Accessibility of compact structures and prion-like protein folding property

Abstract

Based on two-dimensional Gō model of proteins and Monte Carlo simulation method, it is found that different compact conformations have different accessibility, i.e., some are easy to reach in the Monte Carlo simulation from a random conformation, while others are not. The logarithm of folding time is approximately a linear function of the contact order of the native conformation, which is consistent with published experimental results. Transition barrier is the main factor to determine the folding time at low temperature when proteins are stable. To fold to native structure with bigger contact order, higher barrier needs to be overcome. To study the folding properties of some prion-like proteins which have two possible conformations, the normal Gō model is extended to double-Gō model with two native states. In folding simulations, the native state with high accessibility is reached with much higher probability than the other. The accessibility of compact structures determines which structure is easy to reach in folding process. © World Scientific Publishing Company.