Transport Dynamics of MtrD: An RND Multidrug Efflux Pump from Neisseria gonorrhoeae

• Published in: Biochemistry (Easton) 2021-10, Vol.60 (41), p.3098-3113
• Main Authors: Ammerman, Lauren, Mertz, Sarah B., Park, Chanyang, Wise, John G.
• Format: Article
• Language: English
• Subjects: Azithromycin - chemistry; Azithromycin - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; Biological Transport; Hydrogen Bonding; Ligands; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Membrane Transport Proteins - chemistry; Membrane Transport Proteins - metabolism; Molecular Dynamics Simulation; Neisseria gonorrhoeae - chemistry; Protein Binding; Streptomycin - chemistry; Streptomycin - metabolism
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/acs.biochem.1c00399

The MtrCDE system confers multidrug resistance to Neisseria gonorrhoeae, the causative agent of gonorrhea. Using free and directed molecular dynamics (MD) simulations, we analyzed the interactions between MtrD and azithromycin, a transport substrate of MtrD, and a last-resort clinical treatment for multidrug-resistant gonorrhea. We then simulated the interactions between MtrD and streptomycin, an apparent nonsubstrate of MtrD. Using known conformations of MtrD homologues, we simulated a potential dynamic transport cycle of MtrD using targeted MD techniques (TMD), and we noted that forces were not applied to ligands of interest. In these TMD simulations, we observed the transport of azithromycin and the rejection of streptomycin. In an unbiased, long-time scale simulation of AZY-bound MtrD, we observed the spontaneous diffusion of azithromycin through the periplasmic cleft. Our simulations show how the peristaltic motions of the periplasmic cleft facilitate the transport of substrates by MtrD. Our data also suggest that multiple transport pathways for macrolides may exist within the periplasmic cleft of MtrD.