Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues.

ABSTRACT: To understand ion permeation, one must assign correct ionization states to titratable amino acid residues in protein channels. We report on the effects of physical and methodological assumptions in calculating the protonation states at neutral bulk pH of titratable residues lining the lumen of the native Escherichia coli OmpF channel, and five mutants. We systematically considered a wide range of assumed protein dielectric constants and all plausible combinations of protonation states for electrostatically interacting side chains, and three different levels of accounting for solute shielding: 1), full nonlinear Poisson-Boltzmann; 2), linearized Poisson-Boltzmann; and 3), neglect of solute shielding. For this system we found it acceptable to neglect solute shielding, a result we postulate t

SUBMITTER: Varma S 

PROVIDER: S-EPMC1303920 | biostudies-literature | 2004 Feb

REPOSITORIES: biostudies-literature