Investigating the Microscopic Dynamics of Solvent Confined Within and Around a β-Barrel Protein

Protein cavity and surface hydration play critical roles in determining a protein's structure, flexibility, dynamics, and overall function. Yet, uncovering the precise relationships among these factors has remained challenging. To address this, atomistic molecular dynamics (MD) simulations were performed on aqueous systems containing rat liver fatty acid-binding protein (rLFABP)─a β-barrel protein─both in its apo or ligand-free and holo or oleate ligand bound forms at room temperature. The dynamic properties of water at the exterior surface of the protein as against those that are confined within the protein internal core were investigated. This study focused on elucidating how structural fluctuations of the protein (in both apo and holo states) and the bound oleate ligands impact the diffusivity and hydrogen-bonding characteristics of these separate water ensembles. A primary finding was the emergence of pronounced spatial heterogeneity and retarded dynamics of water molecules within the protein's internal cavity, contrasting sharply with the comparatively uniform solvent dynamics at the exterior surface. The structural reorganization of the β-barrel cavity in the holo form was notably correlated with a dynamical transition in the trapped water population. It has been demonstrated that the restricted mobility of core water arises directly from alterations in the kinetics of hydrogen bond formation and dissociation, reflecting a restructured hydrogen-bond network within the confined core volume. Importantly, our findings highlight heterogeneous dynamical behavior of interfacial water across different surface regions of the protein, thus emphasizing intricate coupling between protein structural transitions and local hydration dynamics.