title: Molecular dynamics simulations of the bacterial ABC transporter SAV1866 in the closed form.
abstract: The ATP binding cassette (ABC) transporter family of proteins contains members involved in ATP-mediated import or export of ligands at the cell membrane. For the case of exporters, the translocation mechanism involves a large-scale conformational change that involves a clothespin-like motion from an inward-facing open state, able to bind ligands and adenosine triphosphate (ATP), to an outward-facing closed state. Our work focuses on SAV1866, a bacterial member of the ABC transporter family for which the structure is known for the closed state. To evaluate the ability of this protein to undergo conformational changes at physiological temperature, we first performed conventional molecular dynamics (MD) on the cocrystallized adenosine diphosphate (ADP)-bound structure and on a nucleotide-free structure. With this assessment of SAV1866's stability, conformational changes were induced by steered molecular dynamics (SMD), in which the nucleotide binding domains (NBD) were pushed apart, simulating the ATP hydrolysis energy expenditure. We found that the transmembrane domain is not easily perturbed by large-scale motions of the NBDs.
authors.affiliation: Département de Physique and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal, C.P. 6128, succursale centre-ville, Montréal (Québec), Canada H3C 3J7.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: St-Pierre
authors.forename: Alex
authors.initials: A
authors.lastname: Bunker
authors.forename: Tomasz
authors.initials: T
authors.lastname: Róg
authors.forename: Mikko
authors.initials: M
authors.lastname: Karttunen
authors.forename: Normand
authors.initials: N
authors.lastname: Mousseau
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000737:chemistry / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation
chemical_list: D018528:ATP-Binding Cassette Transporters