Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB

Description

RND family proteins are transmembrane proteins identified as large spectrum drug trans-porters involved in multi-drug resistance. A prototypical case in this superfamily, responsiblefor antibiotic resistance in selected gram negative bacteria, is AcrB. AcrB forms a trimer usingthe proton motive force to efflux drugs, implementing a functional rotation mechanism. Unfor-tunately, the size of the system (1049 amino-acid per monomer and membrane) has preventeda systematic dynamical exploration, so that the mild understanding of this coupled transportjeopardizes our ability to counter it.The large number of crystal structures of AcrB prompts studies to further our understandingof the mechanism. To this end, we present a novel strategy based on two key ingredientswhich are to study dynamics by exploiting information embodied in the numerous crystalstructures obtained to date, and to systematically consider subdomains, their dynamics, andtheir interactions. Along the way, we identify the subdomains responsible for dynamic events,refine the states (A,B,E) of the functional rotation mechanism, and analyze the evolution ofintramonomer and intermonomer interfaces along the functional cycle.Our analysis shows the relevance of AcrB's efflux mechanism as a template within theHAE1 family but not beyond.It also paves the way to targeted simulations exploiting themost relevant degrees of freedom at certain steps, and also to a targeting of specific interfacesto block the drug efflux.Our work shows that complex dynamics can be unveiled from static snapshots, a strategythat may be used on a variety of molecular machines of large size

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