DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate.

ABSTRACT: DelPhiPKa is a widely used and unique approach to compute pK_a 's of ionizable groups that does not require molecular surface to be defined. Instead, it uses smooth Gaussian-based dielectric function to treat computational space via Poisson-Boltzmann equation (PBE). Here, we report an expansion of DelPhiPKa functionality to enable inclusion of salt in the modeling protocol. The method considers the salt mobile ions in solvent phase without defining solute-solvent boundary. Instead, the ions are penalized to enter solute interior via a desolvation penalty term in the Boltzmann factor in the framework of PBE. Hence, the concentration of ions near the protein is balanced by the desolvation penalty and electrostatic interactions. The study reveals that correlation between experimenta

SUBMITTER: Pahari S 

PROVIDER: S-EPMC6294708 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature