Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations

Abstract

Infections in many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine(DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA) anαtoxin with its inserted wedge shaped bundle of insertedαhelices induces significant asymmetry across the membrane leaflets in comparison withαhemolysin (AHL) aβtoxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbation to lipid order as reflected in the tilt angle and order parameters, and membrane thinning is short ranged, lying within ∼ 2.5 nm from the periphery of the either pore complex, commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extend outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with residues tyrosine, tryptophan, lysine and arginine show increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests an inherent plasticity of membrane lipids enabling recovery of structure and membrane fluidity even in the presence of these large oligomeric trans-membrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.