Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.

ABSTRACT: Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well understood. We have addressed the energetics and the position specificity of nonnative hydrophobic interactions by developing a continuum coarse-grained chain model with a native-centric potential augmented by sequence-dependent hydrophobic interactions. By modeling the effect of different hydrophobicity values at various positions in the Fyn SH3 domain, we predicted energetically significant nonnative interactions that led to acceleration or deceleration of the folding rate depending on whether they were more populated in the transition state or unfolded state. These nonnative contacts were ce

SUBMITTER: Zarrine-Afsar A 

PROVIDER: S-EPMC2481363 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature