a lysine residue located in the seventh helix (helix G), about midway between the cytosolic and
extracellular aqueous phases (Figs. 1.23D and 1.24B). In the resting state of “light-adapted” BR,
retinal is in the all-trans conformation. Because the terminal ring at the free extremity of retinal is
solidly held in a binding pocket comprising aromatic residues carried by helices C and F (Fig. 1.23E,
F), any isomerization it undergoes will exercise on the protein a pressure tending to induce structural
changes.
Free all-trans retinal has a strong peak of absorbance at ~380 nm. When bound to membraneinserted BR by a Schiff base, which, in the resting state, is protonated (Fig. 1.23C), it absorbs
maximally at ~570 nm, in the visible part of the spectrum, giving the protein its characteristic purple
color. Light-induced isomerization of retinal from the all-trans to the 13-cis form initiates a conformational cycle during which the Schiff base transfers its proton to an aspartate residue (Asp85), and
from there to the external medium, whereas another aspartate residue (Asp96) reprotonates it and picks
up a proton from the cytosol (Fig. 1.24). The whole process requires 10–15 ms, and most of the many
structural intermediates in the cycle can be distinguished spectroscopically (Fig. 1.24A). Of practical
interest is the fact that, in the dark, a conformational equilibrium is reached in which part of the retinal
is in the all-trans and part in the 13-cis conformation. This “dark-adapted” protein has a visible
absorbance maximum at ~560 nm. Upon illumination, photocycling progressively converts all of the
resting-state retinal to the all-trans form. The resulting ~10-nm red shift, which can be observed
Fig. 1.23 (A) Chemical structure of retinal and lysine 216. (B) Formation of an unprotonated Schiff base.
(C) Protonation of the Schiff base. (D) Ribbon representation of the 3D structure of bacteriorhodopsin,
viewed from within the membrane, with the front-most helices rendered transparent and the critical
residues forming the retinal binding pocket in space-filling representation. The cytosol is on top. (E, F)
Enlarged views of all-trans retinal (yellow), in either stick (E) or space-filling (F) representation,
surrounded by aromatic residues W86, W182, and Y185 (PDB 1QM8) (Panels D–F are from Kandori
2015. # 2015 H. Kandori).
1.6 Dynamics of Transmembrane Regions and the Function of Membrane Proteins
33
extracellular aqueous phases (Figs. 1.23D and 1.24B). In the resting state of “light-adapted” BR,
retinal is in the all-trans conformation. Because the terminal ring at the free extremity of retinal is
solidly held in a binding pocket comprising aromatic residues carried by helices C and F (Fig. 1.23E,
F), any isomerization it undergoes will exercise on the protein a pressure tending to induce structural
changes.
Free all-trans retinal has a strong peak of absorbance at ~380 nm. When bound to membraneinserted BR by a Schiff base, which, in the resting state, is protonated (Fig. 1.23C), it absorbs
maximally at ~570 nm, in the visible part of the spectrum, giving the protein its characteristic purple
color. Light-induced isomerization of retinal from the all-trans to the 13-cis form initiates a conformational cycle during which the Schiff base transfers its proton to an aspartate residue (Asp85), and
from there to the external medium, whereas another aspartate residue (Asp96) reprotonates it and picks
up a proton from the cytosol (Fig. 1.24). The whole process requires 10–15 ms, and most of the many
structural intermediates in the cycle can be distinguished spectroscopically (Fig. 1.24A). Of practical
interest is the fact that, in the dark, a conformational equilibrium is reached in which part of the retinal
is in the all-trans and part in the 13-cis conformation. This “dark-adapted” protein has a visible
absorbance maximum at ~560 nm. Upon illumination, photocycling progressively converts all of the
resting-state retinal to the all-trans form. The resulting ~10-nm red shift, which can be observed
Fig. 1.23 (A) Chemical structure of retinal and lysine 216. (B) Formation of an unprotonated Schiff base.
(C) Protonation of the Schiff base. (D) Ribbon representation of the 3D structure of bacteriorhodopsin,
viewed from within the membrane, with the front-most helices rendered transparent and the critical
residues forming the retinal binding pocket in space-filling representation. The cytosol is on top. (E, F)
Enlarged views of all-trans retinal (yellow), in either stick (E) or space-filling (F) representation,
surrounded by aromatic residues W86, W182, and Y185 (PDB 1QM8) (Panels D–F are from Kandori
2015. # 2015 H. Kandori).
1.6 Dynamics of Transmembrane Regions and the Function of Membrane Proteins
33