Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments

Area of Science:

• Biophysics
• Computational Chemistry
• Materials Science

Background:

• Atomistic resolution molecular dynamics (MD) simulations are crucial for understanding lipid bilayer structures.
• Experimental data (C-H bond order parameters, relaxation rates, scattering factors) provide benchmarks for MD models.
• Phosphatidylcholine lipid bilayers are extensively studied, offering a large dataset for validation.

Purpose of the Study:

• To assess the accuracy of classical atomistic MD simulations in describing phosphatidylcholine lipid bilayer structures and dynamics.
• To compare simulation-derived parameters with experimental data to evaluate model quality.
• To identify discrepancies and limitations of MD models, particularly at the lipid bilayer interfacial region.

Main Methods:

• Calculation of C-H bond order parameters, spin relaxation rates, and scattering form factors from MD simulations.
• Comparison of simulated parameters with experimentally obtained data for phosphatidylcholine lipid bilayers.
• Joint interpretation of diverse experimental data using a unified structural model.

Main Results:

• MD simulations generally provide a good description of the acyl chain structure and rotational dynamics in lipid bilayers.
• Simulations qualitatively reproduce changes in lipid bilayers due to temperature, dehydration, and cholesterol concentration.
• Significant inaccuracies are observed in the simulation of interfacial regions, including glycerol backbone, choline structures, and cation binding.

Conclusions:

• While MD simulations excel at modeling the hydrophobic core of lipid bilayers, their accuracy diminishes at the interfacial regions.
• Extreme caution is advised when using MD simulations to investigate phenomena critically dependent on the lipid bilayer interfacial region.
• Further refinement of MD models is necessary to accurately capture the complex behavior of lipid bilayer interfaces.