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J Chem Inf Model. 2014 Oct 27;54(10):2846-55. doi: 10.1021/ci500397y. Epub 2014 Oct 6.

Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study.

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  • 1Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Universit√† di Padova , via Marzolo 5, 35131 Padova, Italy.

Abstract

Recent advances in structural biology revealed that water molecules play a crucial structural role in the protein architecture and ligand binding of G protein-coupled receptors. In this work, we present an alternative approach to monitor the time-dependent organization of water molecules during the final stage of the ligand-receptor recognition process by means of membrane molecular dynamics simulations. We inspect the variation of fluid dynamics properties of water molecules upon ligand binding with the aim to correlate the results with the binding affinities. The outcomes of this analysis are transferred into a bidimensional graph called water fluid dynamics maps, that allow a fast graphical identification of protein "hot-spots" characterized by peculiar shape and electrostatic properties that can play a critical role in ligand binding. We hopefully believe that the proposed approach might represent a valuable tool for structure-based drug discovery that can be extended to cases where crystal structures are not yet available, or have not been solved at high resolution.

PMID:
25245783
DOI:
10.1021/ci500397y
[PubMed - indexed for MEDLINE]
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