1. Studying dynamics without explicit dynamics: a structure-based study of the export mechanism by AcrB
- Author
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Simsir, Méliné, Broutin, Isabelle, Mus-Veteau, Isabelle, Cazals, Frédéric, Algorithms, Biology, Structure (ABS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Physiologie cellulaire et moléculaire des systèmes intégrés (PCMSI), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), ANR: 15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Cibles Thérapeutiques et conception de médicaments (CiTCoM - UMR 8038), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Cazals, Frederic, Idex UCA JEDI - - UCA JEDI2015 - ANR-15-IDEX-0001 - IDEX - VALID, and 3IA Côte d'Azur - - 3IA@cote d'azur2019 - ANR-19-P3IA-0002 - P3IA - VALID
- Subjects
interfaces ,allostery ,molecular distances ,transporters ,conformational changes ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] ,clustering - Abstract
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.
- Published
- 2020