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Motifs for molecular recognition exploitinghydrophobic enclosure in protein ligand bindingTom Young, Robert Abel, Byungchan Kim, Bruce J. Berne*, and Richard A. FriesnerDepartment of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 Contributed by Bruce J. Berne, November 17, 2006 (sent for review October 12, 2006)The thermodynamic properties and phase behavior of water inconfined regions can vary significantly from that observed in thebulk. This is particularly true for systems in which the confinementis on the molecular -length scale. In this study, we use moleculardynamics simulations and a powerful solvent analysis techniquebased on inhomogenous solvation theory to investigate the prop-erties of water molecules that solvate the confined regions ofprotein active sites. Our simulations and analysis indicate that thesolvation of protein active sites that are characterized by hydro-phobic enclosure and correlated hydrogen bonds induce atypicalentropic and enthalpic penalties of hydration.
proposed motifs (i.e., they entropically perturb the binding-cavity solvent) and motivates an atomistic description of their solvation. The most striking feature of the solvation of the streptavidin binding cavity was the formation of a five-membered water ring.
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