Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

ABSTRACT: Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest el

SUBMITTER: Fiorucci S 

PROVIDER: S-EPMC2862153 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature