Study of Protein Hydration Water with the V4S Structural Index: Focus on Binding Site Description

Abstract

V_4S, a new structural indicator for water specially designed to be suitable for hydration and nanoconfined contexts, has been recently introduced and preliminarily applied for water in contact with self-assembled monolayers and graphene-like systems. This index enabled an accurate detection of defective high local density water molecules (called HDA-like given their structural resemblance with the high-density amorphous ice, HDA). In the present work, we shall apply this new metric to characterize protein hydration water with particular interest in protein binding sites. As a first result, we shall find that protein hydration water has a higher concentration of HDA-like molecular arrangements compared to the bulk. Significantly, we shall show that the concentration of HDA-like molecules sharply decreases beyond the first hydration layer. Finally, we shall also reveal a highly nonuniform spatial distribution of the V_4S values for the first hydration shell on the protein surface, where the higher hydrophobicity inherent to the ligand binding site will be evident from an enrichment in HDA-like molecules as compared to the population exhibited by the global protein surface.