Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states. [Display omitted] •Near-atomic-resolution structure of isocitrate dehydrogenase, a < 100 kDa enzyme•1.8 Å resolution cryo-EM map of 334 kDa glutamate dehydrogenase•2.8 Å resolution cryo-EM map of lactate dehydrogenase, a 145 kDa protein•Localization of small-molecule inhibitors bound to metabolic protein complexes By using cryo-EM methods, the structure of small metabolic enzymes as well as the localization of small-molecule inhibitors that bind to them can be determined at near-atomic resolution.