title: Native geometry and the dynamics of protein folding.
abstract: In this paper, we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids, the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the Go model show that the effect of long-range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.
authors.affiliation: CFTC, Av. Prof. Gama Pinto 2, 1649-003 Lisboa Codex, Portugal. patnev@alfl.cii.fc.ul.pt
authors.forename: P F N
authors.initials: PF
authors.lastname: Faisca
authors.forename: M M
authors.initials: MM
authors.lastname: Telo da Gama
mesh_terms: D007700:Kinetics; D008956:Models, Chemical; D009010:Monte Carlo Method; D011108:Polymers / Q000737:chemistry; D011336:Probability; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013997:Time Factors
chemical_list: D011108:Polymers; D011506:Proteins