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DOI no:
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J Mol Biol
258:322-333
(1996)
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PubMed id:
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H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus.
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J.C.Martins,
D.Maes,
R.Loris,
H.A.Pepermans,
L.Wyns,
R.Willem,
P.Verheyden.
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ABSTRACT
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The conformation in water of antimicrobial protein 2 from Amaranthus caudatus
(Ac-AMP2) was determined using 1H NMR, DIANA and restrained molecular modeling.
Ac-AMP2 is a 30 amino acid residue, lectin-like protein that specifically binds
to chitin, a polymer of beta-1,4-N-acetyl-D-glucosamine. After sequence specific
resonance assignments, a total of 198 distance restraints were collected from 2D
NOESY buildup spectra at 500 MHz at pH 2, supplemented by a 2D NOESY spectrum at
600 MHz. The location of the three previously unassigned disulfide bridges was
determined from preliminary DIANA structures, using a statistical analysis of
intercystinyl distances. The solution structure of Ac-AMP2 is presented as a set
of 26 DIANA structures, further refined by restrained molecular dynamics using a
simulated annealing protocol in the AMBER force field, with a backbone r.m.s.d.
for the well defined Glu3-Cys28 segment of 0.69(+/-0.12) angstroms. The main
structural element is an antiparallel beta-sheet from Met13 to Lys23 including a
betaI-turn over Gln17-Phel8 with a beta bulge at Gly19. In addition, a beta'I
turn over Arg6-Gly7, a beta'III turn over Ser11-Gly12 and a helical turn from
Gly24 to Cys28 are identified. This structure is very similar to the equivalent
regions of the X-ray structure of wheat germ agglutinin and the NMR structure of
hevein.
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Selected figure(s)
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Figure 4.
Figure 4. Average intercystinyl S
g
--S
g
distances observed
in the set of 48 conformers for each of the three possible
disulfide bridge patterns, Cys4-Cys15, Cys9-Cys21,
Cys14-Cys28 (I), Cys4-Cys21, Cys9-Cys15, Cys14-Cys28
(II) and Cys4-Cys9, Cys14-Cys28, Cys15-Cys21 (III).
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Figure 5.
Figure 5. Stereo view of the 26 conformers representing the solution conformation of Ac-AMP2 in solution.
Conformers 2 to 26 were superimposed for minimum r.m.s.d. of the backbone atoms of residues 3 to 28 with conformer
1. Black lines represent the backbone atoms, gray lines the disulfide bridges. For clarity, the N and C-terminal residues
1-2 and 29-30 are not displayed. The structure features the Cys4-Cys15, Cys9-Cys21 and Cys14-Cys28 disulfide bridges
from top to bottom.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
258,
322-333)
copyright 1996.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's
key reference
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PubMed id
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Reference
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S.Yokoyama,
Y.Iida,
Y.Kawasaki,
Y.Minami,
K.Watanabe,
and
F.Yagi
(2009).
The chitin-binding capability of Cy-AMP1 from cycad is essential to antifungal activity.
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J Pept Sci, 15,
492-497.
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M.I.Chávez,
C.Andreu,
P.Vidal,
N.Aboitiz,
F.Freire,
P.Groves,
J.L.Asensio,
G.Asensio,
M.Muraki,
F.J.Cañada,
and
J.Jiménez-Barbero
(2005).
On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues.
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Chemistry, 11,
7060-7074.
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PDB codes:
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H.Hemmi,
J.Ishibashi,
T.Tomie,
and
M.Yamakawa
(2003).
Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.
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J Biol Chem, 278,
22820-22827.
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PDB code:
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P.Karisola,
H.Alenius,
J.Mikkola,
N.Kalkkinen,
J.Helin,
O.T.Pentikäinen,
S.Repo,
T.Reunala,
K.Turjanmaa,
M.S.Johnson,
T.Palosuo,
and
M.S.Kulomaa
(2002).
The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping strategy.
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J Biol Chem, 277,
22656-22661.
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J.C.Martins,
M.Enassar,
R.Willem,
J.M.Wieruzeski,
G.Lippens,
and
S.J.Wodak
(2001).
Solution structure of the main alpha-amylase inhibitor from amaranth seeds.
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Eur J Biochem, 268,
2379-2389.
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PDB code:
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S.C.Ha,
K.Min,
J.C.Koo,
Y.Kim,
D.J.Yun,
M.J.Cho,
and
K.K.Kim
(2001).
Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis nil.
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Acta Crystallogr D Biol Crystallogr, 57,
263-265.
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J.L.Asensio,
H.C.Siebert,
C.W.von Der Lieth,
J.Laynez,
M.Bruix,
U.M.Soedjanaamadja,
J.J.Beintema,
F.J.Cañada,
H.J.Gabius,
and
J.Jiménez-Barbero
(2000).
NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
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Proteins, 40,
218-236.
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N.F.Dawson,
D.J.Craik,
A.M.McManus,
S.G.Dashper,
E.C.Reynolds,
G.W.Tregear,
L.Otvos,
and
J.D.Wade
(2000).
Chemical synthesis, characterization and activity of RK-1, a novel alpha-defensin-related peptide.
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J Pept Sci, 6,
19-25.
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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
codes are
shown on the right.
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30 a.a.
