Network of Hydrogen Bonds Around Proteins

Abstract

In crystallographic studies, the distribution of hydration water molecules on protein surfaces are visualized at atomic resolution. Almost hydration water molecules classified in the first-layer class associate with polar protein atoms and adjoining water molecules via hydrogen bonds. Then, hydration water molecules form local patchwork-like aggregates. Those aggregates are connected further by hydrogen bonds mediated by polar protein atoms, and result in a network of hydrogen bonds extending over large surface areas with a percolation property. To examine whether such large hydrogen bond networks are present over protein surfaces in solution, hydrogen bond patterns on and around protein surfaces are studied using molecular dynamics simulations for protein molecules immersed in explicit water. Local hydrogen bond patterns appear only in the vicinity of protein surfaces and produce a network of hydrogen bonds over the whole surface of the protein, as observed in cryogenic crystal structure analysis. The reorganization of the network in the hydration layer proceeds much slower than that in bulk.