Microtubule Studies on Lattice Dynamics and Severing Machine Guided Regulation

Microtubules (MTs) are dynamically unstable biofilaments composed of tubulin dimers that undergo stochastic phases of polymerization and depolymerization, induced by single-event transitions known as catastrophe and rescue. Due to low kinetic resolution, studies on MTs have yet to agree on what drives catastrophe and rescue events. Here, we used very long (20 seconds) coarse-grained simulations of MT assembly and disassembly to collect parameters for the characterization of catastrophe, rescue, growth, and shortening of MTs. Utilizing Machine Learning techniques, we found that features related to the energetics of the lattice are crucial to distinguish between the four kinetic states. Catastrophe and rescue can also arise due to MT interactions with severing enzymes, such as spastin. Spastin is a complex machine made of an ATPase motor, a flexible linker, and a MIT domain that collectively form a hexamer. It is known to have a specific binding and alignment to tubulin monomer terminal tails and a non-specific orientation onto the MT lattice, and that it applies mechanical force to remove dimers from the MT. Employing different coarse-grained model simulations, we found strong correlations between the strength of the interactions between the MIT domains and an MT lattice, and the orientation of spastin on the MT surface, the tubulin extraction pathways, and the fate of the machine upon the start of severing. In turn, these results can shed light on this machine's role in catastrophe and rescue events.