How cytoplasmic dynein couples ATP hydrolysis cycle to diverse stepping motions: kinetic modeling

Abstract Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of a microtubule (MT) by ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein exhibits various bipedal stepping motions; inchworm and hand-over-hand motions, as well as non-alternating steps of one head. However, the molecular basis to achieve such diverse stepping manners remains unclear because of the lack of an experimental method to observe stepping and ATPase reaction of dynein simultaneously. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and performed Gillespie Monte Carlo simulations that qualitatively reproduce most experimental data obtained to date. The model represents the status of each motor domain as five states according to conformation, and nucleotide- and MT-binding conditions of the domain. In addition, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, similarly to experimental data. The model reproduced key experimental motility-related properties including velocity and run length as functions of the ATP concentration and external force, therefore, provides plausible explanation how dynein achieves various stepping manners with explicit characterization of nucleotide states. Our model highlights uniqueness of dynein in the coupling of ATPase with its movement during both inchworm and hand-over-hand stepping.