Compaction and folding in model proteins

Abstract

Protein folding is modeled as diffusion on a free-energy landscape, allowing use of the diffusion equation to study the impact of energetic parameters on the folding dynamics. The free-energy landscape is characterized by two different order parameters, one representing the degree of compactness, the other a measure of the progress towards the folded state. For marginally stable proteins, fastest folding is achieved when the nonspecific interactions favoring compaction are strong, resulting in a high folding temperature. Such proteins fold by rapid collapse followed by slower accumulation of correct contacts.