title: Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF.
abstract: BtuF is the periplasmic binding protein (PBP) in the vitamin B(12) uptake system in Escherichia coli where it is associated with the ABC transporter BtuCD. When the ligand binds, PBPs generally display large conformational changes, commonly termed the Venus flytrap mechanism. BtuF belongs to a group of PBPs that, on the basis of crystal structures, does not appear to display such behavior. Using 480 ns multicopy molecular dynamics simulations of apo and holo forms of the protein, we investigate the dynamics of BtuF. We find BtuF to be more flexible than previously assumed, displaying clear opening and closing motions which are more pronounced in the apo form. The protein behavior is compatible with a PBP functional model that postulates a closed conformation for the ligand-bound state, whereas the empty form fluctuates between open and closed conformations. Elastic network normal-mode analysis suggests that all BtuF-like PBPs are capable of similar opening and closing motions. It also makes the typical Venus flytrap domain motions a likely common means of how PBP-ABC transporter interaction could occur.
authors.affiliation: Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
authors.forename: Christian
authors.initials: C
authors.lastname: Kandt
authors.forename: Zhitao
authors.initials: Z
authors.lastname: Xu
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman
mesh_terms: D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D019897:Periplasm / Q000378:metabolism*; D033902:Periplasmic Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation
chemical_list: D029968:Escherichia coli Proteins; D008024:Ligands; D033902:Periplasmic Binding Proteins; C446048:btuF protein, E coli