Brownian dynamics simulation of protein folding: A study of the diffusion‐collision model

The dynamic aspects of protein folding are described by a series of diffusion‐collision steps involving structural units (microdomains) of various sizes that combine to form the protein in its native state. A method is introduced for obtaining the rate constants for the basic diffusion‐collision step by use of Brownian dynamics. The method is applied to an investigation of the folding dynamics of two α‐helices connected by a flexible (random‐coil) polypeptide chain. The results of this full three‐dimensional treatment are compared with simplified model calculations for the diffusion‐collision step. Of particular interest are the nature of the collision dynamics and the role of the intervening peptide chain.