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Why is alpha helical membrane channels better suited than beta barrell channels?

  1. Oct 1, 2005 #1
    I have this question I need to answer and I am confused. I've checked my notes and book and can't find an answer. Here is the question:

    "Even though the beta barrel configuration for a transmembrane protein channel would seem an ideal channel, most of the channel proteins have multipass alpha helical domains. Why would this configuration be so well suited to membrane channels?"

    Is it just because the alpha helical proteins form a hole, where the inside is hydropholic and the exterior is hydrophobic (thus interacting with the phospholipids), and the hydrophilic interior makes it easier for the molecules to interact with the protein? I don't get why "beta barrell configuration would seem an ideal channel" in the first place. Confused here, lol. :redface:
  2. jcsd
  3. Oct 2, 2005 #2
    Do you have a good representation (perhaps a drawing in your text) of where the side groups lie, on an alpha helix and beta sheet (I'm presuming a beta barrel is a beta sheet that curls up into a barrel.)?

    I think you're close to the right track with your answer, but I haven't looked at the locations of side groups (R groups) on these structures, in a few years. Double check that and see if your answer is consistent with the 3D structure of each of these motifs.

    (Another question for you: Why do we focus on the R groups in these sorts of questions?)

    (I'd guess, but it's only a guess, that the phrase the beta barrel configuration for a transmembrane protein channel would seem an ideal channel" is an appeal to the (oversimplified) human intuition that a "big channel" lets "stuff" go through "easier." I could be wrong. Is this an introductory course, or an advanced course?)
  4. Oct 2, 2005 #3
    Hi patty, thanks for the reply! Yes, it is an introductory course, Bio 201 (Cell and Molecular Biology). It's the first class required for Bio majors. The only picture I could find in my book is of a channel protein called gramicidin. And it's basically just a picture of a protein with a hydropholic interior with the hydrophobic exterior around it. It says, "gramicidin as an alpha helix consisting of only 15 amino acids. In top view, the molecule forms a hole or pore. In side view, a green helix traces the peptide bonded backbone of they polypeptide. R gropus hang off the backbone to the outside." So I guess the r groups are just drawn to the nonpolar, hydrophobic lipids inside the lipid bilayer. And so the hydrophilic part of the protein is shoved inward to get away from the nonpolar bilayer and forms a hole This stuff is very confusing! Maybe I am making it too hard and there is a very simple answer.
  5. Oct 2, 2005 #4


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    You seem to be on the right track there. You probably aready understand the material well enough to not be sure why a beta barrel would make a good channel in the first place (I think your teacher might be alluding to the apparent "donut" shape of the structure). Here is a site with some illustrations that might help if you're not finding it in your textbook. Take note of the space-filling model shown.

    I'm also assuming by beta barrel that you're really talking about what's known as an alpha/beta barrel, which is a configuration including both alpha helices and beta sheets all "rolled" into a "barrel" shape.
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