Martini 3 Limitations in Phospholipid Flip-Flop.

Area of Science:

• Computational Biophysics
• Molecular Dynamics Simulations
• Membrane Biophysics

Background:

• Phospholipid membranes are crucial biological barriers, and lipid flip-flop is vital for maintaining membrane homeostasis and cellular functions.
• Coarse-grained (CG) force fields, like the Martini force field, are valuable for simulating membrane dynamics due to their balance of efficiency and accuracy.
• The accuracy of the latest Martini 3 force field for simulating phospholipid flip-flop energetics was previously unassessed.

Purpose of the Study:

• To evaluate the accuracy of the Martini 3 force field in describing the free energy barriers of phospholipid flip-flop.
• To compare the Martini 3 results with older Martini 2.2 and CHARMM36m force fields, as well as all-atom simulations.
• To identify potential causes for discrepancies in Martini 3's predictions and suggest model refinements.

Main Methods:

• Umbrella sampling simulations were performed for six different phospholipids (POPC, DPPA, POPE, POPG, POPS, DPTAP) within a POPC membrane.
• Simulations were conducted using Martini 3, Martini 2.2, and CHARMM36m force fields, with comparisons to all-atom simulations.
• Systematic parameter testing was employed to investigate the impact of specific force field parameters on flip-flop energetics, particularly for DPTAP.

Main Results:

• Martini 3 predicted significantly lower free energy barriers for lipid flip-flop compared to Martini 2.2 and all-atom simulations.
• The underestimation of flip-flop barriers by Martini 3 was particularly severe for the positively charged lipid DPTAP.
• Altered Lennard-Jones parameters between choline and alkyl tail beads in Martini 3 were identified as a likely cause for the DPTAP discrepancy.

Conclusions:

• The Martini 3 force field exhibits limitations in accurately parameterizing the energetics of lipid flip-flop, especially for charged lipids.
• These findings necessitate careful consideration when using Martini 3 for simulating molecular transport across membranes.
• Potential refinements to Martini 3's parametrization are suggested to improve its accuracy for membrane transport phenomena.