  How molecular motors like Kinesin regulates the affinity to the rail protein
in the process of ATP hydrolysis remains to be uncovered. To understand the
regulation mechanism, we investigate the structural fluctuation of KIF1A in
different nucleotide states that are realized in the ATP hydrolysis process by
molecular dynamics simulations of Go-like model. We found that "alpha4 helix",
which is a part of the microtubule (MT) binding site, changes its fluctuation
systematically according to the nucleotide states. In particular, the frequency
of large fluctuations of alpha4 strongly correlates with the affinity of KIF1A
for microtubule. We also show how the strength of the thermal fluctuation and
the interaction with the nucleotide affect the dynamics of microtubule binding
site. These results suggest that KIF1A regulates the affinity to MT by changing
the flexibility of alpha4 helix according to the nucleotide states.
