Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model

Abstract

The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The proteins are modeled as self-avoiding 27-mer chains on a cubic lattice, with compact native states and structure-based Gō potentials. Each residue that makes no contact with other residues in a given protein conformation is assigned a solvation energy ɛs, representing its full exposure to the solvent. We find that a negative ɛs, indicating a favorable solvation, increases the cooperativity of the folding transition by lowering the free energy of the unfolded state, increasing the folding free energy barrier, and narrowing the folding routes. This favorable solvation also significantly improves the correlation between folding rates and the native topology, measured by the relative contact order. Our results suggest that the Gō model may overestimate the importance of native interactions, and a solvation potential countering the native bias can play a significant role. The solvation energy in our model can be related to the polar interaction between water and peptide groups in the protein backbone. It is, therefore, suggested that the solvation of peptide groups may significantly contribute to the exceptional folding cooperativity and the pronounced topology-dependence of folding rates observed in two-state proteins.