Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels

Biophys J. 2006 Nov 1;91(9):3230-41. doi: 10.1529/biophysj.105.078782. Epub 2006 Jul 21.


Gramicidin A/gramicidin M heterodimer conductances were measured in planar lipid bilayers and found to form two distinguishable populations about halfway between the gramicidin A and gramicidin M homodimer conductances. This implies that the principle difference in the gramicidin A and gramicidin M transport free-energy profiles occurs at the channel center, where it would produce similar effects on the rate-limiting barrier for the two heterodimers. Kinetic analysis based on this and nearly all previously published homodimer conductance data for both gramicidin A and gramicidin M channels confirms this conclusion, indicating that the translocation step is approximately 100-fold slower in gramicidin M homodimers than in gramicidin A homodimers and that first- and second-ion exit-rate constants are higher by factors of 24 and 10, respectively. Assuming that the ratios of rate constants are related to the free-energy difference between gramicidin A and gramicidin M, we construct an effective ion-Trp free-energy interaction profile that has a minimum at the channel center.

MeSH terms

  • Computer Simulation
  • Dimerization
  • Energy Transfer
  • Gramicidin / analogs & derivatives*
  • Gramicidin / chemistry*
  • Ion Channel Gating*
  • Lipid Bilayers / chemistry*
  • Models, Chemical*
  • Models, Molecular*
  • Tryptophan / chemistry*


  • Lipid Bilayers
  • Gramicidin
  • gramicidin A, 15-des-Trp-Phe-
  • Tryptophan