Structure and Dynamics of Macromolecular Assemblies from Electron Microscopy Maps

Electron microscopy (EM) and electron tomography (ET) have found extensive applica‐ tion to probe structural and dynamic properties of macromolecular assemblies. As an im‐ portant complementary to X-ray and NMR in atomic structural determination, EM has reached a milestone resolution of 2.2Å, enough for understanding atomic interactions, in‐ terpreting mechanism of functions, and for structure-based drug design. This work de‐ scribes approaches to derive structural information from EM/ET images and methods to study dynamics of macromolecular systems using EM/ET images as starting or ending targets. For low-resolution EM/ET maps, X-ray or NMR atomic structures of molecular components are needed to reduce the number of degrees of uncertainty. Depending on the resolution of EM/ET maps and the conformational differences from the X-ray or NMR structures, either rigid fitting or flexible fitting is used to obtain atomic structures. To il‐ lustrate the procedures of the atomic structure derivation, this work describes the coreweighted grid-threading Monte Carlo (CW-GTMC) rigid fitting and the map-restrained self-guided Langevin dynamics (MapSGLD) flexible fitting methods. Their applications are highlighted with four examples: architecture of an icosahedral pyruvate dehydrogen‐ ase complex, dynamics of a group II chaperonin, high-resolution structure of the cell-per‐ meant inhibitor phenylethyl β-D-thiogalactopyranoside, and the mechanism of kinesin walking on microtube.