SMPB: A More Accurate Mean-Field Electrostatic Method for Biomolecules

Nuo Wang
Department of Chemistry and Biochemistry
UC San Diego


ABSTRACT

The modeling of electrostatics for molecular systems is an essential tool for a quantitative understanding of biological systems. In living organisms, biomolecules are typically solvated in electrolytes, within which the electrostatic potential (EP) and ion distributions are commonly calculated by the Poisson-Boltzmann equation (PBE). The PBE models ions as point charges and as a consequence, it usually overestimates ion densities near partially charged biomolecules. Motivated by the importance of ion-biomolecule interaction in biological function, we adapted an improved electrostatics theory, the size-modified Poisson-Boltzmann equation (SMPBE), to biomolecular electrostatics calculations. Here, we demonstrate that, compared to the traditional PBE, SMPBE gives significantly more accurate ion distributions for partially charged biomolecules. The predictions afforded by the advanced electrostatics model provide a better understanding of ion adsorption to, and diffusion about, biomolecules essential to biological function.