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

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 prot

SUBMITTER: Furuta T 

PROVIDER: S-EPMC2267155 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature