Free-energy landscape of kinesin by a realistic lattice model.

Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Gō interactions. By means of the multi-self-overlap ensemble Monte Carlo method and the principal component analysis, 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. (c) 2007 Wiley-Liss, Inc.