Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

摘要

Hexameric ring-shaped AAA+ molecular motors have a key function of active translocation of a macromolecular chain through the central pore. By performing multiscale molecular dynamics (MD) simulations, we revealed that HsIU, a AAA+ motor in a bacterial homologue of eukaryotic proteasome, translocates its substrate polypeptide via paddling mechanism during ATP-driven cyclic con-formational changes. First, fully atomistic MD simulations showed that the HsIU pore grips the threaded signal peptide by the highly conserved Tyr-91 and Val-92 firmly in the closed form and loosely in the open form of the HsIU. The grip depended on the substrate sequence. These features were fed into a coarse-grained MD, and conformational transitions of HsIU upon ATP cycles were simulated. The simulations exhibited stochastic unidirectional translocation of a polypeptide. This unidirectional translocation is attributed to paddling motions of Tyr-91 s between the open and the closed forms: downward motions of Tyr-91 s with gripping the substrate and upward motions with slipping on it. The paddling motions were caused by the difference between the characteristic time scales of the pore-radius change and the up-down displacements of Tyr-91 s. Computational experiments on mutations at the pore and the substrate were in accord with several experiments.