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