2MZ6

NMR structure of Protegrin-3 (PG3) in the presence of DPC micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2015) J.Biomol.Nmr 62: 71-79

  • DOI: 10.1007/s10858-015-9920-0

  • PubMed 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 ...

    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.


    Organizational Affiliation

    NMR Laboratory, Institute of Physics, Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation, k.usachev@kpfu.ru.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protegrin-3
A, B
18Sus scrofaGene Names: NPG3
Find proteins for P32196 (Sus scrofa)
Go to UniProtKB:  P32196
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Database references