Gale Rhodes Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Topic: Lipids and Membranes For graphics from other topics, see Topics List.
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Molecules to Study Thanks for Eric Martz for preparing these files.
They are part of a RasMol animation of lipids and bilayers.
This animation is available at the RasMol Home Page.
Click here to go directly to information about this and other animations.
Click the name of each file to download the model described.
Cholesterol A single cholesterol molecule: choleste.pdb
NOTES · Cholesterol in amphipathic, having both polar and nonpolar regions. The polar region, a single hydroxyl group, is relatively small.
· Cholesterol is a normal component of cell membranes. It resides at the surface of the lipid portion of the bilayer, with its hydroxyl protruding into the polar regions.
· Cholelsterol stiffens the outer parts of the phospholipid tails, thus making the membrane less fluid.
· Counterintuitively, cholesterol also acts as an impurity, lowering the "freezing" temperature of the membrane -the temperature at which the membrane undergoes a transition from the fluid phase to the gel phase. So it lowers membrane fluidity, but widens the temperature range over which the membrane remains fluid. Phosphatidyl Choline (PC) A single PC molecule: pc-oph.pdb
An idealized model of18 molecules of PC in a monolayer: PCmono18.pdb
An idealized model 40 molecules of PC in a bilayer: PCbi40.pdb
Non-idealized model: Fluid.pdb (NOTE: 1.2 Mbyte file. Requires a fast connection or plenty of patience.)
NOTES · Note the amphipathic nature of PC.
· Can you identify the fatty acids in these PC molecules? Each molecule has two different fatty acids esterified to it.
· In all these models except Fluid.pdb, all fatty-acid tails are shown with the same conformation. On the other hand, Fluid.pdb shows a large bilayer model after about 100 picoseconds of computer-simulated motion, starting from an idealized model like those above. This model is probably much like a real bilayer.
· For a smaller non-idealized bilayer model, see the gramicidin model below.
Gramicidin A model of the gramicidin dimer in a lipid bilayer: gramisl.pdb.
Prepared view (RasMol script) of gramicidin/bilayer: GcdnMemb.spt.
These two files are large (314 and 99 kb) and will take awhile to download and execute. To view the script, download both the pdb file and script. Put them both in the same folder or directory as RasMol. Run RasMol; then type script GcdnMemb.spt on the command line. Allow 20-30 seconds (or more for older computers) for the scene to appear.
NOTES · Gramicidin is an ionophore, or ion carrier. It make membranes permeable to water and protons, and is blocked by Ca2+ ion.
· In the script, water molecules are green, hydrophobic side chains of gramicidin are yellow, and all other atoms are colored CPK.
· Notice that the lipid side chains from the two monolayers intermingle with each other. This model was produced by computer simulation of the motion of all molecules, starting from an idealized model like those above. This model is probably much like a real bilayer.
· Notice the water molecules in the gramicidin channel.
· Rotate the model to look at it end-on. Only half the bilayer needed to enclose the gramicidin molecule is shown in the model.
· Notice that the ionophore is polar inside and hydrophobic outside -- just the opposite of water-soluble proteins.
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