Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L−1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.