title: Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates.
abstract: The prediction of protein folding rates and mechanisms is currently of great interest in the protein folding community. A close comparison between theory and experiment in this area is promising to advance our understanding of the physical-chemical principles governing the folding process. The delicate interplay of entropic and energetic/enthalpic factors in the protein free energy regulates the details of this complex reaction. In this article, we propose the use of topological descriptors to quantify the amount of heterogeneity in the configurational entropy contribution to the free energy. We apply the procedure to a set of 16 two-state folding proteins. The results offer a clean and simple theoretical explanation for the experimentally measured folding rates and mechanisms, in terms of the intrinsic entropic roughness along the populated folding routes on the protein free energy landscape.
authors.affiliation: Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: Leslie L
authors.initials: LL
authors.lastname: Chavez
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
authors.forename: Cecilia
authors.initials: C
authors.lastname: Clementi
mesh_terms: D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins