title: An analytical study of the interplay between geometrical and energetic effects in protein folding.
abstract: Analytical studies have several advantages for an understanding of the mechanisms of protein folding such as the interplay between geometrical and energetic effects. In this paper, we introduce a Gaussian filament with a C(alpha) structure-based (Go) potential as a new theoretical scheme based on a Hamiltonian approach. This model takes into account geometrical information in a realistic fashion without the need of phenomenological descriptions. In order to make this model more appropriate for comparison with protein folding simulations and experiments, we introduce a many-body interaction into the potential term to enhance cooperativity. We apply our new analytical model to a beta-hairpin-type peptide and compare our results with a molecular dynamics simulation of a structure-based model.
authors.affiliation: Department of Physics, School of Sciences and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan. youko@phys.meisei-u.ac.jp
authors.forename: Yoko
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Jeff K
authors.initials: JK
authors.lastname: Noel
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
mesh_terms: D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D010455:Peptides