Binding Mode of Actin-Aplyronine A-Tubulin Heterotrimeric Complex Revealed by Molecular Dynamics Simulation

The antitumor macrolide aplyronine A (ApA) disturbs microtubule (MT) dynamics by inducing the protein -protein interaction (PPI) between actin and tubulin. However, the detailed binding mode of the actin-ApA-tubulin heterotrimeric complex (HTC) and the molecular mechanism by which ApA inhibits MT are unclear. To establish the binding modes of the actin-ApA complex on the tubulin alpha/beta-heterodimer, blind protein -protein docking and molecular dynamics simulations were performed. Two plausible HTC models having enough conformational and ligand stabilities were obtained, in which the C7 N,N,O-trimethylserine ester of ApA, an essential group for its potent cytotoxicity and PPI-inducing effect, interacted with Glu336/Asn337 or Arg123/Glu127 of beta-tubulin. Based on the superposed models with the MT lattice, two possible mechanisms were proposed: the HTC would bind to the plus end of MT to potently inhibit tubulin assembly, or the actin- ApA complex would bind to the middle part of MT to form the internal HTC and destabilize MT structure. Our proposed models can explain why the actin-ApA complex inhibits MT dynamics at a much lower concentration than those of fibrous actin and tubulin proteins in cells.