Conformational changes in the M state |
Part 3 (next) |
| Both states of Bacteriorhodopsin are shown simultaneously. The ground state is shown in cyan. The M state is shown in blue. Here helices F and G are shown. Lys 216 in helix G is bonded to retinal. These are the last two helices in the protein. Conformational changes can be noticed by observing the side chains, especially the aromatic rings between the helices. These changes allow a water channel to form at the cytoplasmic side, at the top, connecting Asp 96 to the surface.
This is a close up in the same coloring scheme. In the M state Lys 216 (oxygen) no longer makes a backbone H-bond. It becomes colored white. Hbonds are colored red. This is the region that has a discontinuity in the normal α-helical H-bonding pattern. A π-helix pattern exists for a couple residues, as a water molecule H-bonds between the two helices, using the carbonyl oxygen of residue Ala 215.
In the late M state Asp 82 has moved only slightly, but the nearby Arg 85 has swung down away from it, probably due to reduced interactions after protonation of the Asp. This movement of the Arg is thought to initiate deprotonation of Glu 204, and release of a proton to the extracellular side. Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin. 1cwq (PDB) |