A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion

SIMPLE SUMMARY: The detailed characterization of urea binding sites in protein structures shows that urea can establish multiple types of interactions, in line with recent findings reported for guanidinium and thiocyanate, thus confirming that promiscuity is a general property of protein denaturants. Our analyses support a denaturing model based on protein-denaturant direct interactions to practically equal and independent sites. We also underscore insightful features that can inform on the milder denaturing power displayed by urea. ABSTRACT: An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.