Laws: Local alignment of water sites-Describing allosteric water networks in enzymes.

Abstract

Water is an essential component of biological systems; it affects the structure and stability of biological machinery. Highly conserved water networks have been shown to play a crucial role in the motion of protein domains and affect protein function by mediating allosteric communication. Perturbations to these networks have also been implicated in human diseases. Data from x-ray crystallography provide the locations of crystallographic water sites (CWS) coordinated by the protein which can be potentially used to study the conserved water networks. Here, we propose a computational method called local alignment for water sites (LAWS) to identify conserved water networks in molecular dynamics (MD) simulations. This method is based on multilateration — an algorithm widely used in GPS tracking. LAWS considers the contacts formed by CWS and protein atoms in the crystal structure and uses these interaction distances to track ordered waters in a simulation. We apply our method to simulations of an enzyme, fluoroacetate dehalogenase, and analyze the occupancy, residence times and correlated motions of individual water molecules coupled to the protein. Our results help to determine a highly conserved water network involved in allosteric regulation.