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Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy

Abstract

Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16. These “inconsistent” with monomer structure NOEs appears due to formation of an additional antiparallel β-sheet between two monomers. It was also suggested that there is a possible association of protegrins dimers to form octameric or decameric β-barrels in an oligomer state. In order to investigate a more detailed oligomerization process of protegrins, in the present article we report the monomer (PDB ID: 2NC7) and octamer pore structures of the protegrin-5 (PG-5) in the presence of DPC micelles studied by solution NMR spectroscopy. In contrast to PG-1, PG-2, and PG-3 studies, for PG-5 we observed not only dimer NOEs but also several additional NOEs between side chains, which allows us to calculate an octamer pore structure of PG-5 that was in good agreement with previous AFM and PMF data.

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Acknowledgments

We thank Dr. Andrey Filippov for the peptide synthesized. The work was performed according 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; by RFBR, according to the research project No. 16-34-60001 mol_a_dk.

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Correspondence to Vladimir V. Klochkov.

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Database: Structural data are available in the Protein Data Bank/BioMagResBank databases under the accession numbers 2nc7/26009.

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Usachev, K.S., Kolosova, O.A., Klochkova, E.A. et al. Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy. Eur Biophys J 46, 293–300 (2017). https://doi.org/10.1007/s00249-016-1167-5

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  • DOI: https://doi.org/10.1007/s00249-016-1167-5

Keywords

  • NMR
  • Structure
  • Protegrin
  • Antimicrobial peptide
  • Pore
  • Antibiotic