A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.

ABSTRACT: Calculations of electrostatic potential and solvation free energy of macromolecules are essential for understanding the mechanism of many biological processes. In the classical implicit solvent Poisson-Boltzmann (PB) model, the macromolecule and water are modeled as two-dielectric media with a sharp border. However, the dielectric property of interior cavities and ion-channels is difficult to model realistically in a two-dielectric setting. In fact, the detection of water molecules in a protein cavity remains to be an experimental challenge. This introduces an uncertainty, which affects the subsequent solvation free energy calculation. In order to compensate this uncertainty, a novel super-Gaussian dielectric PB model is introduced in this work, which devices an inhomogeneous dielectric di

SUBMITTER: Hazra T 

PROVIDER: S-EPMC9841320 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature