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PDBsum entry 1dum
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Antimicrobial protein PDB id
1dum

 

 

 

 

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Contents
Protein chains
23 a.a.
PDB id:
1dum
Name: Antimicrobial protein
Title: Nmr structure of [f5y, f16w] magainin 2 bound to phospholipid vesicles
Structure: Magainin 2. Chain: a, b. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: the peptide was prepared by solid-phase synthesis. The sequence of this peptide naturally occurs in xenopus laevis (african clawed frog)
NMR struc: 10 models
Authors: A.Takeda,K.Wakamatsu,T.Tachi,K.Matsuzaki
Key ref: T.Hara et al. (2001). Effects of peptide dimerization on pore formation: Antiparallel disulfide-dimerized magainin 2 analogue. Biopolymers, 58, 437-446. PubMed id: 11180056
Date:
18-Jan-00     Release date:   27-Jun-01    
PROCHECK
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 Headers
 References

Protein chains
P11006  (MAGA_XENLA) -  Magainins from Xenopus laevis
Seq:
Struc: 		303 a.a.
23 a.a.*
Key:    Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Biopolymers 58:437-446 (2001)
PubMed id: 11180056  
 
 
Effects of peptide dimerization on pore formation: Antiparallel disulfide-dimerized magainin 2 analogue.
T.Hara, H.Kodama, M.Kondo, K.Wakamatsu, A.Takeda, T.Tachi, K.Matsuzaki.
 
  ABSTRACT  
 
To elucidate the effects of peptide dimerization on pore formation by magainin 2 (MG2), a covalently linked antiparallel dimer of the MG2 analogue [(F5Y, L6C, F16W, I20C-MG2)(2): II] was synthesized based on the dimer structure revealed by our NMR study. The interactions of the dimer with lipid bilayers were investigated by CD and fluorescence in comparison with a monomer analogue (F5Y, F16W-MG2: I). Similar to I, II was found to form a peptide-lipid supramolecular complex pore accompanied with lipid flip-flop and peptide translocation. The pore formed by II was characterized by a slightly larger pore diameter and a threefold longer lifetime than that of I, although the pore formation rate of the dimer was lower than that of the monomer. The coexistence of the dimer and the monomer exhibited slight but significant synergism in membrane permeabilization, which was maximal at a monomer/dimer ratio of 3. Therefore, we concluded that a pentameric pore composed of one pore-stabilizing dimer and three monomers maximized the overall leakage activity in keeping with our kinetic prediction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19470516 F.Yoneyama, Y.Imura, K.Ohno, T.Zendo, J.Nakayama, K.Matsuzaki, and K.Sonomoto (2009).
Peptide-lipid huge toroidal pore, a new antimicrobial mechanism mediated by a lactococcal bacteriocin, lacticin Q.
  Antimicrob Agents Chemother, 53, 3211-3217.  
19413970 L.Shi, A.Cembran, J.Gao, and G.Veglia (2009).
Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes.
  Biophys J, 96, 3648-3662.  
19591202 R.W.Davis, D.C.Arango, H.D.Jones, M.H.Van Benthem, D.M.Haaland, S.M.Brozik, and M.B.Sinclair (2009).
Antimicrobial peptide interactions with silica bead supported bilayers and E. coli: buforin II, magainin II, and arenicin.
  J Pept Sci, 15, 511-522.  
18284588 A.A.Handler, J.E.Lim, and R.Losick (2008).
Peptide inhibitor of cytokinesis during sporulation in Bacillus subtilis.
  Mol Microbiol, 68, 588-599.  
18616463 J.Y.Lee, S.T.Yang, S.K.Lee, H.H.Jung, S.Y.Shin, K.S.Hahm, and J.I.Kim (2008).
Salt-resistant homodimeric bactenecin, a cathelicidin-derived antimicrobial peptide.
  FEBS J, 275, 3911-3920.  
15841277 D.C.de Lima, P.Alvarez Abreu, C.C.de Freitas, D.O.Santos, R.O.Borges, T.C.Dos Santos, L.Mendes Cabral, C.R.Rodrigues, and H.C.Castro (2005).
Snake Venom: Any Clue for Antibiotics and CAM?
  Evid Based Complement Alternat Med, 2, 39-47.  
15840728 D.Raimondo, G.Andreotti, N.Saint, P.Amodeo, G.Renzone, M.Sanseverino, I.Zocchi, G.Molle, A.Motta, and A.Scaloni (2005).
A folding-dependent mechanism of antimicrobial peptide resistance to degradation unveiled by solution structure of distinctin.
  Proc Natl Acad Sci U S A, 102, 6309-6314.
PDB code: 1xkm
15880793 O.Toke (2005).
Antimicrobial peptides: new candidates in the fight against bacterial infections.
  Biopolymers, 80, 717-735.  
15273301 L.A.Plesniak, J.I.Parducho, A.Ziebart, B.H.Geierstanger, J.A.Whiles, G.Melacini, and P.A.Jennings (2004).
Orientation and helical conformation of a tissue-specific hunter-killer peptide in micelles.
  Protein Sci, 13, 1988-1996.  
15240501 O.Toke, R.D.O'Connor, T.K.Weldeghiorghis, W.L.Maloy, R.W.Glaser, A.S.Ulrich, and J.Schaefer (2004).
Structure of (KIAGKIA)3 aggregates in phospholipid bilayers by solid-state NMR.
  Biophys J, 87, 675-687.  
12878508 W.S.Jang, C.H.Kim, K.N.Kim, S.Y.Park, J.H.Lee, S.M.Son, and I.H.Lee (2003).
Biological activities of synthetic analogs of halocidin, an antimicrobial peptide from the tunicate Halocynthia aurantium.
  Antimicrob Agents Chemother, 47, 2481-2486.  
12470734 A.C.Rinaldi (2002).
Antimicrobial peptides from amphibian skin: an expanding scenario.
  Curr Opin Chem Biol, 6, 799-804.  
11933020 J.M.Boon, and B.D.Smith (2002).
Chemical control of phospholipid distribution across bilayer membranes.
  Med Res Rev, 22, 251-281.  
12124849 K.Wakamatsu, A.Takeda, T.Tachi, and K.Matsuzaki (2002).
Dimer structure of magainin 2 bound to phospholipid vesicles.
  Biopolymers, 64, 314-327.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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