Author
Keywords
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.

Year of Publication
1999
Journal
Proteins: Structure, Function, and Bioinformatics
Volume
37
Issue
4
Number of Pages
565-755
Date Published
1999 Dec 1
Type of Article
Research Article
ISSN Number
0887-3585
Alternate Journal
Proteins
PMID
10651272
Download citation