Electron microscopy (EM) and electron tomography (ET) have found extensive application to probe structural and dynamic properties of macromolecular assemblies. As an important complementary to X-ray and NMR in atomic structural determination, EM has reached a milestone resolution of 2.2Å, enough for understanding atomic interactions, interpreting mechanism of functions, and for structure-based drug design. This work describes 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 illustrate the procedures of the atomic structure derivation, this work describes the core-weighted 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 dehydrogenase complex, dynamics of a group II chaperonin, high-resolution structure of the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside, and the mechanism of kinesin walking on microtube.
Part of the book: Modern Electron Microscopy in Physical and Life Sciences