Dynamics of folding and unfolding transition in a globular protein studied by time correlation functions from computer simulation

Abstract

Abstract A method of calculating time correlation functions from records of computer simulated equilibrium conformational fluctuations in a globular protein is discussed. Use of the calculated time correlation function for discussions of dynamics of folding and unfolding transition in the two‐dimensional lattice model of proteins. The time correlation functions can be approximated in general by a sum of two simple exponential terms. The relaxation time of the slower mode does not depend on the nature of the physical quantity with respect to which the time correlation function is calculated. This time characterizes the overall folding and unfolding transition. The relaxation time of the faster mode depends on the nature of the physical quantity and characterizes conformational fluctuations within each of the native and denatured states. The mechanism of a previously observed phenomenon of the acceleration of the folding and unfolding transition by short‐range interactions is discussed.