Structure, dynamics, and energetics of water at the surface of a small globular protein: A molecular dynamics simulation

Abstract

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.

Transport properties of water at functionalized molecular interfaces

“…The diffusion rate perpendicular to the peptide surface is slower than the overall diffusion while the parallel diffusion is found to be faster. As observed in other simulations 14,32 and experimental results, 33 the anisotropy in the parallel and perpendicular water mobility seems to be connected to the dipole and H-bonding of structured water, especially in the first hydration layer of the protein surface. 10,34 Interactions of protein residues with neighboring water molecules can orient water dipoles normal to the protein surface.…”

“…7,10,14,16,32,33 The self-diffusion coefficient of solvent is expected to decrease when approaching the protein surface. We evaluate the diffusion coefficient of water, along with its parallel and perpendicular components, as a function of distance to the peptide surface ͑Fig.…”

Collapse of the hydration shell of a protein prior to thermal unfolding

“…They showed the existence of a hydration shell whose average density is around 10% larger than that of the bulk water. Molecular dynamics simulation studies also suggested that the variation in the first hydration shell density is subject to the electrostatic properties of the protein surface and local surface topography (Makarov et al, 1998(Makarov et al, , 2000Dastidar & Mukhopadhyay, 2003). However, the properties of the hydrated water shells are still the subject of many experimental and theoretical investigations.…”

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

“…Further, at a particular temperature, the value of D is minimum for the water molecules around the minor groove of the DNA and maximum for bulk water. The value of the diffusion coefficient, D for the bulk water corresponding to a temperature of 300 K is 2.62 × 10 −5 cm 2 /s, closely matched with the value obtained from simulation of pure water [92]. Additionally, if we assume homogeneous, isotropic, three dimensional liquids, then < r 2 > ∼ t. Due to the presence of anomalous diffusion, the MSD follows the law,…”