2NC7 image
Deposition Date 2016-03-21
Release Date 2017-04-19
Last Version Date 2024-11-27
Entry Detail
PDB ID:
2NC7
Title:
Antimicrobial peptide protegrin PG-5
Biological Source:
Source Organism:
Sus scrofa (Taxon ID: 9823)
Method Details:
Experimental Method:
Conformers Calculated:
1000
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protegrin-5
Gene (Uniprot):NPG5
Chain IDs:A
Chain Length:18
Number of Molecules:1
Biological Source:Sus scrofa
Ligand Molecules
Primary Citation
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)
PMID: 27589857 DOI: 10.1007/s00249-016-1167-5

Abstact

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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