Computational Insights into pH Effects on Protein Conformation, Membrane Curvature, and Water Permeation in E. coli Multidrug Efflux Transporter

Abstract MdfA, a multidrug efflux pump in Escherichia coli and a member of the major facilitator superfamily (MFS), is pivotal in bacterial antibiotic resistance due to its ability to expel diverse toxic compounds. This study explores the molecular mechanisms by which pH modulates MdfA's structural dynamics, membrane curvature, and water permeation, leveraging molecular dynamics simulations to provide detailed insights into its functional adaptability and transport efficiency. At acidic pH (4.5), MdfA adopts a highly compact and stable conformation characterized by reduced solvent-accessible surface area (SASA), limited water permeation, and heightened membrane curvature. These features reflect protonation-driven rigidity that preserves structural integrity but diminishes transport efficiency. Near-neutral pH (6.0) represents an optimal balance between rigidity and flexibility, where increased SASA, moderate hydration, and transient water pores enable maximal substrate transport. In contrast, at alkaline pH (7.5), deprotonation induces enhanced flexibility and membrane relaxation, increasing water permeability and pore radius while compromising structural stability over time. Curvature profiles of the membrane leaflets reveal that acidic conditions induce pronounced asymmetry and stress, while neutral and basic pH environments promote planar configurations, reducing deformation. The pH-dependent interplay between MdfA’s conformational states, membrane hydration, and curvature dynamics underpins its functional efficiency, with the physiological pH environment emerging as the most conducive for substrate transport. These findings advance our understanding of how pH modulates efflux pump behavior, offering a molecular framework for designing pH-sensitive drug delivery systems and inhibitors targeting multidrug-resistant pathogens. By linking structural and functional dynamics to environmental pH, this study provides valuable insights into the biophysics of efflux pumps and highlights potential avenues for therapeutic intervention in combating antibiotic resistance.