Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors

Cryo-electron microscopy (cryo-EM) is a powerful tool for atomic- and molecular-resolution structure determination, whereas molecular dynamics (MD) simulations are similarly powerful tools for predicting molecular trajectories. Given the challenges in estimating biomolecule dynamics with cryo-EM alone, MD simulations are employed to forecast molecular motions and to interpret cryo-EM reconstructions. Few methods, however, can evaluate MD predictions directly. Here, we use multislice wave propagation to project sampled snapshots of MD trajectories, either coarse grained or all atom, into simulated cryo-EM 3D reconstructions. We compared simulated and experimental images of low- and high-curvature membranes to show that MD simulations qualitatively reflect the fluidity and thus the contrast of biological membranes observed by cryo-EM. MD simulations also correctly predicted bilayer dimensions for single-component flat bilayers observed in cryo-EM images. However, Martini3 coarse-grained MD simulations failed to predict changes in membrane thickness induced by high curvature and with heterogeneous lipid compositions. We pinpointed the misbehavior of polyunsaturated lipid tails and cholesterol in Martini3 simulations as the main error sources contributing to inaccurate bilayer thicknesses. Our comparisons also explain membrane structure discrepancies between cryo-EM and small angle x-ray scattering. Further testing of MD predictions by direct comparisons between simulated and experimental cryo-EM images should lead to the development of more accurate MD force fields.