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 transporters. A prototypical case in this superfamily, responsible for antibiotic resistance in selected gram negative bacteria, is AcrB. AcrB forms a trimer, which uses the proton motive force to efflux drugs, implementing a functional rotation mechanism. Unfortunately, the size of the system (1049 amino-acid per monomer and membrane) has prevented a systematic dynamical exploration, so that the mild understanding of this coupled transport jeopardizes our ability to counter it. To further our understanding, we present a novel strategy based on two key ingredients which are to study dynamics by exploiting information embodied in the numerous crystal structures of AcrB obtained to date, and to systematically consider subdomains, their dynamics, and their 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 of intra-monomer and inter-monomer interfaces along the functional cycle. Our analysis paves the way to targeted simulations exploiting the most relevant degrees of freedom at certain steps, and also to a targeting of specific interfaces to block the drug efflux. More generally, our work shows that complex dynamics can be unveiled from static snapshots, and our strategy may be used on a variety of molecular machines of large size.

Additional details