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Hydrophobicity at the surface of proteins

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M. Scarsi; N. Majeux; A. Caflisch

Journal: Proteins
Year: 1999
Volume: 37
Issue: 4
Pages: 565-755
Type of Publication: Journal Article

Alkyl 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


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.