Title: De natura denaturantium - On the molecular basis of urea-induced protein denaturation
Protein unfolding by denaturants such as urea is a widely used technique to study protein folding and stability. Despite the widespread use of urea, however, the mechanism of urea-induced protein denaturation is not yet fully understood on the molecular level. In particular, it is controversially discussed whether unfolding is driven by direct interactions of urea with the protein or, alternatively, indirect interactions via urea-induced changes in the water structure. Moreover, it is unclear whether polar or apolar interactions are the main driving force for unfolding. To advance understanding of the process at the molecular level, we have performed comprehensive molecular dynamics of small peptides as well as different proteins in aqueous urea solution. Our results suggest that urea molecules interact preferentially with less polar parts of the protein as well as the peptide backbone. As a result, water is displaced from the solvation shell and the hydrophobic effect is reduced. Further, the ability of urea to form hydrogen bonds helps to avoid unsatisfied hydrogen bond sites at the backbone, but this is only a secondary contribution. In summary, our results suggest a mechanism which is a synthesis of seemingly opposing viewpoints.