Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.

ABSTRACT: The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries. In a systematic investigation using haloalkane dehalogenase as a model system, we focused on the well-established TIP3P, OPC, and TIP4P-Ew water models to explore their impact on the use of t

SUBMITTER: Thirunavukarasu AS 

PROVIDER: S-EPMC11733929 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature