Sidechain Dynamics and Protein Folding

Abstract

The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein structure, with the fastest relaxing sidechains being involved in kinetically important positions. Traversal of the major folding transition state corresponds to the freezing of a small number of residues, while the rest of the chain proceeds towards equilibrium via backbone fluctuations around the native fold. The post-nucleation processes by which sidechains relax are characterized by very slow dynamics, and many barrier crossings, and thus resemble the behavior of a glass. At optimal temperature, however, the nucleated ensemble is energetically very close to equilibrium; slow relaxation is still observed. At lower temperatures, sidechain relaxation becomes a significant and very noticeable part of the folding reaction.