Biomolecular Simulations under Realistic Macroscopic Salt Conditions
Gregory A Ross1, Ariën S Rustenburg1,2, Patrick B Grinaway1,2
1Computational and Systems Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.
The Journal of Physical Chemistry. B
|April 14, 2018
Summary
Biomolecular simulations can now dynamically adjust ion concentrations using a novel Monte Carlo osmostat, providing more realistic local salt environments. This method enhances accuracy by simulating fluctuating ion conditions, unlike traditional fixed-salt simulations.
Area of Science:
- Computational chemistry
- Biophysics
- Molecular dynamics
Background:
- Biomolecular simulations traditionally use fixed ion concentrations, not reflecting dynamic biological conditions.
- Real biological systems exhibit local salt concentrations that fluctuate and differ from bulk.
- The extent of these salt concentration variations in biological systems is largely unknown.
Purpose of the Study:
- To introduce a Monte Carlo osmostat for dynamic ion concentration sampling in simulations.
- To enable simulations to sample the semigrand canonical ensemble with fluctuating salt pairs.
- To accurately model environments where local salt concentration varies.
Main Methods:
- Developed a Monte Carlo osmostat for explicit solvent molecular dynamics or Monte Carlo simulations.
- Implemented nonequilibrium candidate Monte Carlo (NCMC) moves for efficient ion and water exchange.
- Utilized a modified Metropolis-Hastings criterion for correct equilibrium statistics in the (Δμ, N, p, T) ensemble.
Main Results:
- The osmostat successfully reproduces equilibrium statistics for ion exchange with a reservoir.
- Achieved significant (∼10^46x) boosts in Monte Carlo acceptance rates using NCMC.
- Demonstrated that protein and nucleic acid systems show salt concentration distributions differing from fixed-salt simulations.
Conclusions:
- The novel osmostat provides a more biologically relevant simulation method.
- Dynamic ion fluctuations in simulations are comparable in magnitude to average concentrations.
- This approach offers a more accurate representation of biomolecular environments.
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