1.A.30.1.1
The flagellar motor (pmf-dependent) (MotA-MotB). TMSs 3 and 4 of MotA and the single TMS of MotB comprise the proton channel, which is inactive until the complex assembles into a motor. Hosking et al. 2006 identify a periplasmic segment of the MotB protein that acts as a plug to prevent premature proton flow. The plug is in the periplasm just C-terminal to the MotB TMS flanked by Pro52 and Pro65. The Pro residues and Ile58, Tyr61, and Phe62 are essential for plug function (Hosking et al. 2006).   Leu46 of MotB acts as the gate for hydronium ion permeation, which induced the formation of a water wire that may mediate the proton transfer to Asp32 in MotB. The free energy barrier for H3O⁺ permeation was consistent with the proton transfer rate deduced from the flagellar rotational speed and number of protons per rotation, which suggests that gating is the rate-limiting step. Structure and dynamics of MotA/B with nonprotonated and protonated Asp32, Val43Met, and Val43Leu mutants in MotB were investigated using molecular dynamics simulation (Nishihara and Kitao 2015). A narrowing of the channel was observed in the mutants, which is consistent with the size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintained a kink whereas the protonation induced a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, which may be correlated to the motion of the flagellar rotor (Nishihara and Kitao 2015). The mechanism of proton passage and coupling to flagellar rotation has been proposed (Nishihara and Kitao 2015).  About a dozen MotA/B complexes are anchored to the peptidoglycan layer around the motor through the C-terminal peptidoglycan-binding domain of MotB (Castillo et al. 2013). Dynamic permeation by hydronium ions, sodium ions, and water molecules has been observed using steered molecular dynamics simulations, and free energy profiles for ion/water permeation were calculated (Kitao and Nishihara 2017). They also examined the possible ratchet motion of the cytoplasmic domain induced by the protonation/deprotonation cycle of the MotB proton binding site, Asp32. The motor (MotAB) consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica have been solved (Liew et al. 2017). Change in the C ring conformation for switching and rotation involve loose and tight intersubunit interactions (Sakai et al. 2019).