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Simulating asymmetric membranes using P2₁ periodic boundary conditions.

Amy Rice¹, Samarjeet Prasad¹, Bernard R Brooks¹

¹Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States.

Methods in Enzymology

|July 18, 2024

Summary

Molecular dynamics (MD) simulations of asymmetric lipid bilayers are challenging due to differing leaflet surface tensions. This study introduces P21 periodic boundary conditions (PBC) to generate asymmetric bilayers, reducing differential stress and aiding equilibration.

Keywords:

Asymmetric membranes Differential stress Membrane surface tension Molecular dynamics simulation Periodic boundary conditions Spontaneous curvature

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Area of Science:

Biophysics
Computational Chemistry
Materials Science

Background:

Molecular dynamics (MD) simulations are established for symmetric lipid bilayers.
Asymmetric lipid bilayers present unique challenges due to differing leaflet surface tensions.
Current methods for simulating asymmetric bilayers often require assumptions or are less developed.

Purpose of the Study:

To describe a method for generating asymmetric lipid bilayers using P21 periodic boundary conditions (PBC).
To provide a guide for applying P21 PBC to various asymmetric membrane systems, including those with peptides and proteins.
To demonstrate how P21 PBC can reduce differential stress in asymmetric bilayers.

Main Methods:

Utilizing P21 periodic boundary conditions (PBC) that allow lipid exchange between leaflets.
Assuming equal chemical potentials of lipids in opposing leaflets for bilayer generation.
Applying surface area-based methods for assembling bilayers followed by equilibration with P21 PBC.

Main Results:

P21 PBC successfully generates asymmetric lipid bilayers with reduced differential stress.
The method is demonstrated across a range of systems, from simple lipid mixtures to complex peptide/protein-containing bilayers.
Equilibration with P21 PBC significantly lowers differential stress compared to surface area-based assembly methods.

Conclusions:

P21 PBC offers a viable approach for simulating asymmetric lipid bilayers, particularly for reducing differential stress.
The assumption of equal chemical potentials is a key aspect of the P21 PBC method.
Despite technical limitations, P21 PBC simulations are recommended for equilibration protocols in most asymmetric membrane MD studies.