Dynamics of biological water: a computational approach

Abstract

In this contribution it is shown how a better understanding of the dynamics of water surrounding proteins, in particular the inhibitor Barstar, may benefit from atomistic deeper approaches. Barstar is a protein of interest in cancer cell investigations, molecular recognition as well as amyloid fibrils research. Using all-atom molecular dynamics simulations, the dynamics of the first hydration shell surrounding that biomolecule (cutoff = 0.4nm) is analysed along 7ns through three different perspectives. Macroscopic view: time correlation functions show the existence of a broad distribution of relaxation times suggesting a complex landscape of the dynamics (averaged decay time = 84.0 ± 0.3 ps). Mesoscopic view: a power law distribution of residence times indicates that this hydration water exhibits a scale free dynamics with scaling exponent α = 0.57 ± 0.04. Microscopic view: evidence, at atomic level, of multiple time scales in the dynamics of such special solvent (10-1 to 103 ps). That particular ultra-slow behaviour (nano second scale) has not been described for bulk water. These computational results are in agreement with recent experiments performed on native Barstar and contribute to throw some light on solvation data collected by timedependent dynamics Stokes shift (TDSS) measurements on some other proteins in solution.