Biomolecular simulations at constant pH.

John Mongan; David A Case

doi:10.1016/j.sbi.2005.02.002

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Biomolecular simulations at constant pH.

John Mongan·David A Case

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Abstract

Like temperature and pressure, the solution pH is an important thermodynamic variable that is commonly varied in experiments and is used by cells to influence biochemical function. It is now becoming feasible to carry out practical molecular dynamics simulations that mimic the thermodynamics of such experiments, by allowing proton transfer between the system of interest and a hypothetical bath of protons at a given pH. These are demanding calculations, because the energetics of charge changes upon protonation or deprotonation must be accurately modeled, and because such simulations must sample both molecular configurations and the large number of protonation states that are possible for a molecule with many titrating sites.

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Algorithms Biopolymers Computer Simulation Hydrogen-Ion Concentration Macromolecular Substances Models, Chemical Models, Molecular Molecular Conformation Protons Solvents Thermodynamics Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.Review

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John Mongan, David A Case. 2005. Biomolecular simulations at constant pH.. https://doi.org/10.1016/j.sbi.2005.02.002

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