during steps 1 and 2 (Figure 17.11). The protein then switches, due to
conformational changes, to be coupled to the other side of the membrane,
leading to the proton uptake during steps 3 and 4. The system then
resets with the reprotonation of Glu-194 and the re-isomerization of the
retinal in step 5.
Comparison of rhodopsins from different organisms
The three-dimensional structure of rhodopsin has also been solved using
X-ray diffraction and was found to be closely related to that of bacterior-
hodopsin, as expected based on the spectroscopic studies and sequence
comparisons. Whereas the 348 amino acid residues form seven long helices
384 PART 3 UNDERSTANDING BIOLOGICAL SYSTEMS USING PHYSICAL CHEMISTRY
N
O
(a) Ground state
all-trans-retinal protonated
Inside
Outside
Membrane
Light
A
B
C
E D
F
G
C
G
F
F C
G
(b) L intermediate
13-cis-retinal protonated
H
O
H
O
O
N
O
(d) N intermediate
13-cis-retinal protonated
O
H
H
O
O
N
O
Asp 96
Asp 85
Arg 82
H
OH
O
O
H
H
C
G
F
N
O
(c) Late M intermediate
13-cis-retinal neutral
H
O
H
O
O
Figure 17.10A summary of the structural changes associated with each of the intermediate states
of bacteriorhodopsin. Modified from Kuhlbrandt (2000).