Exploring the interplay between topology and secondary structural formation in the protein folding problem

Simple models with a single bead representation (C-alpha models) have been successful in providing a qualitative understanding of the folding mechanism of small globular proteins. Can we go beyond this qualitative understanding and make more detailed quantitative connections to experiments? To achieve this goal, a tractable framework of protein representations whose complexity falls between C-alpha and all-atom representations is needed to address different energetic competing factors during folding events. Such a model conserves the low computational expense inherent in minimalist models while enhancing the understanding of side-chain packing not existent in simple C-alpha models. In this work, we present a minimalist representation of protein structures that are used to investigate the competition between native side-chain contacts and nonspecific backbone hydrogen bonds. Our results suggest that native tertiary contacts and dihedrals force the nonspecific hydrogen bonds to adopt native configurations and retain a funneled landscape. In addition, the use of an angular component in the hydrogen bond interaction prevents non-native conformations.