Molecular Dynamics Investigation of MFS Efflux Pump MdfA Reveals an Intermediate State between Its Inward and Outward...

Area of Science:

• Structural Biology
• Molecular Dynamics
• Antimicrobial Resistance

Background:

• Multidrug resistance (MDR) is a significant threat to antibiotic therapy, driven by bacterial efflux pumps.
• Major Facilitator Superfamily (MFS) efflux pumps, like MdfA from E. coli, are implicated in quinolone resistance.
• The precise mechanisms of MFS efflux pump conformational transitions, often described by a rocker-switch model, are not fully understood.

Purpose of the Study:

• To investigate the factors influencing the conformational transition of the MFS efflux pump MdfA.
• To elucidate the intermediate states and molecular mechanisms underlying MdfA's transport cycle in silico.

Main Methods:

• Utilized molecular dynamics (MD) simulations to model MdfA's inward and outward conformations.
• Analyzed subtle differences between simulated states to identify key transition events.
• Focused on changes in protonation, hydration, structural alterations, and salt bridge dynamics.

Main Results:

• Identified a distinct intermediate conformational state during MdfA's transition.
• Conformational change from outward to inward is initiated by periplasmic protonation, promoting hydration and helix 1 alteration.
• Increased hydrophobic interactions with the membrane store energy for reverse transition; altered cytoplasmic salt bridges facilitate substrate entry.

Conclusions:

• Detailed the total and local molecular changes during MdfA's conformational transition.
• Provided insights into the energy storage and release mechanisms governing efflux pump function.
• Findings offer a basis for designing novel inhibitors targeting MFS efflux pumps to combat antibiotic resistance.