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Article
Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem
The Journal of Physical Chemistry B
  • Margaret S. Cheung
  • John M. Finke, University of Washington Tacoma
  • Benjamin Callahan
  • José N. Onuchic
Publication Date
10-1-2003
Document Type
Article
Abstract

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.

DOI
10.1021/jp034441r
Version
pre-print, post-print
Citation Information
Margaret S. Cheung, John M. Finke, Benjamin Callahan and José N. Onuchic. "Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem" The Journal of Physical Chemistry B Vol. 107 Iss. 40 (2003) p. 11193 - 11200
Available at: http://works.bepress.com/john_finke/23/