25-06-2012, 01:06 PM
Seminar on Bacteriorhodopsin
Bacteriorhodopsin.ppt (Size: 970.5 KB / Downloads: 42)
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.
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.
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 pKa of 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.
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.