Parsing the Contributions of Polypeptide Backbones and Sidechains to Denaturation in Concentrated Aqueous Solutions of Urea and Guanidinium Chloride

The mechanistic details of protein denaturation are relevant for understanding the nature of the collapse transition that is induced by dilution from denaturing to predominantly aqueous solutions. Concentrated solutions of urea and GdnCl are thought to be good solvents for generic proteins. Here we report results from a series of systematic molecular dynamics simulations. We show that the solvent quality of a denaturing solution depends on the chemical details of the polypeptide system. Polyglycine prefers collapsed states in highly concentrated aqueous solutions of GdnCl, implying that these solvents are poor solvents for polypeptide backbones. The induction of chain expansion in 6 M GdnCl requires the addition of specific categories of sidechains including those with aromatic groups, primary amides, and charged groups. Polyglycine expands in highly concentrated aqueous solutions of urea. However, we show that intra-chain and chain-solvent interactions are almost perfectly counterbalanced in 8 M urea, implying that these conditions are theta solvents for generic polypeptide backbones. The degree of chain expansion can be enhanced in urea by the addition of sidechains that interact favorably with urea molecules. Polypeptide backbones and sidechains contribute to chain expansion through preferential interactions with denaturant molecules in 6 M GdnCl and 8 M urea, although the contributions from sidechain and backbone specific interactions are different in the two milieus. Importantly, we observe that the degree of expansion falls short of the upper limit that is achievable for self-avoiding random walks. This implies that the degree of chain expansion can be sequence-specific and be impacted by residual intra-chain attractions. This should influence the details of the collapse transition upon dilution from denaturants.