Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

Abstract

The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.