Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem
Simple models with a single bead representation (Cα 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 Cα 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 Cα 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.
The Journal of Physical Chemistry B
Cheung, Margaret S.; Finke, John M.; Callahan, Benjamin; and Onuchic, José N., "Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem" (2003). SIAS Faculty Publications. 520.