Neck-region-microtubule interactions direct counterclockwise stepping of kinesin-1

Abstract

The "neck" region of kinesin is a structurally conserved element critical for force generation, stepping directionality, and cargo transport along microtubules, yet its atomic-scale structure in a functional context remains unresolved. Here, we employ all-atom replica exchange molecular dynamics simulations to resolve a high-confidence conformation of the neck region in dimeric human kinesin-1 bound to a realistic microtubule lattice, and use this structure to simulate kinesins initial stepping motion. Our simulations reveal that the neck coiled-coil is oriented perpendicular to the microtubules axis and positioned near its surface--a conformation consistent with earlier proposals but lacking high-resolution validation. Importantly, simulations indicate that neck-microtubule interactions bias the stepping trajectory, directing the rear kinesin head to overtake the front head from the right (counterclockwise stepping). These findings establish a mechanism by which neck-microtubule interactions govern directional bias in kinesins initial step, offering new insight into the molecular basis of its motility.