In recent years it has become evident that, in contrast to the passive role of embedding medium usually ascribed to solvent, water plays a major role in non-covalent protein-ligand binding. In this work, we apply molecular simulations to study cavity-ligand binding in a model system through the analysis of the structure, dynamics and associated spectral signatures of water at different stages of the binding process. Connection with the corresponding thermodynamic properties is discussed and reveals that the different phases of water emerging at different stages of the binding process could be detected from infrared spectroscopy. We anticipate that the integration of computer simulations and spectra calculations will play a primary role in the characterization of the molecular mechanisms responsible for cavity-ligand binding in complex biomolecular systems.

Water in cavity-ligand binding: Structure, dynamics, and spectroscopic signatures

244th National Meeting (2012)

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