Holo-BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD.
While there is evidence that other ABC transporters can tell between empty and loaded substrate binding protein, reconstitution experiments suggest otherwise for the Escherichia coli vitamin B12 importer BtuCD-F. Here, we address the question of BtuCD-F substrate sensitivity in a combined protein-protein docking and molecular dynamics simulation approach. Starting from the BtuCD and holo-BtuF crystal structures, we model two holo-BtuCD-F docking complexes differing by a 180 degrees orientation of BtuF. One of these is similar to the apo-BtuCD-F crystal structure. Both docking complexes were embedded in a lipid/water environment to investigate their dynamics and BtuCD's conformational response to the presence and absence of BtuF, vitamin B12, and Mg-ATP in a series of 28 independent MD simulations. We find holo-BtuF stabilizing the open conformation of BtuCD, whereas the transporter begins to close again when BtuF or vitamin B12 is removed-suggesting BtuCD-F is capable of substrate sensitivity. We identified BtuC transmembrane helices 3 and 5, the L-loops and the adjacent helices comprised of BtuC residues 170-180 as hotspots of conformational change. We propose the latter to act as substrate sensors. BtuF-Trp44 appears to act as a lid on the vitamin B12 binding cleft in BtuF X-ray structures and protrudes into the BtuCD transport channel in one of our simulations, which might represent an initial step in vitamin B12 uptake. On an average, we observe subunit motions where the nucleotide binding domains approach each other while the transmembrane domains display an opening trend toward the periplasm.
Department of Life Science Informatics B-IT, University of Bonn, 53113 Bonn, Germany. kandt@bit.uni-bonn.de
Christian
C
Kandt
D Peter
DP
Tieleman
D018528:ATP-Binding Cassette Transporters / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D020035:Holoenzymes / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D033902:Periplasmic Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D014805:Vitamin B 12 / Q000737:chemistry* / Q000378:metabolism
D018528:ATP-Binding Cassette Transporters; C050021:BtuC peptide, E coli; C050022:BtuD peptide, E coli; D029968:Escherichia coli Proteins; D020035:Holoenzymes; D033902:Periplasmic Binding Proteins; C446048:btuF protein, E coli; D014805:Vitamin B 12