Premium
Hydrophobicity at the surface of proteins
Author(s) -
Scarsi Marco,
Majeux Nicolas,
Caflisch Amedeo
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19991201)37:4<565::aid-prot7>3.0.co;2-v
Subject(s) - van der waals force , electrostatics , polar , chemistry , curvature , surface (topology) , surface protein , chemical physics , molecular dynamics , static electricity , crystallography , computational chemistry , molecule , physics , biology , organic chemistry , geometry , mathematics , virology , astronomy , quantum mechanics
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. Proteins 1999;37:565–575. ©1999 Wiley‐Liss, Inc.