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The Way Things Move: Looking Under the Hood of Molecular Motor Proteins
Ronald D. Vale and Ronald A. Milligan

Supplementary Material

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  • Movie 1
    An animated model for muscle myosin-based motility.

    Muscle myosin is a dimer of two identical motor heads that are anchored to the thick filament (top) by a coiled-coil (gray rod extending to the upper right). The helical actin filament is shown at the bottom (gray). Myosin's catalytic core is blue and its mechanical elements (converter, lever arm helix and surrounding light chains) are colored yellow or red. In the beginning of the movie, the myosin heads are in the prestroke ADP-Pi state (yellow) and the catalytic cores bind weakly to actin. Once a head docks properly onto an actin subunit (green), phosphate (Pi) is released from the active site. Phosphate release increases the affinity of the myosin head for actin and swings the converter/lever arm to the poststroke, ADP state (transition from yellow to red). The swing of the lever arm moves the actin filament by ~100 Å the exact distance may vary from cycle to cycle depending upon the initial prestroke binding configuration of the myosin on actin. After completing the stroke, ADP dissociates and ATP binds to the empty active site, which causes the catalytic core to detach from actin. The lever arm then recocks back to its prestroke state (transition from red to yellow). The surface features of the myosin head and the actin filament were rendered from X-ray crystal structures by Graham Johnson (fiVth media: www.fiVth.com) using the programs MolView, Strata Studio Pro and Cinema 4D. PDB files used were ADP-AlF4- smooth muscle myosin (prestroke, yellow: #1BR2) and nucleotide-free chicken skeletal myosin (poststroke, red: #2MYS). Transitions between myosin crystal structure states were performed by computer-coordinated extrapolations between the known prestroke and poststroke positions.

  • Movie 2
    An animated model for processive motility by conventional kinesin.

    The two heads of the kinesin dimer work in a coordinated manner to move processively along the microtubule. The catalytic core (blue) is bound to a tubulin heterodimer (green, β-subunit; white, α-subunit) along a microtubule protofilament (the cylindrical microtubule is composed of 13 protofilament tracks). In solution, both kinesin heads contain ADP in the active site (ADP release is rate-limiting in the absence of microtubules). The chaotic motion of the kinesin molecule reflects Brownian motion. One kinesin head makes an initial weak binding interaction with the microtubule and then rearranges to engage in a tight binding interaction. Only one kinesin head can readily make this tight interaction with the microtubule, due to restraints imposed by the coiled-coil and pre-stroke conformation of the neck linker in the bound head. Microtubule binding releases ADP from the attached head. ATP then rapidly enters the empty nucleotide binding site, which triggers the neck linker to zipper onto the catalytic core (red to yellow transition). This action throws the detached head forward and allows it to reach the next tubulin binding site, thereby creating a 2-head-bound intermediate in which the neck linkers in the trailing and leading heads are pointing forward (post-stroke; yellow) and backwards (pre-stroke; red) respectively. The trailing head hydrolyzes the ATP (yellow flash of ADP-Pi), and reverts to a weak microtubule binding state (indicated by the bouncing motion) and releases phosphate (fading Pi). Phosphate release also causes the unzippering of the neck linker (yellow to red transition). The exact timing of the strong-to-weak microtubule binding transition and the phosphate release step are not well-defined from current experimental data. During the time when the trailing head executes the previously described actions, the leading head releases ADP, binds ATP, and zippers its neck linker onto the catalytic core. This neck linker motion throws the trailing head forward by 160 Å to the vicinity of new tubulin binding site. After a random diffusional search, the new lead head docks tightly onto the binding site, which completes the 80 Å step of the motor. The movie shows two such 80 Å steps of the kinesin motor. The surface features of the kinesin motor domains and the microtubule protofilament were rendered from X-ray and EM crystallographic structures by Graham Johnson (fiVth media: www.fiVth.com) using the programs MolView, Strata Studio Pro and Cinema 4D. PDB files used were human conventional kinesin (prestroke, red: #1BG2) and rat conventional kinesin (poststroke, yellow: #2KIN). In human conventional kinesin, the neck linker is mobile and its located in the prestroke state is estimated from cryo-electron microscopy data. Transitions between states were performed by performing computer-coordinated extrapolations between the prestroke and poststroke positions. The durations of the events in this sequence were optimized for clarity and do not necessarily reflect the precise timing of events in the ATPase cycle.

    Supplemental Figure 1. Shown here are cross-eyed (left pair of trio) and wall-eyed (right pair) stereos of the human and rat kinesin structures. On the basis of arguments outlined in the article, we propose that these two structures represent the ADP/nucleotide-free and ATP/ADP-Pi states of kinesin, respectively. In the ADP/nucleotide-free state (human), the neck linker is mobile and only a small portion of it is seen in the x-ray structure (red and orange). ATP binding to the active site causes the relay helix and polymer loop to move (white arrow) from the downstroke position (light green) to the upstroke position (dark green), creating a pocket on the surface of the motor core. Insertion of Ile325 (orange, Ile327 in rat kinesin) into this pocket triggers zippering of the neck linker onto the core. In the docked rat kinesin neck linker (yellow), pockets for additional residues can also be identified, e.g., a conserved Asn329, two residues to the right of Ile327. The black arrowhead indicates where the visible portion of the neck linker originates on the rendered surface. Acknowledgments: Human kinesin, PDB file 1BG2; rat kinesin, PDB file 2KIN. B. Sheehan made the renderings using AVS modules written by M. Pique. A. Lin composed the final illustration.

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