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ATP-binding cassette (ABC) transporters mediate the movement of molecules across cell membranes in both prokaryotes and eukaryotes. In ABC transporters, solute translocation occurs after ATP is either bound or hydrolyzed at the intracellular nucleotide-binding domains (NBDs). Molecular dynamics (MD) simulations have been employed to study the interactions of nucleotide with NBD. The results of extended (approximately 20 ns) MD simulations of HisP (total simulation time approximately 80 ns), the NBD of the histidine transporter HisQMP2J from Salmonella typhimurium, are presented. Analysis of the MD trajectories reveals conformational changes within HisP that are dependent on the presence of ATP in the binding pocket of the protein, and are sensitive to the presence/absence of Mg ions bound to the ATP. These changes are predominantly confined to the alpha-helical subdomain of HisP. Specifically there is a rotation of three alpha-helices within the subdomain, and a movement of the signature sequence toward the bound nucleotide. In addition, there is considerable conformational flexibility in a conserved glutamine-containing loop, which is situated at the interface between the alpha-helical subdomain and the F1-like subdomain. These results support the mechanism for ATP-induced conformational transitions derived from the crystal structures of other NBDs.

Original publication

DOI

10.1529/biophysj.104.046870

Type

Journal article

Journal

Biophys J

Publication Date

12/2004

Volume

87

Pages

3703 - 3715

Keywords

ATP-Binding Cassette Transporters, Adenosine Triphosphate, Amino Acid Transport Systems, Basic, Bacterial Proteins, Binding Sites, Computer Simulation, Kinetics, Models, Chemical, Models, Molecular, Motion, Nucleotides, Protein Binding, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Structure-Activity Relationship