Literature DB >> 17242738

Water at biomolecular binding interfaces.

Zheng Li1, Themis Lazaridis.   

Abstract

Water molecules are often found at the binding interface of biomolecular complexes mediating the interaction between polar groups via hydrogen bonds, or simply filling space providing van der Waals interactions. Recent studies have demonstrated the importance of taking such water molecules into account in docking and binding affinity prediction. Here, we review the recent experimental and theoretical work aimed at quantifying the influence of interfacial water on the thermodynamic properties of binding. We highlight especially our recent results obtained by inhomogeneous fluid solvation theory in several systems and the prediction of the thermodynamic consequences of displacement of the bound water molecule by ligand modification. Finally, we discuss possible directions for further progress in this field.

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Year:  2006        PMID: 17242738     DOI: 10.1039/b612449f

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  55 in total

1.  Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors:  Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

2.  Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: computer simulation studies in model tyrosine-cysteine peptides in solution.

Authors:  Ariel A Petruk; Silvina Bartesaghi; Madia Trujillo; Darío A Estrin; Daniel Murgida; Balaraman Kalyanaraman; Marcelo A Marti; Rafael Radi
Journal:  Arch Biochem Biophys       Date:  2012-05-26       Impact factor: 4.013

3.  A bulk water-dependent desolvation energy model for analyzing the effects of secondary solutes on biological equilibria.

Authors:  Daryl K Eggers
Journal:  Biochemistry       Date:  2011-02-21       Impact factor: 3.162

Review 4.  Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

Authors:  N Moitessier; P Englebienne; D Lee; J Lawandi; C R Corbeil
Journal:  Br J Pharmacol       Date:  2007-11-26       Impact factor: 8.739

5.  Involvement of water in carbohydrate-protein binding: concanavalin A revisited.

Authors:  Renuka Kadirvelraj; B Lachele Foley; Jane D Dyekjaer; Robert J Woods
Journal:  J Am Chem Soc       Date:  2008-12-17       Impact factor: 15.419

Review 6.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

7.  Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

Authors:  Kamran Haider; Lauren Wickstrom; Steven Ramsey; Michael K Gilson; Tom Kurtzman
Journal:  J Phys Chem B       Date:  2016-06-02       Impact factor: 2.991

8.  A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

Authors:  Rajat Kumar Pal; Kamran Haider; Divya Kaur; William Flynn; Junchao Xia; Ronald M Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio
Journal:  J Comput Aided Mol Des       Date:  2016-09-30       Impact factor: 3.686

Review 9.  Computations of standard binding free energies with molecular dynamics simulations.

Authors:  Yuqing Deng; Benoît Roux
Journal:  J Phys Chem B       Date:  2009-02-26       Impact factor: 2.991

10.  Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization.

Authors:  Julien Michel; Julian Tirado-Rives; William L Jorgensen
Journal:  J Am Chem Soc       Date:  2009-10-28       Impact factor: 15.419

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