Three-Dimensional Structures of Peptaibols 

This compilation provides information on three-dimensional (3D) structures of peptaibols.

The peptaibols are a family of peptides characterized by the presence of AIB (amino isobutyric acid) residues, an acetylated N-terminus and a hydroxylated C-terminal amino acid. Other non-natural amino acids occurring in peptaibols are iso-valine (IVA) and hydroxy-proline (HYP). Peptaibols exhibit an antibiotic activity that is assumed to be due to their ability to form ion-channels in lipid membranes.

Peptaibol structures for which co-ordinates have been deposited at either the Cambridge Structural Database (CSD) or the Protein Data Bank (PDB):

Name Sequence Length Method of Structure Determination Database Code (Database) Reference
Alamethicin 20 X-ray
(3 molecules in asymmetric unit)
1AMT (PDB | JenaLib) Fox RO, Richards FM.
Nature 1982, 300, 325-330.
A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5 Å resolution.
Ampullosporin A 15 X-ray
(1 molecule in asymmetric unit)
AMPA - internal code (deposited at CSD; CCDC 195231) Kronen M, Goerls H, Ngyuen HH, Reissmann S, Bohl M, Suehnel J, Graefe U.
J. Peptide Sci. 2003, 9, 729-744.
Crystal structure and conformational analysis of ampullosporin A.
Antiamoebin I 16 X-ray
(2 molecules in asymmetric unit)
1JOH (PDB | JenaLib)
Snook CF, Woolley GA, Oliva G, Pattabhi V, Wood SF, Blundell TL, Wallace BA.
Structure 1998, 6, 783-792.
The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide
.
Antiamoebin I
16 X-ray
(2 molecules in asymmetric unit)
FEJQOA (CSD) Karle IL, Perozzo MA, Mishra VK, Balaram P.
Proc Natl Acad Sci U S A 1998, 95, 5501-5504.
Crystal structure of the channel-forming polypeptide antiamoebin in a membrane-mimetic environment.
Antiamoebin I 16 NMR
(20 models)
1GQ0 (PDB | JenaLib) Galbraith TP, Harris R, Driscoll PC, Wallace BA.
Biophys J. 2003, 84, 185-194.
Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide.
Cephaibol A

Cephaibol B

Cephaibol C
16

16

16
X-ray
(1 molecule in asymmetric unit
X-ray
(2 molecules in asymmetric unit)
X-ray
(2 molecules in asymmetric unit)
1OB4 (PDB | JenaLib)

1OB6 (PDB | JenaLib)

1OB7 (PDB | JenaLib)
Bunkoczi G, Schiell M, Vertesy L, Sheldrick GM.
J. Peptide Sci. 2003, 9, 745-52.
Crystal structures of cephaibols.
Chrysopermin C 19 NMR
(average structure)
1EE7 (PDB | JenaLib) Anders R, Ohlenschlager O, Soskic V, Wenschuh H, Heise B, Brown LR.
Eur J Biochem. 2000, 267, 1784-1794.
The NMR solution structure of the ion channel peptaibol chrysospermin C bound to dodecylphosphocholine micelles.
Trichotoxin_A50E 18 X-ray
(2 molecules in asymmetric unit)
1M24 (PDB | JenaLib) Chugh JK, Bruckner H, Wallace BA.
Biochemistry 2002, 41, 12934-12941.
Model for a helical bundle channel based on the high-resolution crystal structure of trichotoxin_A50E.
Zervamicin IIb 16
NMR
(20 models, isotropic solvent)
1DLZ (PDB | JenaLib)
Balashova TA, Shenkarev ZO, Tagaev AA, Ovchinnikova TV, Raap J, Arseniev AS.
FEBS Lett. 2000 , 466, 333-336.
NMR structure of the channel-former zervamicin IIB in isotropic solvents.
Zervamicin IIb 16 NMR
(20 models, bound to DPC micelles)
1IH9 (PDB | JenaLib) Shenkarev ZO, Balashova TA, Efremov RG, Yakimenko ZA, Ovchinnikova TV, Raap J, Arseniev AS.
Biophys J. 2002, 82, 762-771.
Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating.
Zervamicin IIb 16 NMR
(24 models)
1R9U (PDB | JenaLib) Shenkarev ZO, Balashova TA, Yakimenko ZA, Ovchinnikova TV, Arseniev AS. Related Articles, Links
Peptaibol zervamicin IIb structure and dynamics refinement from transhydrogen bond J couplings.
Biophys J. 2004, 86, 3687-3699.
Leu1-Zervamicin 16 X-ray
(1 molecule in asymmetric unit)
KIYPUD (CSD) Karle IL, Flippen-Anderson JL, Agarwalla S, Balaram P.
Proc Natl Acad Sci U S A 1991, 88, 5307-5311.
Crystal structure of [Leu1]zervamicin, a membrane ion-channel peptide: implications for gating mechanisms.

Further papers describing complete peptaibol structures with structural information not deposited at a database:

Condamine E, Rebuffat S, Prigent Y, Segalas I, Bodo B, Davoust D.
Biopolymers 1998, 46. 75-88.
Three-dimensional structure of the ion-channel forming peptide trichorzianin TA VII bound to sodium dodecyl sulfate micelles.
Toniolo C, Peggion C, Crisma M, Formaggio F, Shui X, Eggleston DS.
Nat Struct Biol 1994,1, 908-914.
Structure determination of racemic trichogin A IV using centrosymmetric crystals.

Bending analysis:

Related link on peptaibol structures:


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