Comparing Multislice Simulations of MD Simulations with CryoEM Exposes Membrane Prediction Errors

Abstract

Cryo-electron microscopy (cryoEM) is a powerful tool for atomic- and molecular-resolution structure determination, while molecular dynamics (MD) simulations are similarly powerful tools for predicting molecular trajectories. Given the challenges in estimating biomolecule dynamics with cryoEM alone, MD simulations are employed to forecast molecular motions and to interpret cryoEM 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 (CG) or all-atom (AA), into simulated cryoEM 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 cryoEM. MD simulations also correctly predicted bilayer dimensions for single component flat bilayers observed in cryoEM images. However, Martini3 CG-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 cryoEM and small angle X-ray scattering (SAXS). Further testing of MD predictions by direct comparisons between simulated and experimental cryoEM images should lead to the development of more accurate MD force fields. Statement of SignificanceMolecular dynamics (MD) simulations are frequently employed to predict the dynamics of biological macromolecules and assemblies, but these predictions remain difficult to validate experimentally. Cryo-electron microscopy (cryoEM) can be used to directly image the conformational ensemble of macromolecules, but images of Coulombic potential cannot be easily compared to snapshots of atoms from MD simulations. Here, we show that a physics-based multislice image projection algorithm accurately converts MD trajectories to simulated cryoEM 2D images and 3D reconstructions. Using this approach, we identify consistencies and discrepancies between MD simulations and cryoEM experiments. Notably, coarse-grained MD performs poorly compared to all-atom MD when simulating membranes composed of mixtures of lipids that include cholesterol and polyunsaturated lipids, providing observables for MD force field improvement.