On the Kinetic Behavior and Folding Properties of an Off-Lattice Heteropolymer Model

Abstract

The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is obtained even for sequences with very different thermodynamic properties. Furthermore, the degree of cooperativity in the folding process is examined by studying the residual number of degrees of freedom, obtained from an eigenvalue analysis of the correlation matrix, contributing to the structural fluctuations. In the compact state, a gradual decrease in this effective number of degrees of freedom take place as the temperature is lowered. This can be interpreted as an increasing asymmetry of the energy landscape.