Profiling charge complementarity and selectivity for binding at the protein surface.

ABSTRACT: 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 towa

SUBMITTER: Sulea T 

PROVIDER: S-EPMC1302852 | biostudies-literature | 2003 May

REPOSITORIES: biostudies-literature