Large-Scale All-Atom Simulations of T4P Filaments Reveal Critical Interactions for T4P Stability

Type IV pili (T4P) are protein filaments that function as molecular “grappling hooks” for bacteria and archaea. They are found to support very large forces, and undergo a force-induced polymorphic transition that is poorly understood. Most of what is known about T4P comes from cryo-electron microscopy based models, for example from the bacterial organisms Neisseria meningitidis and Neisseria gonorrhoeae. However, these models are static structures, and do not shed light on the underlying dynamics of T4P filaments. In this study we have run more than 1.5 microseconds molecular dynamics simulation on the largest T4P systems that have been studied using all-atom models. Simulations have been carried out for both the N. meningitidis (Nm) and N. gonorrhoeae (Ng) T4P, which exhibit very similar quaternary structure, with slightly different primary sequences for their pilin subunits. The simulations are run in explicit solvent using the AMBER molecular dynamics software, and in order to enhance the sampling in these simulations the hydrogen mass repartitioning method is implemented. All simulations are carried out on graphics processing units (GPUs). These large-scale simulations are used to calculate various filament physical properties including the pilin subunit rise, subunit twist around the helical axis, and the filament persistence length and torsional rigidity. Additionally, the filaments from the Nm and Ng systems are compared to one another based on these metrics, as well as based on the results of the clustering of conformations that the pilin subunits in each filament system explore over microsecond timescales. Pilin-pilin interactions are also studied in order to ascertain the most stable contacts in the system, including hydrogen-bonding, salt-bridge formation, and hydrophobic packing interactions within the filament core, and interactions between pilin globular domains along the T4P surface.