Breaking down microtubule severing motors: A computational study of lower order katanin oligomers

Katanin is a microtubule (MT) severing motor from the AAA+ family that forms asymmetric spiral hexamers, which undergo a conformational change to a ring structure through ATP hydrolysis. The presence of ATP and of the carboxy terminal tails (CTTs) of tubulin dimers in a MT is required for oligomerization of severing proteins prior to severing. The CTT binds to loops found in the central pore of the hexamer. Studies showed that the hexamer dissociates into lower order oligomers in the absence of at least one binding partner, but there is no consensus on the order(s) of the oligomers, beyond being up to three, nor on the dissociation dynamics. To address these questions, we carried out molecular dynamics simulations of oligomeric states of katanin, starting from recently solved cryo-EM structures of the hexamers. A central finding is that for hexameric katanin the absence of the ATP and CTT leads to the dissociation of the central pore loops into trimers. We use the combination of structural, kinetic, and Machine Learning approaches to shed light on the stability of lower order oligomers, and the influence of the nucleotide and the substrate on the networks of interactions responsible for the dynamic stability of oligomers.