A Membrane Protein for Modern/Cell Biology

 

The Bacteriorhodopsin protein embedded in a portion of phospholipid bilayer membrane is shown using the Cartoon display, colored by Structure. The retinal pigment is Spacefill, colored purple. H2O molecules, small red spheres, cover the bottom and top surfaces.
The yellow box enclosing this piece is about 80Å on each side. Each phospholipid, shown as Spacefill, has a polar phosphatidyl choline headgroup and hydrophobic tails of oleic and palmitic fatty acids.

"Dissect" the model as follows to see specific portions of the bilayer (e.g. the mostly hidden protein):
Color the carbon atoms in the lower layer a darker gray.

Remove all of the H2O molecules.
  Add the H2O molecules back to both sides of the bilayer.

Show a chunk of the upper layer as Wireframe.
  Remove a chunk of the upper layer completely.
  Restore the chunk of the upper layer to its original Spacefill display.

Viewing Tip: Rotate the model after each of the above operations to get a 3-D perspective on the way the various portions of the bilayer are related to one another and oriented around the protein.

Back to Molecules for Modern/Cell Biology at CMU.

The image displayed on this page requires the Chemscape Chime plug-in.
A Chime Viewer's Guide and the download site for this plug-in are linked under Viewing Tips on the Molecules for Modern/Cell Biology at CMU page.

Credits: The coordinates are from the work of H. Heller, M. Schaefer, and K. Schulten (1993) "Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases", J. Phys. Chem. 97, 8343-60.
Those coordinates were modified slightly from the popc-br-equi.pdb.Z file downloaded from Dr. Heller's Membrane Page.