3.E.1.1.1
Bacteriorhodopsin. Proton efflux occurs via a transient linear water-molecule chain in a hydrophobic section of the Brho channel between Asp96 and Asp85 (Freier et al., 2011).  It can be converted to a chloride uptake pump by a single amino acid substitution at position 85.  However, halorhodopsin (3.E.1.2.1), which pumps chloride ions (Cl^-) into the cell, apparently does not use hydrogen-bonded water molecules for Cl^- transport (Muroda et al. 2012).  Nango et al. 2016 used time-resolved serial femtosecond crystallography and an x-ray free electron laser to visualize conformational changes in bRho from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bRho transports protons uphill against a transmembrane concentration gradient. Nango et al. 2016 have created a 3-d movie of structural changes in the protein showing that an initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. Brho has light-independent lipid scramblase activity (Verchère et al. 2017). This activity occurs  at a rate >10,000 per trimer per second, comparable to that of other scramblases including bovine rhodopsin and fungal TMEM16 proteins. BR scrambles fluorescent analogues of common phospholipids but does not transport a glycosylated diphosphate isoprenoid lipid. In silico analyses suggested that membrane-exposed polar residues in transmembrane helices 1 and 2 of BR may provide the molecular basis for lipid translocation by coordinating the polar head-groups of transiting phospholipids. Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR trimer in a phospholipid membrane revealed water penetration along transmembrane helix 1 with the cooperation of a polar residue (Y147 in transmembrane helix 5) in the adjacent protomer. These findings suggest that the lipid translocation pathway may lie at or near the interface of the protomers of the BR trimer (Verchère et al. 2017). Retinal isomerization has been observed in the using a femtosecond x-ray laser (Nogly et al. 2018). S-TGA-1, a halobacterium-derived glycolipid, has the highest specificity to bRho, with a nanomolar dissociation constant (Inada et al. 2019). Weinert et al. 2019 recorded the structural changes in bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release. From 10 to 15 milliseconds onwards, large additional structural rearrangements, up to 9 Å on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle (Weinert et al. 2019).  The effect of membrane composition on the orientation and activity of bR has been reported (Palanco et al. 2017).  Efficient transfer of bRho from native membranes to covalently circularized nanodiscs has been accomplished (Yeh et al. 2018). The oligomeric status of BRho plays a role in the photocycle associated with short-range processes, such as retinal isomerization and deprotonation of the protonated Schiff base at the retinal pocket (Kao et al. 2019).