BPS2026 – Investigating the role of the HflK/C-FtsH protease complex on membrane modulation in E. coli using molecular dynamics simulation

FtsH, an AAA (ATPases associated with diverse cellular activities) protease, associates with the HflK/C assembly to form a massive inner-membrane complex in bacteria, where it degrades both soluble and membrane proteins and contributes to recovery from environmental stress. Homologs of FtsH and HflK/C are conserved in eukaryotic organelles, and mutations in specific isoforms have been linked to neurological disorders. Despite its biological significance, the dynamic interactions between FtsH and HflK/C within the assembly, and their role in modulating membrane properties, remain incompletely understood. Using the enhanced sampling technique Gaussian accelerated molecular dynamics, we investigated the dynamics of the cryo-EM structure of the open, nautilus-like conformation of the complex (PDB ID: 9CZ2) and evaluated its effects on the lipid bilayer. Guided by experimental data, the complex was embedded in a membrane composed of 74% PG, 20% CL, and 6% PE. Our simulations reveal that the protein induces pronounced negative membrane curvature near its edges, with overall curvature intensity approximately 2-fold higher than in the control membrane system lacking the complex, demonstrating that the assembly actively drives membrane deformation beyond the effects of lipid composition alone. We also observed dissociation of an HflC subunit during the simulation, accompanied by direct contacts between neighboring HflK subunits and an FtsH protease. This dynamic behavior is consistent with experimental observations of a secondary opening, proposed to facilitate membrane protein access to FtsH. Change in lipid composition is also observed over the simulation, including 4.3% absolute enrichment of cardiolipins around HflC subunits. These results provide insight into how the complex both modulates its surrounding membrane and undergoes conformational changes as a result.