Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

• Published in: Biophysical journal 2018-05, Vol.114 (10), p.2352-2362
• Main Authors: Zavadlav, Julija, Sablić, Jurij, Podgornik, Rudolf, Praprotnik, Matej
• Format: Article
• Language: English
• Subjects: DNA - chemistry; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleic Acids and Genome Biophysics; Pressure; Salts - pharmacology; Solutions; Solvents - chemistry
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2018.02.042

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system’s electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.