Journal article
A Combined Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin
Biophysical journal, Vol.79(6), pp.2840-2857
2000
Handle:
https://hdl.handle.net/2376/118233
PMCID: PMC1301164
PMID: 11106593
Abstract
We develop a model for proton conduction through gramicidin based on the molecular dynamics simulations of Pomès and Roux (Biophys. J. 72:A246, 1997). The transport of a single proton through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained from the molecular dynamics. In addition, the model incorporates the dynamics of a defect in the hydrogen bonding structure of pore waters without an excess proton. Proton entrance and exit were not simulated by the molecular dynamics. The single proton conduction model includes a simple representation of these processes that involves three free parameters. A reasonable value can be chosen for one of these, and the other two can be optimized to yield a good fit to the proton conductance data of Eisenman et al. (1980,
Ann. N. Y. Acad. Sci. 339:8–20) for pH≥ 1.7. A sensitivity analysis shows the significance of this fit.
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Details
- Title
- A Combined Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin
- Creators
- Mark F Schumaker - Department of Pure and Applied Mathematics, Washington State University, Pullman, Washington 99164-3113 USARégis Pomès - Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 USABenoît Roux - Groupe de Recherche en Transport Membranaire, Départements de Physique et de Chimie, Université de Montréal, Québec H3C 3J7, Canada
- Publication Details
- Biophysical journal, Vol.79(6), pp.2840-2857
- Academic Unit
- Mathematics and Statistics, Department of
- Publisher
- Elsevier Inc
- Identifiers
- 99900548585401842
- Language
- English
- Resource Type
- Journal article