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PDBsum entry 1g8c
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Antimicrobial protein
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PDB id
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1g8c
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DOI no:
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Biochemistry
39:15765-15774
(2000)
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PubMed id:
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Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles.
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A.Rozek,
C.L.Friedrich,
R.E.Hancock.
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ABSTRACT
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Indolicidin is a cationic, 13-residue antimicrobial peptide
(ILPWKWPWWPWRR-NH(2)) which is unusually rich in tryptophan and proline. Its
antimicrobial action involves the bacterial cytoplasmic membrane. Fluorescence
and circular dichroism spectra demonstrated the structural similarity of
indolicidin in complexes with large unilamellar phospolipid vesicles and with
detergent micelles. The structure of indolicidin bound to zwitterionic
dodecylphosphocholine (DPC) and anionic sodium dodecyl sulfate (SDS) micelles
was determined using NMR methods and shown to represent a unique
membrane-associated peptide structure. The backbone structure in DPC, well
defined between residues 3 and 11, was extended, with two half-turns at residues
Lys-5 and Trp-8. The backbone structure in SDS, well defined between residues 5
and 11, was also extended, but lacked the bend in the C-terminal half.
Indolicidin in complexes with DPC had a central hydrophobic core composed of
proline and tryptophan, which was bracketed by positively charged regions near
the peptide termini. The tryptophan side chains, with one exception, folded flat
against the peptide backbone, thus giving the molecule a wedge shape.
Indolicidin in complexes with SDS had an arrangement of hydrophobic and cationic
regions similar to that found in the presence of DPC. The tryptophan side chains
were less well defined than for indolicidin in DPC and extended away from the
peptide backbone. The preferred location of indolicidin in DPC micelles and
lipid bilayers, analyzed using spin-label probes, was at the membrane interface.
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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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E.Ahmad,
A.Ahmad,
S.Singh,
M.Arshad,
A.H.Khan,
and
R.H.Khan
(2011).
A mechanistic approach for islet amyloid polypeptide aggregation to develop anti-amyloidogenic agents for type-2 diabetes.
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Biochimie,
93,
793-805.
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T.Godballe,
L.L.Nilsson,
P.D.Petersen,
and
H.Jenssen
(2011).
Antimicrobial β-peptides and α-peptoids.
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Chem Biol Drug Des,
77,
107-116.
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H.Y.Yu,
K.C.Huang,
B.S.Yip,
C.H.Tu,
H.L.Chen,
H.T.Cheng,
and
J.W.Cheng
(2010).
Rational design of tryptophan-rich antimicrobial peptides with enhanced antimicrobial activities and specificities.
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Chembiochem,
11,
2273-2282.
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M.Wieczorek,
H.Jenssen,
J.Kindrachuk,
W.R.Scott,
M.Elliott,
K.Hilpert,
J.T.Cheng,
R.E.Hancock,
and
S.K.Straus
(2010).
Structural studies of a peptide with immune modulating and direct antimicrobial activity.
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Chem Biol,
17,
970-980.
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A.Sayyed-Ahmad,
H.Khandelia,
and
Y.N.Kaznessis
(2009).
Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles.
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Mol Simul,
35,
986-997.
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A.Zumbuehl,
P.Stano,
M.Sohrmann,
R.Dietiker,
M.Peter,
and
E.M.Carreira
(2009).
Synthesis and investigation of tryptophan-amphotericin B conjugates.
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Chembiochem,
10,
1617-1620.
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G.Diamond,
N.Beckloff,
A.Weinberg,
and
K.O.Kisich
(2009).
The roles of antimicrobial peptides in innate host defense.
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Curr Pharm Des,
15,
2377-2392.
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M.M.Waegele,
M.J.Tucker,
and
F.Gai
(2009).
5-Cyanotryptophan as an Infrared Probe of Local Hydration Status of Proteins.
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Chem Phys Lett,
478,
249-253.
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R.Gopal,
S.C.Park,
K.J.Ha,
S.J.Cho,
S.W.Kim,
P.I.Song,
J.W.Nah,
Y.Park,
and
K.S.Hahm
(2009).
Effect of Leucine and Lysine substitution on the antimicrobial activity and evaluation of the mechanism of the HPA3NT3 analog peptide.
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J Pept Sci,
15,
589-594.
