The Journal of Membrane Biology

, Volume 251, Issue 5–6, pp 633–640 | Cite as

Effect of Site-Specific Intermolecular Lysine–Tryptophan Interactions on the Aggregation of Gramicidin-Based Peptides Leading to Pore Formation in Lipid Membranes

  • Alexander M. Firsov
  • Irina D. Pogozheva
  • Sergey I. Kovalchuk
  • Elena A. Kotova
  • Yuri N. AntonenkoEmail author


In contrast to the parent pentadecapeptide gramicidin A (gA), some of its cationic analogs have been shown previously to form large-diameter pores in lipid membranes. These pores are permeable to fluorescent dyes, which allows one to monitor pore formation by using the fluorescence de-quenching assay. According to the previously proposed model, the gA analog with lysine substituted for alanine at position 3, [Lys3]gA, forms pores by a homopentameric assembly of gramicidin double-stranded β-helical dimers. Here, we studied the newly synthesized analogs of [Lys3]gA with single, double and triple substitutions of isoleucines for tryptophans at positions 9, 11, 13, and 15. Replacement of any of the tryptophans of [Lys3]gA with isoleucine resulted in suppression of the pore-forming activity of the peptide, the effect being significantly dependent on the position of tryptophans. In particular, the peptide with a single substitution of tryptophan 13 showed much lower activity than the analogs with single substitutions at positions 9, 11, or 15. Of the peptides with double substitutions, the strongest suppression of the leakage was observed with tryptophans 13 and 15. In the case of triple substitutions, only the peptide retaining tryptophan 11 exhibited noticeable activity. It is concluded that tryptophans 11 and 13 contribute most to pore stabilization in the membrane, whereas tryptophan 9 is not so important for pore formation. Cation–π interactions between the lysine and tryptophan residues of the peptide are suggested to be crucial for the formation of the [Lys3]gA pore.


Peptide Liposome Leakage Pore Channel Permeability Gramicidin A 



Gramicidin A


gA with lysine in the position 3 instead of alanine




Bilayer lipid membrane



The authors are grateful to Andrei Lomize from the University of Michigan and Tatyana Rokitskaya from Belozersky Institute of Physico-Chemical Biology for fruitful discussions and a help in conducting several experiments. We acknowledge the financial support from the Russian Science Foundation (Grant Number 16-14-10025) to Yuri Antonenko for synthesis of gA derivatives and liposome leakage studies and the financial support from the Division of Biological Infrastructure of the National Science Foundation (Award Number 1458002) to Irina Pogozheva for modeling part of the research.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.


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Authors and Affiliations

  1. 1.Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
  2. 2.Department of Medicinal ChemistryUniversity of MichiganAnn ArborUSA
  3. 3.M.M.Shemyakin and Y.A.Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia

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