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Martini 3 Limitations in Phospholipid Flip-Flop.

Ondřej Kroutil1, Ladislav Bartoš1,2, Ivo Kabelka1

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Journal of Chemical Theory and Computation
|September 25, 2025
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The Martini 3 force field underestimates lipid flip-flop energy barriers in membranes, unlike Martini 2.2. This impacts simulations of molecular transport across membranes, suggesting needed parameter refinements for Martini 3.

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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.