Abstract
Amino acid/polyamine/organocation (APC) transporters belong to a large family (∼250) of secondary transport proteins that catalyze bilayer translocation of a broad range of substrates. Monte Carlo Normal Mode Following [Miloshevsky & Jordan, Structure 14, 1241 (2006); 15, 1654 (2007)] is used to explore possible conformational change mechanisms in a proton-dependent APC transporter, ApcT, a bacterial homologue from Methanocaldococcus jannaschii [Shaffer et al., Science 325, 1010 (2009)]. ApcT was captured in an inward-facing apo state. Gating is initiated by global counter-torsions of the intracellular and extracellular domains of ApcT around the pore axis, with the extracellular half rotating clockwise and the intracellular half anticlockwise, and vice versa. The domain motions are highly concerted and cooperative. The stationary plane relative to which counter-torsion occurs passes through the center of ApcT parallel to the membrane. Intracellularly, overall rotation of the peripheral helices (TM7, TM5, TM8, TM3, TM4, TM9, TM10, TM11 and TM12) reconfigures TM6a significantly and TM1b slightly. These helices alternately approach and separate from the opposed peripheral TM10 and TM11, affecting the intracellular mouth. TM6a and TM1b move toward the protein's perimeter and become buried inside the protein. Loops and small helices on the intracellular surface of ApcT undergo large-scale rotations. Extracellular motion is similar. Overall peripheral helix rotation affects TM1a significantly and TM6b slightly, displacing them from and collapsing them onto TM8 and TM5. TM8 and TM5 alternately undergo large-scale bending near their midpoints. Normal mode following along the lowest-frequency eigenvector(s) reveals details of the gating transition in the ApcT transporter.