Anisotropic unbinding and location-dependent hovering of a kinesin motor head over microtubule

The motor protein kinesin moves over the microtubule (MT) by undergoing a motility cycle involving MT-bound and -unbound states. Compared with the structurally well-defined MT-bound state, very little is known about the behaviors of kinesin in the unbound state at the atomistic level. In order to maintain motility, the unbound head hovers near the MT, where the near-range interaction remains undefined. To this end, we perform a total of over 82-μs all-atom molecular dynamics simulations of a Kinesin-1 motor head detaching and hovering over the MT lattice by using the Anton-2 supercomputer. Resistance to unbinding depended strongly on the loading direction due to the uneven response of the MT-binding elements to pulling. Such directional anisotropy is consistent with easier unbinding of the rear head and resistance to load by the front head in a kinesin dimer. The interaction between a hovering head with the MT surface was evaluated across a 102-point grid with sufficient size and overlap to cover the periodic MT lattice. Interaction with the MT C-terminal tails (CTTs) versus MT surface was strongly location dependent, which results in regions of weak repulsion, relatively free diffusion, and a landing zone formed directly behind the next binding site where attraction to the MT surface is pronounced. The hovering head tends to stay upright with a reduced footprint on the MT and interacts differently between the α-tubulin CTT (αCTT) and β-tubulin CTT (βCTT), where it can "vine-swing" between the two, or brachiate. Unexpectedly, there were a few residues forming notable contacts, including L317 on α6 of kinesin, Y451 at the C terminus of αCTT, and F446 in the middle of βCTT. These results provide a foundation for studying the stepping or diffusion of kinesins, as well as the effects of MT post-translational modifications or interaction with other MT-associated proteins.