In silico chaperonin-like cycle helps folding of proteins for structure prediction

¹ Graduate School of Agricultural and Life Sciences, The University of Tokyo
² Graduate School of Science and Technology, Kobe University
³ Graduate School of Engineering, Nagoya University
⁴ Graduate School of Science, Kyoto University

^* To whom correspondence should be addressed. E-mail: takada{at}biophys.kyoto-u.ac.jp.

Submitted on July 3, 2007
Revised on August 21, 2007
Accepted on 16 November 2007

	Abstract

Currently, one of the most serious problems in protein-folding simulations for de novo structure prediction is conformational sampling of medium-to-large proteins. In vivo, folding of these proteins is mediated by molecular chaperones. Inspired by the functions of chaperonins, we designed a simple chaperonin-like simulation protocol within the framework of the standard fragment assembly method: in our protocol, the strength of the hydrophobic interaction is periodically modulated to help the protein escape from misfolded structures. We tested this protocol for 38 proteins and found that, using a certain defined criterion of success, our method could successfully predict the native structures of 14 targets, whereas only those of 10 targets were successfully predicted using the standard protocol. In particular, for non--helical proteins, our method yielded significantly better predictions than the standard approach. This chaperonin-inspired protocol that enhanced de novo structure prediction using folding simulations may, in turn, provide new insights into the working principles underlying the chaperonin system.

Key Words: conformational sampling, energy landscape, fragment assembly, hydrophobic interaction, simulated annealing