Hydrophobicity at the surface of proteins

TitleHydrophobicity at the surface of proteins
Publication TypeJournal Article
Year of Publication1999
AuthorsScarsi M., Majeux N., Caflisch A.
JournalProteins: Structure, Function, and Bioinformatics
Volume37
Issue4
Pagination565-755
Date Published1999 Dec 1
Type of ArticleResearch Article
ISSN0887-3585
KeywordsAlkyl and Aryl Transferases, Annexin A2, Binding Sites, Dipeptides, DNA, DNA-Binding Proteins, Farnesyltranstransferase, Homeodomain Proteins, Macromolecular Substances, Models, Molecular, Nuclear Proteins, Peptides, Piperidines, Polyisoprenyl Phosphates, Protein Binding, Protein Conformation, Protein Structure, Quaternary, Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-mdm2, S100 Proteins, Sesquiterpenes, Static Electricity, Surface Properties, Thermodynamics, Thrombin, Tumor Suppressor Protein p53
Abstract

A new method is presented to quantitatively estimate and graphically display the propensity of nonpolar groups to bind at the surface of proteins. It is based on the calculation of the binding energy, i.e., van der Waals interaction plus protein electrostatic desolvation, of a nonpolar probe sphere rolled over the protein surface, and on the color coding of this quantity on a smooth molecular surface (hydrophobicity map). The method is validated on ten protein-ligand complexes and is shown to distinguish precisely where polar and nonpolar groups preferentially bind. Comparisons with existing approaches, like the display of the electrostatic potential or the curvature, illustrate the advantages and the better predictive power of the present method. Hydrophobicity maps will play an important role in the characterization of binding sites for the large number of proteins emerging from the genome projects and structure modeling approaches.

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Alternate JournalProteins
PubMed ID10651272
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