Quantitative Comparison Against Experiments Reveals Imperfections in Force Fields' Descriptions of Phospholipid-Cholesterol Interactions

15 June 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Cholesterol is a central building block in biomembranes, where it induces orientational order, slows down diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level, yet it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses towards simulations of complex membranes mimicking the in vivo conditions: Pertinent multi-component simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation on the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of phosphatidylcholine and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions, but the Slipids parameters provide the best overall performance. The quality-evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multi-component membranes using automated approaches.

Keywords

molecular dynamics simulations
lipid membranes
cholesterol
x-ray scattering
nuclear magnetic resonance

Supplementary materials

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Title
Supporting Information: Quantitative Comparison Against Experiments Reveals Imperfections in Force Fields’ Descriptions of Phospholipid–Cholesterol Interactions
Description
Simulation parameters. Form factor plots from simulations and experiments with the traced minima at various cholesterol concentrations. Electron density profiles from simulation and experiment at various cholesterol concentrations. C-H bond order parameters of both acyl chains of POPC from simulation and experiment at various cholesterol concentrations. Deviation of POPC head group order parameters from experiment as a function of cholesterol concentration. Lateral diffusion coefficients with varying cholesterol concentrations as a function of simulation box size from simulations together with the extrapolation of these values to an infinite box size. Diffusion coefficients as a function of cholesterol concentration from simulations with varying box sizes together with comparison to experiment. Effect of simulation box size on the area per phospholipid across the studied cholesterol concentrations. Effect of simulation box size on the density profiles across the studied cholesterol concentrations. Cholesterol tilt as a function of cholesterol concentration from simulations.
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