Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.

ABSTRACT: A central problem in computational biophysics is the treatment of titratable residues in molecular dynamics simulations of large biological macromolecular systems. Conventional simulation methods ascribe a fixed ionization state to titratable residues in accordance with their pK_a and the pH of the system, assuming that an effective average model will be able to capture the predominant behavior of the system. While this assumption may be justifiable in many cases, it is certainly limited, and it is important to design alternative methodologies allowing a more realistic treatment. Constant-pH simulation methods provide powerful approaches to handle titratable residues more realistically by allowing the ionization state to vary statistically during the simulation. Extending

SUBMITTER: Bignucolo O 

PROVIDER: S-EPMC9483922 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature