Bacteriorhodopsin(bR) Crystallized From Bicelles

"bR is a light driven proton pump from Halobacterium salinarum and contains a covalently bound retinal chromophore that gives it its purple color. bR occurs naturally as a two-dimensional crystal in the inner membrane, forming a specialized membrane structure called the purple membrane. In the purple membrane, the protein subunits are organized in trimeric units which is the form seen in the layers of the crystals grown from the lipid cubic phase."(Faham)

Original Settings

Backbone

The difference in colors shows the mobility of different parts of the protein. Blue is immobile and as you move to red it is more mobile.  There is really no red in this protien, which goes to show that it is very immobile.

Cartoon

In this rendering, the protein can be seen as a monomer with 7 helices and an antiparallel beta sheet.

Basic Sites

Red designates basic sites

Acidic sites

Blue designates acidic sites

Retinal(spacefill) Bound to Protein(wireframe)

Retinal(spacefill) Bound to Protein(cartoon)

With the Retinal in spacefill mode, it becomes easier to see how close it is to the protein.

Retinal(wireframe) Bound to Protein(cartoon)

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Retinal Alone

"Retinal is a conjugated polyene derived from beta-carotene. It is analogous to the visual pigment protein rhodopsin in retinal cells. Absorption of light by the retinal induces a conformation changes in the retinal and protein, which leads to vectorial discharge of protons."(Jakubowski)

Dissolve to Retinal Alone.

This display dissolves the protein to the frame with Retinal, rotates 360 degrees, and then rebuilds itself. (Please wait for it to finish)

Original Settings

Pic by: Lehninger

Retinal active site

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According to the picture above and the retinal active site depicted in the chime, the retinal is contacted by Leu 93, Trp 182, and Trp 86 through different interactions which are probably hydrophobic. It is also supposed to be covalently linked to Lys 216.

Move to Retinal active site

Like stated above, the retinal is normally covantly linked to the Lys 216 via what looks like a schiff base. We're not sure why it's not here in the chime.  It should look like the below picture.

by: Stryer.

Water binding Regions

Notice that the water molecules are located primarily at the turns of the helices. This is important because those parts are more likely to be outside of the hyrdrophobic area of the bilayer. Also, the placement of the water matches well with the lipophilicity surface potential below.  However, there are some water molecules located in between the helices.  The importance of this is discussed below.

Retinal Proton Pumping

Zoom In 200X Zoom Normal

The amino acids in this rendering are important to the proton pumping model that is suggested in the below diagram which shows Retinal in a schiff base arrangement. The water is also an important factor in the bacteriorhodopsin's proton pumping because it provides stability through H-bonding and protons.

Move through Retinal Proton Pumping

Use the diagram below to help follow the movements. The first stop is what is supposed to be a schiff base. In the M_N state, the schiff donates its proton to the Asp 85. Conformational changes cause the Arg 82 to somehow interact with the waters associated with the two Glu 204 and 194.  Then  a proton is released from Glu 204 and through the hole created by the 7 helices.

Original Settings

Straight through Retinal Proton Pumping Helices: Feel the speed. In one side and out the other.

This display takes you through the helices. The running time is about 30 sec. It's more fun than informative.

Original Settings

Normal Surface: Transparent

Normal Surface: Opaque

Lipophilic Surface Potential

The lipophilicity surface potential reaffirms the water binding regions depiction above by showing that the helices are mostly lipophilic.  An interesting point here is the spots of red indicating lipophobic areas located in the holes the helices create.  This may be important in how protons are acquired and pumped through to the other side.

Original Settings

Hydrophobic Normal View

Green indicates hydrophobic sites.

Electrostatic Surface Potential

Notice again that there are regions of interest in the holes created by the helices.  This again may point to how protons are pumped.

Original Settings

Charged Normal View

Yellow indicates charged sites.

Sources:

First diagram of Retinal by Stryer: Biochemistry, Fourth Edition copyright 1995 by W.H. Freeman and company. Figure 12-49, page 320.

Second diagram of Retinal by Gennis & Ebry, Sciene 286, 252 (1999) Copyright (1999) American Association for the Advancement of Science