Conformational Changes of the ABC Transporter McjD Revealed by Molecular Dynamics Simulations

Abstract

ATP-Binding Cassette (ABC) transporters constitute one of the largest protein superfamilies and are involved in a variety of physiological processes such as drug resistance in cancer chemotherapy and maintaining of the blood-brain barrier. Mutations of these proteins are associated with many diseases including cystic fibrosis. ABC transporters utilize the energies of ATP hydrolysis to translocate ligands with diverse chemical properties (such as ions, lipids, and peptides) across the membrane bilayer. An alternating access mechanism has been proposed for their translocation mechanism, in which the protein switches between an inward-facing state and an outward-facing state. Although several ABC transporters have been crystallized in inward- or outward-facing states, the mechanism and extent of the conformational changes remains uncertain. The structure of the ABC exporter McjD from E. coli was recently published in an outward occluded conformation (PDB ID: 4PL0). McjD confers immunity to cells that are producing the antibacterial lasso peptide MccJ25. The cavity of the McjD is accessible from neither the intracellular side nor the extracellular side and may be an intermediate state between the inward- and outward-facing states.After manual docking of the MccJ25 peptide in the cavity of the McjD transporter [1], we applied steered molecular dynamics simulations to pull the ligand out of the extracellular side to investigate the conformational changes during this process. The resulting putative outward-facing state opens to a lesser degree than observed in outward-facing crystal structures. We repeated our simulations with different parameters and the results were reproducible. Therefore, we propose that the large conformational changes implied by some crystal structures are not necessary and that the transporter could accomplish the translocation process with minor structural changes.[1] H. G. Choudhury, et al., Proc Natl Acad Sci USA, 2014, 111 (25), 9145-9150.