title: Configuration-dependent diffusion dynamics of downhill and two-state protein folding.
abstract: Configuration-dependent diffusion (CDD) is important for protein folding kinetics with small thermodynamic barriers. CDD can be even more crucial in downhill folding without thermodynamic barriers. We explored the CDD of a downhill protein (BBL), and a two-state protein (CI2). The hidden kinetic barriers due to CDD were revealed. The increased ~1 k(B)T kinetic barrier is in line with experimental value based on other fast folding proteins. Compared to that of CI2, the effective free-energy profile of BBL is found to be significantly influenced by CDD, and the kinetics are totally determined by diffusion. These findings are consistent with both earlier bulk and single-molecule fluorescence measurements. In addition, we found the temperature dependence of CDD. We also found that the ratio of folding transition temperature against optimal kinetic folding temperature can provide both a quantitative measure for the underlying landscape topography and an indicator for the possible appearance of downhill folding. Our study can help for a better understanding of the role of diffusion in protein folding dynamics.
authors.affiliation: Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States.
authors.forename: Weixin
authors.initials: W
authors.lastname: Xu
authors.forename: Zaizhi
authors.initials: Z
authors.lastname: Lai
authors.forename: Ronaldo J
authors.initials: RJ
authors.lastname: Oliveira
authors.forename: Vitor B P
authors.initials: VB
authors.lastname: Leite
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
mesh_terms: D004058:Diffusion; D007700:Kinetics; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins