Statistical mechanics of simple models of protein folding and design

• Published in: Biophysical journal Vol. 73; no. 6; pp. 3192 - 3210
• Main Authors: Pande, V.S., Grosberg, A.Y., Tanaka, T.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.1997
• Subjects: Biophysical Phenomena; Biophysics; Drug Design; Freezing; Mathematics; Models, Molecular; Protein Conformation; Protein Engineering; Protein Folding; Thermodynamics
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/S0006-3495(97)78345-0

It is now believed that the primary equilibrium aspects of simple models of protein folding are understood theoretically. However, current theories often resort to rather heavy mathematics to overcome some technical difficulties inherent in the problem or start from a phenomenological model. To this end, we take a new approach in this pedagogical review of the statistical mechanics of protein folding. The benefit of our approach is a drastic mathematical simplification of the theory, without resort to any new approximations or phenomenological prescriptions. Indeed, the results we obtain agree precisely with previous calculations. Because of this simplification, we are able to present here a thorough and self contained treatment of the problem. Topics discussed include the statistical mechanics of the random energy model (REM), tests of the validity of REM as a model for heteropolymer freezing, freezing transition of random sequences, phase diagram of designed ("minimally frustrated") sequences, and the degree to which errors in the interactions employed in simulations of either folding and design can still lead to correct folding behavior.