Compare and contrast the structural features of the ion carrier valinomycin with those of a channel former like gramicidin. How does the structural information help explain the mechanism by which these molecules conduct ions across membrane bilayers?

Biochemistry by Geoffrey

Your answers should be concise but not too brief: no more than two pages for the entire assignment (typically several sentences or a paragraph per question).  To have a chance to get full credit on the assignment you must use a word processor (ie., typed!).  Hand-written answers will only receive minimal credit.

 

Kranse et. al., (1971) Freezing and Melting of Lipid Bilayers and the Mode of Action of Nonactin.

 

This classic paper compares the membrane conductance of two small molecule ion carriers with a small molecule ion channel former across bilayers at different temperatures.  You should review the structure of the a-helix on pp 135-137 of your textbook to answer question #2 below, and read about membrane proteins and the structure of valinomycin on pp 295-297 of your textbook.

 

Background Questions

 

  1. 1. Compare and contrast the structural features of the ion carrier valinomycin with those of a channel former like gramicidin. How does the structural information help explain the mechanism by which these molecules conduct ions across membrane bilayers?
  2. 2. A typical integral membrane protein has a stretch (or stretches) of ~20 hydrophobic amino acids that form an a-helix that spans the bilayer (as is found in membrane proteins such as glycophorin A and bacteriorhodopsin). Compare and contrast the molecular and structural features of gramicidin with a membrane-spanning a-helix.  Explain how gramicidin can form an ion channel when a typical membrane-spanning a-helix cannot (eg, glycophorin A).

 

 Results

 

  1. 3. What is the specific question being addressed in Figure 1B? What are the results and what conclusions do the authors draw from the results?
  2. 4. What is the specific question being addressed in Figure 3? What are the results and how are they different from the results in Figure 1B?  What conclusions did they draw?
  3. 5. Why did the authors worry about the temperature-dependent solubility of the carriers in the bilayer? How did the authors determine whether the effect of freezing the lipid bilayer was to decrease the solubility of the carriers (nonactin and valinomycin) or whether the effect was to impair their ability to diffuse through the membrane (decrease their mobility)?

General

 

  1. Gramicidin A can adopt more than one structure; NMR spectroscopy has revealed an “end-to-end” dimer form, and x-ray crystallography has revealed an “anti-parallel double helical” form. Briefly outline and describe an experimental approach/strategy (not detailed experiments) to investigate WHICH configuration (“end-to-end dimer” vs “anti-parallel double helical”) gramicidin adopts in an actual lipid bilayer.
  2. Kranse et. al. measured the temperature dependence of membrane conductance using bilayers containing the phospholipids glyceryl dipalmitate and glyceryl distearate. Describe the modifications in membrane content that you would employ to (a) shift the temperature of the phase transition and (b) make the ion conductance curve for valinomycin and nonactin more like that of gramicidin (ie., lacking a steep discontinuity).