The rigidization of water dynamics around proteins: A molecular dynamics study.

Abstract

The interaction between a solvated protein and its solvent is a rich area of biophysics that has yet to be fully explored. While a wealth of research suggests that the dynamics of a protein are intimately related to the dynamics of its surrounding solvent, the degree and the intensity of this modulation has not been fully quantified. To elucidate this phenomenon, we modeled multiple protein structures of various sizes and shapes in an explicit TIP4P-2005 water solvent. Motivated by past findings which related it to the α-relaxation process of the intermediate scattering function, the Debye-Waller factor u2 was used to characterize the local mobility of the protein and the water atoms. In all the solvated protein systems considered, we observed the presence of two regimes of water behavior: the hydration layer and the bulk. Aligning with previous findings in THz microscopy, the hydration layer had a thickness on the order of 1 nm. Moreover, as seen before in studies of the interfacial region of glass-forming and crystalline inorganic materials, the interfacial water u2 exponentially approached the bulk water u2 over the length of the hydration shell. Among all the water molecules in the hydration shell, the u2's obeyed a -distribution. The right tails in these distributions were associated with pockets of fast-moving water molecules clustered near the positively-charged regions of the protein surface. Put together, these in silica findings lend credence to Karplus’ analogy between the dynamics of solvated proteins and inorganic nanoparticles.