Chapter 6 Minimal Models for Proteins and RNA: From Folding to Function

• Published in: Progress in nucleic acid research and molecular biology Vol. 85; no. 1; pp. 203 - 250
• Main Authors: Pincus, David L, Cho, Samuel S, Hyeon, Changbong, Thirumalai, D
• Format: Journal Article
• Language: English
• Published: 2008
• ISSN: 0079-6603
• DOI: 10.1016/S0079-6603(08)00406-6

Background: Recent data have suggested two principles that are central to the work we describe here. First, proteins are the result of evolutionary 'sequence selection' to optimize the energy of the native state. Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established. Results Employing only these two principles, we have constructed a non-phenomenological, correlated energy landscape theory that predicts single barrier protein folding kinetics. Moreover, we are able to analytically describe the nature of the free energetic barrier between the denatured and native states of a protein and to detail the nature of folding kinetics for short proteins. Our model predicts Hammond behavior and also describes how mutations can lead to drastic differences in folding times. Conclusion We find that folding and unfolding kinetics can be characterized by a single thermodynamic parameter and, moreover, that Monte Carlo simulation data on folding and unfolding rates with different temperatures and mutations collapse with this characterization. Our results also delineate a regime in which kinetics may proceed via a single unique nucleus.