An analytical study of the interplay between geometrical and energetic effects in protein folding.
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.
Suzuki
Yoko
Y
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
Noel
Jeff K
JK
Onuchic
José N
JN
D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D010455:Peptides