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Bacteriorhodopsin

Bacteriorhodopsin. or form is function. The bR photocycle.

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Bacteriorhodopsin

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  1. Bacteriorhodopsin or form is function

  2. The bR photocycle bR is a thermally driven proton pump, with at least 6 intermediate states, understood to varying degrees. It operates on time scales spanning 11 orders of magnitude, from the initial femtosecond electronic and Franck-Condon transitions to the eventual recovery of the retinal chromophore.

  3. the retinal active site The chromophore retinal is bonded covalently as a Schiff base, a reversible and easily protonated bond between amide and carboxyl groups. The absorption maximum depends strongly on the surrounding environment, as do the kinetics and conformational energy landscape of retinal. Recent spectroscopic experimentsat 5 femtosecond time resolution show that a three state system is likely.

  4. The L intermediate Here we see the first structural rearrangements of the protein. Re-isomerization of retinal to 13-cis shortens the ScB-complex counterion distance and breaks up a complex network of hydrogen bonds, freeing water molecules to move. These changes result in the pKaof the Schiff base, just enough to lower it below that of D85, and proton transfer occurs (Some argue that this is a hydrolysis reaction, involving a water molecule.) K216 and W182 move (forced by C20?), causing the G helix to be less stiff.

  5. The M intermediate pKa changes propagate to the EC surface, h-bond network changes result in release of proton, probably from E194 or E204, or both. The mysterious and crucial “switch” occurs sometime in the M state, but no correlation between spectroscopic states and states has been made. The mechanism of the switch is unknown but may result from linear translation or simple rotation of the Schiff Base linkage (e.g. bicycle pedal pathway).

  6. The N and O intermediates Less is known about these states. The N intermediate is marked by the beginnings of reprotonation from the CP side, but it is not at all clear how this happens (proton antennae? Structural changes leading to a new channel?). D96 ultimately donates a proton to the Schiff base, but this process is also a mystery. The O intermediate is where reisomerization of the retinal begins, and the photocycle completes itself.

  7. References, in no particular order • Kobayashi, et al, Nature 414, 29.Nov.2001, p. 531-534 • Lanyi and Pohorille, Trends Biotech., April 2001 v19:140-144 • Lanyi and Luecke, Curr. Op. Struct. Biol. 2001, 11:415-419 • Oesterhelt, Curr. Op. Struct. Biol. 1998, 8:489-500 • Edman, et al., Nature 401, 21.Oct.1999, p. 822-826 • Genick et al., Science, 275:1471-1475, 7 March 1997 (time resolved x-rays) • Luecke et al., Science 286:255-260, 8 October 1999

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