II. Lipid Bilayers
Jmol Visualization Tutorial:
Lipid Bilayers - Membrane Channel
Key Words: amphipathic, cholesterol, phospholipid, zwitterion, bilayer, fluid phase, gel phase, protein channel
Open the tutorial: http://biomodel.uah.es/en/model2/bilayer/inicio.htm (Chrome browser recommended)
Select the JSmol button: I do not have Java or I prefer not to use it.
Click on Start the presentation to load the Cholesterol start page.
Note: the presentation works best if you click on the grey buttons one at a time in the order they appear in the text.
page 1: Cholesterol
http://biomodel.uah.es/en/model2/bilayer/colester.htm
Select Load the model and then click on the sticks button. A molecule should appear in the lower right. Rotate your view by dragging your left mouse button over the molecule.
Question 1a: Why do more atoms appear in the molecular representation than in the skeletal formula at the top of the page for cholesterol?
Q1b: Which atom of which group is the white 'H' label next to the molecule referring to?
Q1c: Assuming you didn't know the structural formula, describe how you could locate a double bond in this stick representation.
Next, click on Spacefilling model, which opens a van der Waals sphere representation, showing the volume occupied by the atoms.
Q2: The vdw representation might give you the impression that the whole molecule is rigid, but this is not the case. Which half of the molecule is flexible, having unrestricted rotation about single bonds? In other word, both halves are roughly in the same plane in the molecular pose shown, but which half can deviate from this plane at room temperature?
Lastly, click on 'This orientation' in the upper right.
Q3: Describe how this button changes the view, referring to each of the following molecular portions in your answer: polar head; steroid nucleus; alkyl tail.
page 2: Phospholipid
To open the page, select the next arrow or the Phospholipids link in the outline on the lower left...
http://biomodel.uah.es/en/model2/bilayer/fosfolip.htm
First, click on the Here button in the first sentence of the tutorial. A 3D map of the molecule's electron density appears as a dotted outline in the lower right.
Q4: What molecule contributed to the chain in yellow (condensation reaction)? the chain in white? Is this chain kinked or straight at the location of the double bond? Spell the names for the conjugate base of the two fatty acids.
Q5: What color is used to represent the phosphorous atom in stick representation? What is the net charge of this OPPC lipid?
Q6: Name the two functional groups present in a molecule of choline. Is it titratable or non-titratable?
Lastly, click on the Next followed by the Play button to omit hydrogen atoms (white) as is common practice when viewing macromolecules. Looking at the "licorice" representation, you can quickly see the structure of the molecule by checking the nitrogen (blue) and oxygen (red) groups.
Q7: Name the two oxygen-containing functional groups in OPPC.
pages 3-6: Building bilayers
To open the page, select the next arrow or the outline link at lower left...
http://biomodel.uah.es/en/model2/bilayer/bicapa-1.htm
Click on the first 3 buttons one at a time, in order. Now, click the next step arrow 4 times. Use your mouse to rotate to a sideways view.
Q8: When the tails interdigitate, do you expect the saturated or unsaturated chains to pack together more tightly?
Click each remaining Play button to complete subsequent steps.
Q9a: POPC has a gel-fluid transition temperature of 271 K. Arrange the bilayer phases in order of increasing disorder and increasing equilibrium temperature (100 K, 250 K, 300 K):
liquid crystal (fluid)
pure crystalline
paracrystalline (gel)
Q9b: The tutorial mentions increasing the head group spacing, which allows the tails to spread out more (less vertical). Do you expect the gel or fluid to have a smaller bilayer thickness (height between head group layers)?
Q9c: If simulations on a modern computer are for 100 nanoseconds, how much longer is that than 100 ps in 1990?
page 7: Peptide channel
To open the page, select the next arrow or the outline link at lower left...
http://biomodel.uah.es/en/model2/bilayer/gramicid.htm
Gramicidin is an antibiotic peptide produced by soil bacteria that forms a dimeric membrane channel. Its backbone forms a rare secondary structure: the beta helix, which is essentially a tighter version of the beta barrel. Every other amino acid in gramicidin has an inverted chirality at the alpha carbon. This places all sidechains on the outside of the channel (unlike beta barrels), making the inside permeable to cations and water and thus serving as an ionophore. You'll want to click the Next arrows repeatedly to observe. The atomic structure can be viewed here (right clicks> Style> Scheme> Wireframe):
http://pdb.org/pdb/explore/jmol.do?structureId=1NRM&bionumber=1