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J Am Chem Soc. 2010 Sep 1;132(34):12091-7. doi: 10.1021/ja1050082.

Water in cavity-ligand recognition.

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  • 1Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California, San Diego, California 92093, USA. rbaron@mccammon.ucsd.edu

Abstract

We use explicit solvent molecular dynamics simulations to estimate free energy, enthalpy, and entropy changes along the cavity-ligand association coordinate for a set of seven model systems with varying physicochemical properties. Owing to the simplicity of the considered systems we can directly investigate the role of water thermodynamics in molecular recognition. A broad range of thermodynamic signatures is found in which water (rather than cavity or ligand) enthalpic or entropic contributions appear to drive cavity-ligand binding or rejection. The unprecedented, nanoscale picture of hydration thermodynamics can help the interpretation and design of protein-ligand binding experiments. Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models.

PMID:
20695475
[PubMed - indexed for MEDLINE]
PMCID:
PMC2933114
Free PMC Article
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