Electrostatics of nanosystems: Application to microtubules and the ribosome

TLDR

Electrostatic analysis of biomolecules is a routine biophysical technique, but the Poisson‑Boltzmann equation has traditionally been limited to small systems due to computational constraints. The study aims to develop numerical methods that allow trivially parallel solutions of the Poisson‑Boltzmann equation for supramolecular structures vastly larger than previously tractable. The authors employ trivially parallel numerical techniques to solve the Poisson‑Boltzmann equation for large supramolecular assemblies. Electrostatic potentials were computed for microtubule and ribosome structures, suggesting that electrostatics likely influence many of their functional activities.

Abstract

Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.