Improved sample preparation, data collection, and image processing pipelines have ushered in a new era in cryo-Electron Tomography (CryoET). Electron density maps of large, conformationally heterogeneous assemblies can be determined at subnanometer resolutions and coupled with high resolution structural information and large scale molecular dynamics simulation to gain atomistic understanding of large and complex cellular machinery that is otherwise unattainable. We use such an integrative approach to investigate the signal transduction in bacterial chemotaxis arrays - large transmembrane protein complex assemblies responsible for modulating the motility of bacteria. These arrays are responsible, in part for appropriately biasing the cell's inherent random walk, and also retaining the memory of recent states of the system. Despite recent advances, fundamental questions on how the components of the system work together to transduce the signal from membrane receptor to kinase molecule, and how the individual signaling unit works cohesively to achieve a large gain in signaling remain unanswered. We devised a novel in vitro reconstitution system to build extended signaling arrays on a lipid monolayer using purified protein components, providing an unprecedented number of signaling units in a thin layer (∼150-200nm) ideal for cryoET. The individual subvolumes from 3D tomograms are extracted, aligned, classified and averaged, resulting in a 3D density map of the basic chemotaxis signaling unit comprising the chemoreceptor, the histidine kinase CheA and the cofactor CheW. The density map reveals an unexpected asymmetry among three kinase CheA dimers, indicating distinct CheA conformations within the unit. Large scale all-atom molecular dynamics simulations further point to the specific side chain contacts that mediate the transition of CheA conformations, which we show, through biochemical assays, to fully abrogate chemotactic function if disrupted.
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