Conformational Changes of the Antibacterial Peptide ATP Binding Cassette Transporter McjD Revealed by Molecular Dynamics Simulations.
The ATP binding cassette (ABC) transporters form one of the largest protein superfamilies. They use the energy of ATP hydrolysis to transport chemically diverse ligands across membranes. An alternating access mechanism in which the transporter switches between inward- and outward-facing conformations has been proposed to describe the translocation process. One of the main open questions in this process is the degree of opening of the transporter at different stages of the transport cycle, as crystal structures and biochemical data have suggested a wide range of distances between nucleotide binding domains. Recently, the crystal structure of McjD, an antibacterial peptide ABC transporter from Escherichia coli, revealed a new occluded intermediate state of the transport cycle. The transmembrane domain is closed on both sides of the membrane, forming a cavity that can accommodate its ligand, MccJ25, a lasso peptide of 21 amino acids. In this work, we investigate the degree of opening of the transmembrane cavity required for ligand translocation. By means of steered molecular dynamics simulations, the ligand was pulled from the internal cavity to the extracellular side. This resulted in an outward-facing state. Comparison with existing outward-facing crystal structures shows a smaller degree of opening in the simulations, suggesting that the large conformational changes in some crystal structures may not be necessary even for a large substrate like MccJ25.
Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada.
Ruo-Xu
RX
Gu
Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada.
Valentina
V
Corradi
Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada.
Gurpreet
G
Singh
Department of Life Sciences, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.|Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom.|Rutherford Appleton Laboratory , Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom.
Hassanul G
HG
Choudhury
Department of Life Sciences, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.|Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom.|Rutherford Appleton Laboratory , Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom.
Konstantinos
K
Beis
Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada.
D Peter
DP
Tieleman
D018528:ATP-Binding Cassette Transporters / Q000737:chemistry / Q000378:metabolism*; D000900:Anti-Bacterial Agents / Q000378:metabolism*; D001430:Bacteriocins / Q000378:metabolism*; D001665:Binding Sites; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
D018528:ATP-Binding Cassette Transporters; D000900:Anti-Bacterial Agents; D001430:Bacteriocins; D029968:Escherichia coli Proteins; C000604081:McjD protein, E coli; C020411:microcin