Protein folding dynamics via quantification of kinematic energy landscape.
We study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. We find that (i) folding rates of these proteinlike sequences of the same length can differ by 4 orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates; rather, a basin analysis of the kinematic energy landscape defined by the moves can provide an excellent account of the observed folding rates.
Kachalo
Sëma
S
Department of Bioengineering, MC-063, University of Illinois at Chicago, Chicago, Illinois 60305, USA.
Lu
Hsiao-Mei
HM
Liang
Jie
J
D001696:Biomechanical Phenomena; D008956:Models, Chemical; D017510:Protein Folding; D013816:Thermodynamics