Profiling charge complementarity and selectivity for binding at the protein surface.
A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins.
Sulea
Traian
T
Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada.
Purisima
Enrico O
EO
D001665:Binding Sites; D003116:Color; D003198:Computer Simulation; D004563:Electrochemistry / Q000379:methods*; D004735:Energy Transfer; D046911:Macromolecular Substances; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055672:Static Electricity; D013499:Surface Properties; D014357:Trypsin / Q000737:chemistry*; D014584:User-Computer Interface
D046911:Macromolecular Substances; D009419:Nerve Tissue Proteins; D011506:Proteins; C033652:postsynaptic density proteins; D014357:Trypsin