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

TL;DR

This study investigates the kinetic and folding behaviors of an off-lattice heteropolymer model, revealing insights into short-term dynamics and the temperature-dependent cooperativity of folding through eigenvalue analysis.

Contribution

It introduces an analysis of off-lattice heteropolymer kinetics and folding cooperativity using eigenvalue analysis of structural fluctuations.

Findings

Similar short-time behavior across sequences with different thermodynamics

Decreasing degrees of freedom with lowering temperature indicating increased landscape asymmetry

Gradual folding transition observed in the compact state

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.