Structural models of dimeric kinesin on microtubule in all four combinations of open and closed heads. (A) Atomic models of kinesin dimer on microtubule in the two-head–bound state (top view): one with both heads nucleotide-free and in the open state (left; termed Topen-Lopen) and another with the trailing head ATP-bound and in the closed state, while the leading head remains the nucleotide-free/open state (right; termed Tclosed-Lopen). Thermally equilibrium conformations of the disordered neck linkers were determined by running MD simulations (Fig. S4). The lower panel shows close-ups of the neck linkers (red), and α4 (green) and α6 (orange) helices. Numbers indicate the distance between the T328 residue in the trailing head and the I325 residue in the leading head. (B) Close-up view (side view) of the atomic model of two-head–bound state with both heads in the closed state (upper; Tclosed-Lclosed), compared with the Tclosed-Lopen model (lower). We modeled the Tclosed-Lclosed such that the initial segment of the neck linker (323–325 residues) of the leading head docks onto the head, while the rest remains detached. Even this partial docking leads to a considerable increase in neck linker extension, prohibiting the open-to-closed conformational change of the leading head (Fig. 9, purple rectangle). (C) Atomic model of Topen-Lclosed state (upper), compared with the Tclosed-Lopen model (lower). This model represents the off-pathway transition where the tethered head binds to the rear tubulin-binding site after ATP-induced isomerization of the microtubule-bound head (Fig. 9, green hexagonal box). In this model, the I325 residue of the leading head is detached from the head, but its position is translated toward the plus-end of the microtubule due to the rotational movement and extension of the α6 helix (orange rectangle).
