title: Quantitative prediction of protein folding behaviors from a simple statistical model.
abstract: The statistical nature of the protein folding process requires the use of equally detailed yet simple models that lend themselves to characterize experiments. One such model is the Wako-Saitô-Muñoz-Eaton model, that we extend here to include solvation effects (WSME-S), introduced via empirical terms. We employ the novel version to analyze the folding of two proteins, gpW and SH3, that have similar size and thermodynamic stability but with the former folding 3 orders of magnitude faster than SH3. A quantitative analysis reveals that gpW presents at most marginal barriers, in contrast to SH3 that folds following a simple two-state approximation. We reproduce the observed experimental differences in melting temperature in gpW as seen by different experimental spectroscopic probes and the shape of the rate-temperature plot. In parallel, we predict the folding complexity expected in gpW from the analysis of both the residue-level thermodynamics and kinetics. SH3 serves as a stringent control with neither folding complexity nor dispersion in melting temperatures being observed. The extended model presented here serves as an ideal tool not only to characterize folding data but also to make experimentally testable predictions.
authors.affiliation: Departamento de Física Teórica & Instituto de Biocomputacíon y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain. pier@unizar.es
authors.forename: Pierpaolo
authors.initials: P
authors.lastname: Bruscolini
authors.forename: Athi N
authors.initials: AN
authors.lastname: Naganathan
mesh_terms: D007700:Kinetics; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D013816:Thermodynamics; D015678:Viral Structural Proteins / Q000737:chemistry; D018909:src Homology Domains
chemical_list: D015678:Viral Structural Proteins; C411883:protein W, bacteriophage lambda