Water dynamics on the surface of the protein barstar

Abstract

Water plays a fundamental function in life and technology. To gain a deeper knowledge to the problem of the hydration of biomolecules, the dynamics of water around a 89-residue protein of interest in molecular recognition, cancer cell research and amyloid fribrils investigations is analyzed. The biomolecule is the ribonuclease inhibitor barstar wild-type. The dynamics of the protein and the 7430 water molecules of the bath in which is immersed, is monitored during a period of 7 ns by using all-atom molecular dynamics simulations. The results confirm the existence of multiple time scales in the dynamics of water (10 -1 to 10 3 ps) at atomic level. That heterogeneity of residence times is not lost if the system of reference is just one atom of the inhibitor. The dehydration process of barstar is considered through the analysis of time correlation functions obtaining an averaged decay time of τ = 84.0 ± 0.3 ps. A power law distribution, with scaling exponent α = 0.57 ± 0.04, suggests that this hydration water exhibits a scale free dynamics (with respect to the residence time of solvent molecules). Most of the water molecules located on the surface of the protein spend times smaller than the picosecond while only about 1% of them stay for periods of time on the nanosecond scale.

Insights into hydrogen bond dynamics at the interface of the charged monolayer-protected Au nanoparticle from molecular dynamics simulation

“…[28][29][30][32][33][34][35][36][37][38][39][40][41][42] Especially, the existence of polar groups at the interface can dominate the formation and breaking of interfacial HBs. 33,36,37,40 Balasubramanian and Bagchi 34 have shown that the HB lifetime between water molecules and the polar head groups (cesium pentadecafluorooctanoate) at a micelle surface is found to be much longer than that of water molecules themselves.…”

Low temperature dependence of protein-water interactions on barstar surface: A nano-scale modelling

“…Classical all-atom molecular dynamics simulations of aqueous solutions of the protein barstar (wild type) were conducted at 300 K [25], 288 K, 273 K, 258 K, 248 K and 243 K. The initial structure of that inhibitor was obtained from the RCSB Protein Data Bank (PDB ID: 1BRS). The water molecules shown in the crystallographic PDB data were not maintained.…”

“…Larger radius will result in taking into account more of the bulk dynamics. It is also the thickness that has been already considered in previous data at ambient temperature [25].…”

“…In order to follow the dynamics and existing interactions between the protein and its hydration water at nanoscopic level, we have carried out all-atoms molecular dynamics simulations at room and low temperature. Those numerical simulations are very useful for providing details of dynamical processes that are not experimentally reachable [25,[39][40].…”

“…relaxation times), the dynamics of biological water is affected only to a small extent (2-4-fold slowdown) when compared with neat water [14,22,23]. However if microscopic data are taken into account, that hydration water dynamics exhibits a slow component neatly smaller than that of bulk water (2-3 orders of magnitude) [24][25][26]. The magnitude and molecular origin of this retardation are still topics for further study [26][27][28][29].…”