Insights into the Mechanical Properties of the Kinesin Neck Linker Domain from Sequence Analysis and Molecular Dynamics Simulations

The 14- to 18-amino acid kinesin neck linker domain links the core motor to the coiled-coil dimerization domain. One puzzle is that the neck linker appears too short for the 4-nm distance each linker must stretch to enable an 8-nm step—when modeled as an entropic spring, high inter-head forces are predicted when both heads are bound to the microtubule. We addressed this by analyzing the length of the neck linker across different kinesin families and using molecular dynamics simulations to model the extensibility of Kinesin-1 and Kinesin-2 neck linkers. The force–extension profile from molecular dynamics agrees with the worm-like chain (WLC) model for Kinesin-1 and supports the puzzling prediction that extending the neck linker 4 nm requires forces multiple times the motor stall force. Despite being three amino acids longer, simulations suggest that extending the Kinesin-2 neck linker by 4 nm requires similarly high forces. A possible resolution to this dilemma is that helix α-6 may unwind to enable the two-head bound state. Finally, simulations suggest that cis/trans isomerization of a conserved proline residue in Kinesin-2 accounts for the differing predictions of molecular dynamics and the WLC model, and may contribute to motor regulation in vivo.