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Among the multiple steps constituting the kinesin's mechanochemical cycle,one of the most interesting events is observed when kinesins move an 8-nm stepfrom one microtubule (MT)-binding site to another. The stepping motion thatoccurs within a relatively short time scale (~100 microsec) is, however, beyondthe resolution of current experiments, therefore a basic understanding to thereal-time dynamics within the 8-nm step is still lacking. For instance, therate of power stroke (or conformational change), that leads to theundocked-to-docked transition of neck-linker, is not known, and the existenceof a substep during the 8-nm step still remains a controversial issue in thekinesin community. By using explicit structures of the kinesin dimer and the MTconsisting of 13 protofilaments (PFs), we study the stepping dynamics withvarying rates of power stroke (kp). We estimate that 1/kp <~ 20 microsec toavoid a substep in an averaged time trace. For a slow power stroke with 1/kp>20microsec, the averaged time trace shows a substep that implies the existence ofa transient intermediate, which is reminiscent of a recent single moleculeexperiment at high resolution. We identify the intermediate as a conformationin which the tethered head is trapped in the sideway binding site of theneighboring PF. We also find a partial unfolding (cracking) of the bindingmotifs occurring at the transition state ensemble along the pathways prior tobinding between the kinesin and MT.

Mechanical control of the directional stepping dynamics of the kinesin motor