Unbinding Simulation of Kinesin’s Neck Linker

Kinesin’s neck linker is known to play a critical role in its nucleotide-dependent motility. However, it remains unclear how the neck linker binds and unbinds on the kinesin motor head as it walks on the microtubule and generates a walking stroke. To elucidate the nature of the interaction between the neck linker and motor head, we performed molecular dynamics simulations in which the neck linker is pulled out of the binding pocket by external forces. We found that it unbinds in a stepwise manner, in which N334 located in the middle of the neck linker keeps it from complete unbinding, creating an intermediate state. The rest of the neck linker rapidly unbinds once N334 releases from the motor head. Furthermore, we found that the N-terminal cover strand forms a β-sheet with the base portion of the neck linker, which can potentially control kinesin motility by affecting its conformational behavior. Our characterization of subdomains in the neck linker and their binding partners will help elucidate the walking mechanism of kinesin.