Hydrophobicity at the surface of proteins.
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.
Scarsi
M
M
Department of Biochemistry, University of Zürich, Switzerland.
Majeux
N
N
Caflisch
A
A
D019883:Alkyl and Aryl Transferases / Q000737:chemistry; D017306:Annexin A2 / Q000737:chemistry; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry; D051231:Farnesyltranstransferase; D018398:Homeodomain Proteins / Q000737:chemistry; D046911:Macromolecular Substances; D008958:Models, Molecular; D009687:Nuclear Proteins; D010455:Peptides / Q000737:chemistry; D010880:Piperidines / Q000737:chemistry; D011106:Polyisoprenyl Phosphates / Q000737:chemistry; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011485:Protein Binding; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry*; D011518:Proto-Oncogene Proteins / Q000737:chemistry; D051736:Proto-Oncogene Proteins c-mdm2; D009418:S100 Proteins; D012717:Sesquiterpenes; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics; D013917:Thrombin / Q000737:chemistry; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry; D000099248:S100 Calcium Binding Protein A10
D019883:Alkyl and Aryl Transferases; D017306:Annexin A2; D004247:DNA; D004268:DNA-Binding Proteins; D004151:Dipeptides; D051231:Farnesyltranstransferase; D018398:Homeodomain Proteins; D046911:Macromolecular Substances; D009687:Nuclear Proteins; D010455:Peptides; D010880:Piperidines; D011106:Polyisoprenyl Phosphates; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011506:Proteins; D011518:Proto-Oncogene Proteins; D051736:Proto-Oncogene Proteins c-mdm2; D009418:S100 Proteins; D012717:Sesquiterpenes; D013917:Thrombin; D016159:Tumor Suppressor Protein p53; D000099248:S100 Calcium Binding Protein A10; C101121:HOXB1 homeodomain protein; C083400:PBX1 protein, human; C004808:farnesyl pyrophosphate; C038708:N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide