Energetics of Protein Folding Kinetics

Abstract

Experimentally observed diversity in protein folding rates for single domain two-state proteins is very challenging phenomena. Although these two-state proteins have comparable chain sizes, the difference in their folding rates between the slowest and fastest ones could be 9 orders of magnitude. in this study, native-centric C_alpha based course-grained molecular dynamics protein models with Langevin dynamics, which contain different protein energetics such as homogenous and heterogenous interactions, short and long range non-local interactions, local interactions, non-native repulsive interactions, have been considered. The folding kinetics of a protein set consists of 26 experimentally studied two-state proteins was examined. We have shown that, besides the topology of the proteins, presence of non-native repulsive interactions and range of non-local interactions are crucial to observe experimental-like high diversity in the folding rates. Among the protein models we have considered, the one which includes heterogenous and short range non-local interactions, and non-native repulsive interactions, provided a significant correlation between experimental and computational folding rates, i.e., r = 0.68. in addition, for the same model and protein set, an excellent agreement in the diversity of folding rates comparing with experimental results, e.g 5 orders of magnitude, was observed. Contributions of each energetics on protein dynamics will also be discussed in details.