Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties

Abstract

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times, $τ_{F}$, and $σ= (T_{θ} - T_{F})/T_{θ} $, where $T_{θ}$ and $T_{F}$ are the equilibrium collapse and folding transition temperatures, respectively. The microscopic dynamics reveals several scenarios for the refolding kinetics depending on the values of $σ$. Proteins with small $σ$ reach the native conformation via a nucleation collapse mechanism and their energy landscape is characterized by single dominant native basin of attraction. Proteins with large $σ$ get trapped in competing basins of attraction, in which they adopt misfolded structures. In this case only a small fraction of molecules $Φ$ access the native state rapidly, the majority of them approach the native state by a three stage multipathway mechanism. The partition factor $Φ$ is determined by $σ$: smaller the value of $σ$ larger is $Φ$. The qualitative aspects of our results are found to be independent of the friction coefficient. Estimates for time scales for folding of small proteins via a nucleation collapse mechanism are presented.