Exploring the conformational space of the NorA efflux pump of Staphylococcus aureus: a microscale conventional molecular dynamics and metadynamics simulation approach

Abstract

Efflux pump (EP) proteins play an important role in the emergence of multidrug-resistant (MDR) Staphylococcus aureus and in reducing the effectiveness of antibiotic therapy. EP, NorA of the Major Facilitator Superfamily (MFS) family, is well known for effluxing fluoroquinolones, thereby reducing the intracellular drug concentrations to sub-inhibitory levels and causing S. aureus to be less susceptible. NorA uses the electrochemical proton gradient to efflux drugs across the cell membrane; however, the mechanism of drug efflux remains to be discovered. In the present study, conventional molecular dynamics of 1.0 μs have been performed and essential dynamics (ED), and global motion of the structure has been observed and further used as reference for specifying collective variables (CVs). A metadynamics (MetaD) simulation of 100 ns was employed to sample the conformational space based on the assigned collective variables (CVs). Five energy minima states, including a global minimum, were identified from the free-energy landscape analysis, demonstrating the opening and closing mechanisms of the NorA efflux pump. Transmembrane helices 1 and 2 are identified as the most flexible helices of the efflux pump, performing the function of a lid in the extracellular section (Leu 21 to Leu 42). The efflux process through the NorA efflux pump can be observed from the resulting conformational states, which may be further utilized for the future design and development of next-generation EP inhibitors to address the drug resistance issue in S. aureus.