle bending and bond stretching force constants

Abstract

Conformational transitions in chain molecules have been shown to proceed via a reaction coordinate which is a localized mode involving rotations about bonds, and also bond angle bending and bond stretching. By investigating the kinetics as a function of the force constants (flexibility) for bond angle bending and bond stretching, the role of the localized mode is probed. The study reported here consists of computer simulations of the Brownian dynamics of chain motions, and of kinetic calculations of rates and reaction modes. The theory accurately predicts the relative effects of force constant variations on transition rates determined by simulation.