Literature DB >> 9000013

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design.

J E Ladbury1.   

Abstract

Recent data have highlighted the enigmatic role that water plays in biomolecular complexes. Water at the interface of a complex can increase the promiscuity of an interaction, yet it can also provide increased specificity and affinity. The ability to engineer water-binding sites into the interface between a drug and its target might prove useful in drug design.

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Year:  1996        PMID: 9000013     DOI: 10.1016/s1074-5521(96)90164-7

Source DB:  PubMed          Journal:  Chem Biol        ISSN: 1074-5521


  126 in total

1.  Contribution of proton linkage to the thermodynamic stability of the major cold-shock protein of Escherichia coli CspA.

Authors:  S A Petrosian; G I Makhatadze
Journal:  Protein Sci       Date:  2000-02       Impact factor: 6.725

2.  Scoring functions: a view from the bench.

Authors:  J R Tame
Journal:  J Comput Aided Mol Des       Date:  1999-03       Impact factor: 3.686

3.  Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

Authors:  G Pujadas; J Palau
Journal:  Protein Sci       Date:  2001-08       Impact factor: 6.725

4.  Thermodynamic analysis of the binding of component enzymes in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.

Authors:  Hyo-Il Jung; Simon J Bowden; Alan Cooper; Richard N Perham
Journal:  Protein Sci       Date:  2002-05       Impact factor: 6.725

5.  Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain.

Authors:  Brian M Swalla; Richard I Gumport; Jeffrey F Gardner
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

6.  Water and proteins: a love-hate relationship.

Authors:  Yaakov Levy; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-01       Impact factor: 11.205

7.  Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design.

Authors:  Benjamin Schaefer; Caroline Kisker; Christoph A Sotriffer
Journal:  J Comput Aided Mol Des       Date:  2011-11-11       Impact factor: 3.686

8.  Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Authors:  Pratyush Tiwary; Jagannath Mondal; Joseph A Morrone; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

9.  Characterization of a novel water pocket inside the human Cx26 hemichannel structure.

Authors:  Raul Araya-Secchi; Tomas Perez-Acle; Seung-Gu Kang; Tien Huynh; Alejandro Bernardin; Yerko Escalona; Jose-Antonio Garate; Agustin D Martínez; Isaac E García; Juan C Sáez; Ruhong Zhou
Journal:  Biophys J       Date:  2014-08-05       Impact factor: 4.033

10.  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

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