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Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2
Francesco Villa1, Alexander D MacKerell2, Benoît Roux3,4
1Laboratoire de Biochimie, CNRS UMR7654, Ecole Polytechnique , Palaiseau 91128 , France.
The Journal of Physical Chemistry. A
|July 4, 2018
Summary
This study optimized molecular dynamics parameters for methyl phosphate (MP) and inorganic phosphate (Pi) to accurately simulate their interactions with magnesium ions. The new parameters enable precise prediction of magnesium binding affinities in aqueous solutions.
Area of Science:
- Computational chemistry
- Biomolecular simulations
- Chemical physics
Background:
- Phosphate groups are crucial for nucleic acids and proteins, influencing folding and binding.
- Methyl phosphate (MP) serves as a model for protein post-translational modifications and nucleic acid termini.
- Accurate molecular simulations require precise force field parameters for phosphate moieties.
Purpose of the Study:
- To optimize polarizable molecular dynamics force field parameters for methyl phosphate (MP) and inorganic phosphate (Pi).
- To validate these parameters by reproducing quantum mechanics and experimental hydration free energies.
- To compute magnesium binding affinities for MP and Pi using advanced simulation techniques.
Main Methods:
- Polarizable molecular dynamics simulations utilizing the classical Drude oscillator model.
- Parameter optimization based on quantum mechanics calculations and experimental hydration free energies.
- Alchemical free energy simulations to determine magnesium binding affinities.
Main Results:
- Optimized parameters for mono- and dianionic methyl phosphate (MP-, MP2-) and inorganic phosphate (Pi2-).
- Parameters showed good agreement with quantum mechanics and experimental hydration data.
- Simulations accurately predicted magnesium binding affinities, with outer sphere binding dominating for MP- and MP2-.
Conclusions:
- The developed Drude oscillator model force field parameters enable accurate simulations of methyl phosphate and inorganic phosphate.
- These parameters facilitate reliable computation of metal ion binding affinities, crucial for understanding biomolecular interactions.
- The findings support the predominant role of outer sphere binding in magnesium-phosphate interactions.
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