  Structural fluctuations in the thermal equilibrium of the kinesin motor
domain are studied using a lattice protein model with Go interactions. By means
of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal
component analysis (PCA), the free-energy landscape is obtained. It is shown
that kinesins have two subdomains that exhibit partial folding/unfolding at
functionally important regions: one is located around the nucleotide binding
site and the other includes the main microtubule binding site. These subdomains
are consistent with structural variability that was reported recently based on
experimentally-obtained structures. On the other hand, such large structural
fluctuations have not been captured by B-factor or normal mode analyses. Thus,
they are beyond the elastic regime, and it is essential to take into account
chain connectivity for studying the function of kinesins.
