Molecular dynamics study of lipid bilayer asymmetry induced by ion concentration gradient and electronic polarizability

ABSTRACT

It has been difficult to reproduce an arbitrary value of a membrane potential in molecular dynamics (MD) simulations for lipid bilayer systems because the membrane potential is sensitively affected by the net charge difference. The membrane potential and membrane properties depend on the intra- and extracellular ion concentrations. In this paper, we present a simple procedure to reproduce an arbitrary value of the membrane potential by all-atom MD simulations for two POPC bilayers system. The calculated membrane capacitance is consistent with an experimental result for the POPC. We show a correlation between the ion imbalance and the number of lipid molecules per leaflet to reproduce an arbitrary value of the membrane potential in MD simulations. Moreover, we show an asymmetry of lipid head group induced by the electronic polarizability and an asymmetry of lipid tail and water molecules on the membrane surface induced by the ion concentration gradient.

KEYWORDS:

• Bilayer asymmetry
• membrane potential
• molecular dynamics simulation
• ion concentration gradient
• electronic polarizability

Acknowledgements

The calculations were partly performed at the research center for computational science of Institute for Molecular Science (IMS), and the center for computational sciences, University of Tsukuba, and the advanced center for computing and communication of RIKEN.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was partly supported by Kanazawa University SAKIGAKE Project and JSPS KAKENHI [grant numbers 26400429 to H.N. and 19K16086 and 20H04791 to H.S.].