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Simulation of the Coupling between Nucleotide Binding and Transmembrane Domains in the ATP Binding Cassette Transporter BtuCD

Jacob Sonne ^*  , Christian Kandt , Günther H. Peters ^* , Flemming Y. Hansen ^*, Morten Ø. Jensen  and D. Peter Tieleman 

^* Department of Chemistry, Technical University of Denmark, DK-2800 Lyngby, Denmark; MEMPHYS - Center for Biomembrane Physics, Physics Department, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark; Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada

Correspondence: Address reprint requests to D. Peter Tieleman, E-mail: tieleman{at}ucalgary.ca.

The nucleotide-induced structural rearrangements in ATP binding cassette (ABC) transporters, leading to substrate translocation, are largely unknown. We have modeled nucleotide binding and release in the vitamin B₁₂ importer BtuCD using perturbed elastic network calculations and biased molecular dynamics simulations. Both models predict that nucleotide release decreases the tilt between the two transmembrane domains and opens the cytoplasmic gate. Nucleotide binding has the opposite effect. The observed coupling may be relevant for all ABC transporters because of the conservation of nucleotide binding domains and the shared role of ATP in ABC transporters. The rearrangements in the cytoplasmic gate region do not provide enough space for B₁₂ to diffuse from the transporter pore into the cytoplasm, which could suggest that peristaltic forces are needed to exclude B₁₂ from the transporter pore.

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