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

Details

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_5DCCD5D6A63D
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.
Journal
The journal of physical chemistry. B
Author(s)
Bignucolo O., Chipot C., Kellenberger S., Roux B.
ISSN
1520-5207 (Electronic)
ISSN-L
1520-5207
Publication state
Published
Issued date
15/09/2022
Peer-reviewed
Oui
Volume
126
Number
36
Pages
6868-6877
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
Publication Status: ppublish
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 <sub>a</sub> 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 the molecular mechanical (MM) potential energy function to a family of potential functions accounting for different ionization states, constant-pH simulations are designed to sample all accessible configurations and ionization states, properly weighted according to their Boltzmann factor. Because protonation and deprotonation events correspond to a change in the total charge, difficulties arise when the long-range Coulomb interaction is treated on the basis of an idealized infinite simulation model and periodic boundary conditions with particle-mesh Ewald lattice sums. Charging free-energy calculations performed under these conditions in aqueous solution depend on the Galvani potential of the bulk water phase. This has important implications for the equilibrium and nonequilibrium constant-pH simulation methods grounded in the relative free-energy difference corresponding to the protonated and unprotonated residues. Here, the effect of the Galvani potential is clarified, and a simple practical solution is introduced to address this issue in constant-pH simulations of the acid-sensing ion channel (ASIC).
Keywords
Hydrogen-Ion Concentration, Membrane Proteins, Molecular Dynamics Simulation, Water/chemistry
Pubmed
Web of science
Open Access
Yes
Create date
26/08/2022 8:46
Last modification date
04/04/2023 6:53
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