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R.Ghiselli,
A.Giacometti,
O.Cirioni,
F.Mocchegiani,
F.Orlando,
C.Silvestri,
F.Di Matteo,
A.Abbruzzetti,
G.Scalise,
and
V.Saba
(2008).
Efficacy of the bovine antimicrobial peptide indolicidin combined with piperacillin/tazobactam in experimental rat models of polymicrobial peritonitis.
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Crit Care Med,
36,
240-245.
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S.A.Vishwanathan,
and
E.Hunter
(2008).
Importance of the membrane-perturbing properties of the membrane-proximal external region of human immunodeficiency virus type 1 gp41 to viral fusion.
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J Virol,
82,
5118-5126.
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S.W.Ho,
D.Jung,
J.R.Calhoun,
J.D.Lear,
M.Okon,
W.R.Scott,
R.E.Hancock,
and
S.K.Straus
(2008).
Effect of divalent cations on the structure of the antibiotic daptomycin.
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Eur Biophys J,
37,
421-433.
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A.A.Langham,
A.J.Waring,
and
Y.N.Kaznessis
(2007).
Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data.
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BMC Biochem,
8,
11.
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H.Khandelia,
and
Y.N.Kaznessis
(2007).
Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations.
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J Phys Chem B,
111,
242-250.
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J.C.Hsu,
and
C.M.Yip
(2007).
Molecular dynamics simulations of indolicidin association with model lipid bilayers.
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Biophys J,
92,
L100-L102.
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J.M.Wu,
S.Y.Wei,
H.L.Chen,
K.Y.Weng,
H.T.Cheng,
and
J.W.Cheng
(2007).
Solution structure of a novel D-naphthylalanine substituted peptide with potential antibacterial and antifungal activities.
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Biopolymers,
88,
738-745.
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V.V.Andrushchenko,
H.J.Vogel,
and
E.J.Prenner
(2007).
Optimization of the hydrochloric acid concentration used for trifluoroacetate removal from synthetic peptides.
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J Pept Sci,
13,
37-43.
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A.A.Langham,
H.Khandelia,
and
Y.N.Kaznessis
(2006).
How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.
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Biopolymers,
84,
219-231.
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D.J.Schibli,
L.T.Nguyen,
S.D.Kernaghan,
Ã.˜.Rekdal,
and
H.J.Vogel
(2006).
Structure-function analysis of tritrpticin analogs: potential relationships between antimicrobial activities, model membrane interactions, and their micelle-bound NMR structures.
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Biophys J,
91,
4413-4426.
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PDB codes:
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H.Jenssen,
P.Hamill,
and
R.E.Hancock
(2006).
Peptide antimicrobial agents.
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Clin Microbiol Rev,
19,
491-511.
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J.Song,
M.S.Lee,
I.Carlberg,
A.V.Vener,
and
J.L.Markley
(2006).
Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications.
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Biochemistry,
45,
15633-15643.
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PDB code:
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N.Y.Yount,
A.S.Bayer,
Y.Q.Xiong,
and
M.R.Yeaman
(2006).
Advances in antimicrobial peptide immunobiology.
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Biopolymers,
84,
435-458.
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S.Y.Wei,
J.M.Wu,
Y.Y.Kuo,
H.L.Chen,
B.S.Yip,
S.R.Tzeng,
and
J.W.Cheng
(2006).
Solution structure of a novel tryptophan-rich peptide with bidirectional antimicrobial activity.
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J Bacteriol,
188,
328-334.
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B.Japelj,
P.Pristovsek,
A.Majerle,
and
R.Jerala
(2005).
Structural origin of endotoxin neutralization and antimicrobial activity of a lactoferrin-based peptide.
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J Biol Chem,
280,
16955-16961.
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PDB codes:
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C.Appelt,
A.Wessolowski,
J.A.Söderhäll,
M.Dathe,
and
P.Schmieder
(2005).
Structure of the antimicrobial, cationic hexapeptide cyclo(RRWWRF) and its analogues in solution and bound to detergent micelles.
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Chembiochem,
6,
1654-1662.
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PDB codes:
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C.H.Hsu,
C.Chen,
M.L.Jou,
A.Y.Lee,
Y.C.Lin,
Y.P.Yu,
W.T.Huang,
and
S.H.Wu
(2005).
Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA.
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Nucleic Acids Res,
33,
4053-4064.
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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?
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Evid Based Complement Alternat Med,
2,
39-47.
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D.M.Bowdish,
D.J.Davidson,
M.G.Scott,
and
R.E.Hancock
(2005).
Immunomodulatory activities of small host defense peptides.
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Antimicrob Agents Chemother,
49,
1727-1732.
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G.Wang,
Y.Li,
and
X.Li
(2005).
Correlation of three-dimensional structures with the antibacterial activity of a group of peptides designed based on a nontoxic bacterial membrane anchor.
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J Biol Chem,
280,
5803-5811.
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PDB codes:
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H.Li,
F.Li,
M.Kwan,
Q.Y.He,
and
H.Sun
(2005).
NMR structures and orientation of the fourth transmembrane domain of the rat divalent metal transporter (DMT1) with G185D mutation in SDS micelles.
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Biopolymers,
77,
173-183.
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O.Toke
(2005).
Antimicrobial peptides: new candidates in the fight against bacterial infections.
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Biopolymers,
80,
717-735.
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H.Li,
F.Li,
Z.M.Qian,
and
H.Sun
(2004).
Structure and topology of the transmembrane domain 4 of the divalent metal transporter in membrane-mimetic environments.
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Eur J Biochem,
271,
1938-1951.
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H.S.Won,
S.J.Jung,
H.E.Kim,
M.D.Seo,
and
B.J.Lee
(2004).
Systematic peptide engineering and structural characterization to search for the shortest antimicrobial peptide analogue of gaegurin 5.
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J Biol Chem,
279,
14784-14791.
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T.S.Ryge,
X.Doisy,
D.Ifrah,
J.E.Olsen,
and
P.R.Hansen
(2004).
New indolicidin analogues with potent antibacterial activity.
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J Pept Res,
64,
171-185.
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A.Rozek,
J.P.Powers,
C.L.Friedrich,
and
R.E.Hancock
(2003).
Structure-based design of an indolicidin peptide analogue with increased protease stability.
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Biochemistry,
42,
14130-14138.
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PDB codes:
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W.Jing,
H.N.Hunter,
J.Hagel,
and
H.J.Vogel
(2003).
The structure of the antimicrobial peptide Ac-RRWWRF-NH2 bound to micelles and its interactions with phospholipid bilayers.
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J Pept Res,
61,
219-229.
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A.Tanaka,
and
E.Hoshino
(2002).
Thermodynamic and activation parameters for the hydrolysis of amylose with Bacillus alpha-amylases in a diluted anionic surfactant solution.
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J Biosci Bioeng,
93,
485-490.
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H.S.Won,
S.H.Park,
H.E.Kim,
B.Hyun,
M.Kim,
B.J.Lee,
and
B.J.Lee
(2002).
Effects of a tryptophanyl substitution on the structure and antimicrobial activity of C-terminally truncated gaegurin 4.
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Eur J Biochem,
269,
4367-4374.
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L.W.Tinoco,
A.Da Silva,
A.Leite,
A.P.Valente,
and
F.C.Almeida
(2002).
NMR structure of PW2 bound to SDS micelles. A tryptophan-rich anticoccidial peptide selected from phage display libraries.
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J Biol Chem,
277,
36351-36356.
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PDB code:
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R.E.Hancock,
and
A.Rozek
(2002).
Role of membranes in the activities of antimicrobial cationic peptides.
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FEMS Microbiol Lett,
206,
143-149.
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S.Nagpal,
K.J.Kaur,
D.Jain,
and
D.M.Salunke
(2002).
Plasticity in structure and interactions is critical for the action of indolicidin, an antibacterial peptide of innate immune origin.
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Protein Sci,
11,
2158-2167.
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Y.Shai
(2002).
Mode of action of membrane active antimicrobial peptides.
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Biopolymers,
66,
236-248.
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P.A.Luchette,
T.N.Vetman,
R.S.Prosser,
R.E.Hancock,
M.P.Nieh,
C.J.Glinka,
S.Krueger,
and
J.Katsaras
(2001).
Morphology of fast-tumbling bicelles: a small angle neutron scattering and NMR study.
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Biochim Biophys Acta,
1513,
83-94.
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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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Links
