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Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study

Journal of Biomolecular NMR volume 62, pages 71–79 (2015)Cite this article

Abstract

A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric β-barrels.

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Acknowledgments

We thank Dr. Andrey Filippov for peptide synthesized. The work is performed accordingly to the Russian Government Program of Competitive Growth of Kazan Federal University; by the subsidy allocated to Kazan Federal University for the project part of the state assignment in the sphere of scientific activities and also supported by Russian Foundation for Basic Research (Grant 14-04-31029 mol_a).

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Authors and Affiliations

  1. NMR Laboratory, Institute of Physics, Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation

    K. S. Usachev, S. V. Efimov, O. A. Kolosova, E. A. Klochkova, A. V. Aganov & V. V.  Klochkov

  2. Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation

    K. S. Usachev

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  1. K. S. Usachev
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  2. S. V. Efimov
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  3. O. A. Kolosova
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  4. E. A. Klochkova
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  5. A. V. Aganov
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  6. V. V.  Klochkov
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Corresponding author

Correspondence to K. S. Usachev.

Additional information

Database Structural data are available in the Protein Data Bank/BioMagResBank databases under the accession numbers 2MZ6/25474.

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Usachev, K.S., Efimov, S.V., Kolosova, O.A. et al. Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study. J Biomol NMR 62, 71–79 (2015). https://doi.org/10.1007/s10858-015-9920-0

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  • DOI: https://doi.org/10.1007/s10858-015-9920-0

Keywords

  • NMR
  • Structure
  • Protegrin
  • Dimer
  • Antimicrobial peptide
  • DPC micelle