Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi.

ABSTRACT: Our group has implemented a smooth Gaussian-based dielectric function in DelPhi (J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) which models the solute as an object with inhomogeneous dielectric permittivity and provides a smooth transition of dielectric permittivity from surface-bound water to bulk solvent. Although it is well-understood that the protein hydrophobic core is less polarizable than the hydrophilic protein surface, less attention is paid to the polarizability of water molecules inside the solute and on its surface. Here, we apply explicit water simulations to study the behavior of water molecules buried inside a protein and on the surface of that protein and contrast it with the behavior of the bulk water. We selected a protein that is experimentally sho

SUBMITTER: Chakravorty A 

PROVIDER: S-EPMC9883665 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature