Energetic frustrations in protein folding at residue resolution: a simulation study of homologous immunoglobulin-like \b{eta}-sandwich proteins

TL;DR

This study systematically characterizes energetic frustrations caused by nonnative inter-residue interactions in the folding of homologous immunoglobulin-like ta-sandwich proteins, revealing their heterogeneous effects and interplay with native-contact networks.

Contribution

It provides a residue-level analysis of energetic frustrations in ta-sandwich protein folding, highlighting their role and potential for folding process redesign.

Findings

Energetic frustrations vary across secondary structures.

Folding mechanisms are conserved despite energetic frustrations.

Manipulating frustrations could alter folding pathways.

Abstract

Nonnative residual interactions have attracted increasing attention in recent protein folding researches. Experimental and theoretical investigations had been set out to catch nonnative contacts that might dominate key events in protein folding. However, energetic frustrations caused by nonnative inter-residue interactions are not systematically characterized, due to the complicated folding mechanism. Recently, we studied the folding of a set of homologous all-{\alpha} proteins and found that nonnative-contact-based energetic frustrations are closely related to protein native-contact networks. In this paper, we studied the folding of nine homologous immunoglobulin-like (Ig-like) \b{eta}-sandwich proteins and examined energetic frustrations caused by nonnative inter-residue interactions, based on analyses of residual phi-values and contact maps of transition state ensembles. The proteins share similar tertiary structures, thus minimize topology frustration differences in protein folding and highlighting the effects of energetic frustrations as caused by hydrophilic-hydrophobic mutations. Our calculations showed that energetic frustrations have highly heterogeneous effects on the folding of most secondary structures and on the folding correlations between different folding-patches of \b{eta}-sandwich proteins. The simulations revealed a strong interplay between energetic frustrations and native-contact networks in \b{eta}-sandwich domains, which ensures that \b{eta}-sandwich domains follow a common folding mechanism. Our results suggested that the folding processes of \b{eta}-sandwich proteins might be redesigned by carefully manipulating energetic frustrations at residue level.