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

Abstract

RND family proteins are transmembrane proteins identified as large spectrum drug transporters involved in multi-drug resistance. A prototypical case in this superfamily, responsible for antibiotic resistance in selected gram negative bacteria, is AcrB. AcrB forms a trimer using 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. The large number of crystal structures of AcrB prompts studies to further our understanding of the mechanism. To this end, we present a novel strategy based on two key ingredients which are to study dynamics by exploiting information embodied in the numerous crystal structures 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 intramonomer and intermonomer interfaces along the functional cycle. Our analysis shows the relevance of AcrB's efflux mechanism as a template within the HAE1 family but not beyond. It also 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. Our work shows that complex dynamics can be unveiled from static snapshots, a strategy that may be used on a variety of molecular machines of large size.

Common recognition topology of mex transporters of Pseudomonas aeruginosa revealed by molecular modelling

“…In comparison, cationic antibiotics such as oleandomycin, erythromycin, and puromycin are pumped out with low efficiency (Tikhonova et al, 2002). The observed changes in electrostatic potential surfaces of AP L and DP T among pre-MD and most populated cluster structures are related to (expected) conformational changes taking place in the transporters during the MD simulations (Simsir et al, 2021).…”

A Model for Allosteric Communication in Drug Transport by the AcrAB-TolC Tripartite Efflux Pump

“…Currently, AcrAB-TolC is the only drug efflux pump for which there are high-resolution structures of the whole pump assembly in a resting and transport state, and these offer structural insight into the pump’s mechanism of action [ 13 ]. Molecular dynamics (MD) simulations have also been used to study AcrAB-TolC’s conformational change, particularly the functionally rotating mechanism of AcrB [ 31 , 32 ]. This was complemented by a recent study of numerous X-ray structures of AcrB with different substrates that revealed several intermediate states of the transport cycle [ 33 ].…”

Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry

“…leave) the active site [1]. Membrane transporters implement complex efflux mechanisms resorting to loops changing the relative position of (essentially) rigid domains [2]. In the humoral immune response, the binding affinity of antibodies for antigens is modulated by the dynamics of loops called complementarity determining regions (CDRs) [3].…”