Comparing Multislice Projections 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 often 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

SUBMITTER: Mohammed A 

PROVIDER: S-EPMC12710634 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature