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PDBsum entry 1hpn
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Glycosaminoglycan
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PDB id
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1hpn
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PDB id:
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Glycosaminoglycan
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Title:
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N.M.R. And molecular-modelling studies of the solution conformation of heparin
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Structure:
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2-o-sulfo-alpha-l-idopyranuronic acid-(1-4)-2-deoxy-6-o- sulfo-2-(sulfoamino)-alpha-d-glucopyranose-(1-4)-2-o-sulfo-alpha-l- idopyranuronic acid-(1-4)-2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d- glucopyranose-(1-4)-2-o-sulfo-alpha-l-idopyranuronic acid-(1-4)-2- deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose-(1-4)-2-o-sulfo- alpha-l-idopyranuronic acid-(1-4)-2-deoxy-6-o-sulfo-2-(sulfoamino)- alpha-d-glucopyranose-(1-4)-2-o-sulfo-alpha-l-idopyranuronic acid-(1- 4)-2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose-(1-4)-2-o- sulfo-alpha-l-idopyranuronic acid-(1-4)-2-deoxy-6-o-sulfo-2-
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Source:
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not given
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NMR struc:
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2 models
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Authors:
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B.Mulloy,M.J.Forster
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Key ref:
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B.Mulloy
et al.
(1993).
N.m.r. and molecular-modelling studies of the solution conformation of heparin.
Biochem J,
293,
849-858.
PubMed id:
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Date:
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17-Jan-95
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Release date:
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31-Mar-95
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Headers
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References
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Biochem J
293:849-858
(1993)
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PubMed id:
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N.m.r. and molecular-modelling studies of the solution conformation of heparin.
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B.Mulloy,
M.J.Forster,
C.Jones,
D.B.Davies.
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ABSTRACT
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The solution conformations of heparin and de-N-sulphated, re-N-acetylated
heparin have been determined by a combination of n.m.r. spectroscopic and
molecular-modelling techniques. The 1H- and 13C-n.m.r. spectra of these
polysaccharides have been assigned. Observed 1H-1H nuclear Overhauser
enhancements (n.O.e.s) have been simulated using the program NOEMOL [Forster,
Jones and Mulloy (1989) J. Mol. Graph. 7, 196-201] for molecular models derived
from conformational-energy calculations; correlation times for the simulations
were chosen to fit experimentally determined 13C spin-lattice relaxation times.
In order to achieve good agreement between calculated and observed 1H-1H n.O.e.s
it was necessary to assume that the reorientational motion of the polysaccharide
molecules was not isotropic, but was that of a symmetric top. The resulting
model of heparin in solution is similar to that determined in the fibrous state
by X-ray-diffraction techniques [Nieduszynski, Gardner and Atkins (1977) Am.
Chem. Soc. Symp. Ser. 48, 73-80].
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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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N.Motamedi-Shad,
T.Garfagnini,
A.Penco,
A.Relini,
F.Fogolari,
A.Corazza,
G.Esposito,
F.Bemporad,
and
F.Chiti
(2012).
Rapid oligomer formation of human muscle acylphosphatase induced by heparan sulfate.
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Nat Struct Mol Biol,
19,
547.
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C.H.Coles,
Y.Shen,
A.P.Tenney,
C.Siebold,
G.C.Sutton,
W.Lu,
J.T.Gallagher,
E.Y.Jones,
J.G.Flanagan,
and
A.R.Aricescu
(2011).
Proteoglycan-specific molecular switch for RPTPĪ clustering and neuronal extension.
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Science,
332,
484-488.
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PDB codes:
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D.A.Keire,
H.Ye,
M.L.Trehy,
W.Ye,
R.E.Kolinski,
B.J.Westenberger,
L.F.Buhse,
M.Nasr,
and
A.Al-Hakim
(2011).
Characterization of currently marketed heparin products: key tests for quality assurance.
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Anal Bioanal Chem,
399,
581-591.
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V.Roldós,
F.J.Cañada,
and
J.Jiménez-Barbero
(2011).
Carbohydrate-protein interactions: a 3D view by NMR.
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Chembiochem,
12,
990.
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A.Rullo,
and
M.Nitz
(2010).
Importance of the spatial display of charged residues in heparin-peptide interactions.
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Biopolymers,
93,
290-298.
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B.Casu,
A.Naggi,
and
G.Torri
(2010).
Heparin-derived heparan sulfate mimics to modulate heparan sulfate-protein interaction in inflammation and cancer.
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Matrix Biol,
29,
442-452.
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E.Seyrek,
and
P.Dubin
(2010).
Glycosaminoglycans as polyelectrolytes.
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Adv Colloid Interface Sci,
158,
119-129.
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L.Y.Yan,
W.Li,
X.F.Fan,
L.Wei,
Y.Chen,
J.L.Kuo,
L.J.Li,
S.K.Kwak,
Y.Mu,
and
M.B.Chan-Park
(2010).
Enrichment of (8,4) single-walled carbon nanotubes through coextraction with heparin.
|
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Small,
6,
110-118.
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M.G.Costa,
P.R.Batista,
C.S.Shida,
C.H.Robert,
P.M.Bisch,
and
P.G.Pascutti
(2010).
How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics.
|
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BMC Genomics,
11,
S5.
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L.Jin,
M.Hricovíni,
J.A.Deakin,
M.Lyon,
and
D.Uhrín
(2009).
Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin.
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Glycobiology,
19,
1185-1196.
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L.R.Teixeira,
P.G.Merzlyak,
A.Valeva,
and
O.V.Krasilnikov
(2009).
Interaction of heparins and dextran sulfates with a mesoscopic protein nanopore.
|
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Biophys J,
97,
2894-2903.
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M.J.Lehtinen,
A.L.Rops,
D.E.Isenman,
J.van der Vlag,
and
T.S.Jokiranta
(2009).
Mutations of factor H impair regulation of surface-bound C3b by three mechanisms in atypical hemolytic uremic syndrome.
|
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J Biol Chem,
284,
15650-15658.
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M.R.Schenauer,
J.K.Meissen,
Y.Seo,
J.B.Ames,
and
J.A.Leary
(2009).
Heparan sulfate separation, sequencing, and isomeric differentiation: ion mobility spectrometry reveals specific iduronic and glucuronic acid-containing hexasaccharides.
|
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Anal Chem,
81,
10179-10185.
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N.S.Gandhi,
and
R.L.Mancera
(2009).
Free energy calculations of glycosaminoglycan-protein interactions.
|
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Glycobiology,
19,
1103-1115.
|
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S.M.Thompson,
D.G.Fernig,
E.C.Jesudason,
P.D.Losty,
E.M.van de Westerlo,
T.H.van Kuppevelt,
and
J.E.Turnbull
(2009).
Heparan sulfate phage display antibodies identify distinct epitopes with complex binding characteristics: insights into protein binding specificities.
|
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J Biol Chem,
284,
35621-35631.
|
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V.Veverka,
A.J.Henry,
P.M.Slocombe,
A.Ventom,
B.Mulloy,
F.W.Muskett,
M.Muzylak,
K.Greenslade,
A.Moore,
L.Zhang,
J.Gong,
X.Qian,
C.Paszty,
R.J.Taylor,
M.K.Robinson,
and
M.D.Carr
(2009).
Characterization of the Structural Features and Interactions of Sclerostin: MOLECULAR INSIGHT INTO A KEY REGULATOR OF Wnt-MEDIATED BONE FORMATION.
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J Biol Chem,
284,
10890-10900.
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PDB code:
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A.Silipo,
Z.Zhang,
F.J.Cañada,
A.Molinaro,
R.J.Linhardt,
and
J.Jiménez-Barbero
(2008).
Conformational analysis of a dermatan sulfate-derived tetrasaccharide by NMR, molecular modeling, and residual dipolar couplings.
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Chembiochem,
9,
240-252.
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M.Mobli,
M.Nilsson,
and
A.Almond
(2008).
The structural plasticity of heparan sulfate NA-domains and hence their role in mediating multivalent interactions is confirmed by high-accuracy (15)N-NMR relaxation studies.
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Glycoconj J,
25,
401-414.
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M.Nitz,
A.Rullo,
and
M.X.Ding
(2008).
Heparin dependent coiled-coil formation.
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Chembiochem,
9,
1545-1548.
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N.S.Gandhi,
and
R.L.Mancera
(2008).
The structure of glycosaminoglycans and their interactions with proteins.
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Chem Biol Drug Des,
72,
455-482.
|
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W.Li,
and
J.A.Huntington
(2008).
The Heparin Binding Site of Protein C Inhibitor Is Protease-dependent.
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J Biol Chem,
283,
36039-36045.
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PDB code:
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Z.Zhang,
S.A.McCallum,
J.Xie,
L.Nieto,
F.Corzana,
J.Jiménez-Barbero,
M.Chen,
J.Liu,
and
R.J.Linhardt
(2008).
Solution structures of chemoenzymatically synthesized heparin and its precursors.
|
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J Am Chem Soc,
130,
12998-13007.
|
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|
|
|
|
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B.E.Prosser,
S.Johnson,
P.Roversi,
A.P.Herbert,
B.S.Blaum,
J.Tyrrell,
T.A.Jowitt,
S.J.Clark,
E.Tarelli,
D.Uhrín,
P.N.Barlow,
R.B.Sim,
A.J.Day,
and
S.M.Lea
(2007).
Structural basis for complement factor H linked age-related macular degeneration.
|
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J Exp Med,
204,
2277-2283.
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PDB codes:
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E.Gemma,
A.N.Hulme,
A.Jahnke,
L.Jin,
M.Lyon,
R.M.Müller,
and
D.Uhrín
(2007).
DMT-MM mediated functionalisation of the non-reducing end of glycosaminoglycans.
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Chem Commun (Camb),
(),
2686-2688.
|
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M.Knappe,
S.Bodevin,
H.C.Selinka,
D.Spillmann,
R.E.Streeck,
X.S.Chen,
U.Lindahl,
and
M.Sapp
(2007).
Surface-exposed amino acid residues of HPV16 L1 protein mediating interaction with cell surface heparan sulfate.
|
| |
J Biol Chem,
282,
27913-27922.
|
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|
|
|
|
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A.Raghuraman,
P.D.Mosier,
and
U.R.Desai
(2006).
Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s).
|
| |
J Med Chem,
49,
3553-3562.
|
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|
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|
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D.J.Johnson,
W.Li,
T.E.Adams,
and
J.A.Huntington
(2006).
Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation.
|
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EMBO J,
25,
2029-2037.
|
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PDB code:
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|
|
|
|
|
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H.Tossavainen,
T.Pihlajamaa,
T.K.Huttunen,
E.Raulo,
H.Rauvala,
P.Permi,
and
I.Kilpeläinen
(2006).
The layered fold of the TSR domain of P. falciparum TRAP contains a heparin binding site.
|
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Protein Sci,
15,
1760-1768.
|
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PDB code:
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L.Jin,
P.E.Barran,
J.A.Deakin,
M.Lyon,
and
D.Uhrín
(2005).
Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling.
|
| |
Phys Chem Chem Phys,
7,
3464-3471.
|
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M.Mohammadi,
S.K.Olsen,
and
O.A.Ibrahimi
(2005).
Structural basis for fibroblast growth factor receptor activation.
|
| |
Cytokine Growth Factor Rev,
16,
107-137.
|
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M.Vacatello,
G.D'Auria,
L.Falcigno,
M.Dettin,
R.Gambaretto,
C.Di Bello,
and
L.Paolillo
(2005).
Conformational analysis of heparin binding peptides.
|
| |
Biomaterials,
26,
3207-3214.
|
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S.A.Cain,
C.Baldock,
J.Gallagher,
A.Morgan,
D.V.Bax,
A.S.Weiss,
C.A.Shuttleworth,
and
C.M.Kielty
(2005).
Fibrillin-1 interactions with heparin. Implications for microfibril and elastic fiber assembly.
|
| |
J Biol Chem,
280,
30526-30537.
|
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S.A.Colebrooke,
C.D.Blundell,
P.L.DeAngelis,
I.D.Campbell,
and
A.Almond
(2005).
Exploiting the carboxylate chemical shift to resolve degenerate resonances in spectra of 13C-labelled glycosaminoglycans.
|
| |
Magn Reson Chem,
43,
805-815.
|
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E.Krieger,
E.Geretti,
B.Brandner,
B.Goger,
T.N.Wells,
and
A.J.Kungl
(2004).
A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.
|
| |
Proteins,
54,
768-775.
|
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G.A.Nicolaes,
K.W.Sørensen,
U.Friedrich,
G.Tans,
J.Rosing,
L.Autin,
B.Dahlbäck,
and
B.O.Villoutreix
(2004).
Altered inactivation pathway of factor Va by activated protein C in the presence of heparin.
|
| |
Eur J Biochem,
271,
2724-2736.
|
|
|
|
|
|
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S.Ricard-Blum,
O.Féraud,
H.Lortat-Jacob,
A.Rencurosi,
N.Fukai,
F.Dkhissi,
D.Vittet,
A.Imberty,
B.R.Olsen,
and
M.van der Rest
(2004).
Characterization of endostatin binding to heparin and heparan sulfate by surface plasmon resonance and molecular modeling: role of divalent cations.
|
| |
J Biol Chem,
279,
2927-2936.
|
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|
|
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A.Kern,
K.Schmidt,
C.Leder,
O.J.Müller,
C.E.Wobus,
K.Bettinger,
C.W.Von der Lieth,
J.A.King,
and
J.A.Kleinschmidt
(2003).
Identification of a heparin-binding motif on adeno-associated virus type 2 capsids.
|
| |
J Virol,
77,
11072-11081.
|
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R.Raman,
G.Venkataraman,
S.Ernst,
V.Sasisekharan,
and
R.Sasisekharan
(2003).
Structural specificity of heparin binding in the fibroblast growth factor family of proteins.
|
| |
Proc Natl Acad Sci U S A,
100,
2357-2362.
|
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G.Rastegar-Lari,
B.O.Villoutreix,
A.S.Ribba,
P.Legendre,
D.Meyer,
and
D.Baruch
(2002).
Two clusters of charged residues located in the electropositive face of the von Willebrand factor A1 domain are essential for heparin binding.
|
| |
Biochemistry,
41,
6668-6678.
|
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|
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H.Lortat-Jacob,
A.Grosdidier,
and
A.Imberty
(2002).
Structural diversity of heparan sulfate binding domains in chemokines.
|
| |
Proc Natl Acad Sci U S A,
99,
1229-1234.
|
|
|
|
|
|
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I.Capila,
and
R.J.Linhardt
(2002).
Heparin-protein interactions.
|
| |
Angew Chem Int Ed Engl,
41,
391-412.
|
|
|
|
|
|
|
K.Tan,
M.Duquette,
J.H.Liu,
Y.Dong,
R.Zhang,
A.Joachimiak,
J.Lawler,
and
J.H.Wang
(2002).
Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication.
|
| |
J Cell Biol,
159,
373-382.
|
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PDB code:
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S.M.Prince,
M.Achtman,
and
J.P.Derrick
(2002).
Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
|
| |
Proc Natl Acad Sci U S A,
99,
3417-3421.
|
|
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PDB code:
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Sachchidanand,
O.Lequin,
D.Staunton,
B.Mulloy,
M.J.Forster,
K.Yoshida,
and
I.D.Campbell
(2002).
Mapping the heparin-binding site on the 13-14F3 fragment of fibronectin.
|
| |
J Biol Chem,
277,
50629-50635.
|
|
|
|
|
|
|
D.Xu,
K.Baburaj,
C.B.Peterson,
and
Y.Xu
(2001).
Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking.
|
| |
Proteins,
44,
312-320.
|
|
|
|
|
|
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I.Capila,
M.J.Hernáiz,
Y.D.Mo,
T.R.Mealy,
B.Campos,
J.R.Dedman,
R.J.Linhardt,
and
B.A.Seaton
(2001).
Annexin V--heparin oligosaccharide complex suggests heparan sulfate--mediated assembly on cell surfaces.
|
| |
Structure,
9,
57-64.
|
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PDB code:
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J.Dong,
C.A.Peters-Libeu,
K.H.Weisgraber,
B.W.Segelke,
B.Rupp,
I.Capila,
M.J.Hernáiz,
L.A.LeBrun,
and
R.J.Linhardt
(2001).
Interaction of the N-terminal domain of apolipoprotein E4 with heparin.
|
| |
Biochemistry,
40,
2826-2834.
|
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PDB code:
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J.T.Gallagher
(2001).
Heparan sulfate: growth control with a restricted sequence menu.
|
| |
J Clin Invest,
108,
357-361.
|
|
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|
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L.C.Chang,
H.F.Lee,
Z.Yang,
and
V.C.Yang
(2001).
Low molecular weight protamine (LMWP) as nontoxic heparin/low molecular weight heparin antidote (I): preparation and characterization.
|
| |
AAPS PharmSci,
3,
E17.
|
|
|
|
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M.Petitou,
A.Imberty,
P.Duchaussoy,
P.A.Driguez,
M.L.Ceccato,
F.Gourvenec,
P.Sizun,
J.P.Hérault,
S.Pérez,
and
J.M.Herbert
(2001).
Experimental proof for the structure of a thrombin-inhibiting heparin molecule.
|
| |
Chemistry,
7,
858-873.
|
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D.E.Hoke,
S.R.LaBrenz,
M.Höök,
and
D.D.Carson
(2000).
Multiple domains contribute to heparin/heparan sulfate binding by human HIP/L29.
|
| |
Biochemistry,
39,
15686-15694.
|
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D.J.Stauber,
A.D.DiGabriele,
and
W.A.Hendrickson
(2000).
Structural interactions of fibroblast growth factor receptor with its ligands.
|
| |
Proc Natl Acad Sci U S A,
97,
49-54.
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PDB code:
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J.Schlessinger,
A.N.Plotnikov,
O.A.Ibrahimi,
A.V.Eliseenkova,
B.K.Yeh,
A.Yayon,
R.J.Linhardt,
and
M.Mohammadi
(2000).
Crystal structure of a ternary FGF-FGFR-heparin complex reveals a dual role for heparin in FGFR binding and dimerization.
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| |
Mol Cell,
6,
743-750.
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PDB code:
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R.Sasisekharan,
and
G.Venkataraman
(2000).
Heparin and heparan sulfate: biosynthesis, structure and function.
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| |
Curr Opin Chem Biol,
4,
626-631.
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W.L.Chuang,
M.D.Christ,
J.Peng,
and
D.L.Rabenstein
(2000).
An NMR and molecular modeling study of the site-specific binding of histamine by heparin, chemically modified heparin, and heparin-derived oligosaccharides.
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| |
Biochemistry,
39,
3542-3555.
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A.Sharma,
J.A.Askari,
M.J.Humphries,
E.Y.Jones,
and
D.I.Stuart
(1999).
Crystal structure of a heparin- and integrin-binding segment of human fibronectin.
|
| |
EMBO J,
18,
1468-1479.
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PDB code:
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H.Zhou,
J.R.Casas-Finet,
R.Heath Coats,
J.D.Kaufman,
S.J.Stahl,
P.T.Wingfield,
J.S.Rubin,
D.P.Bottaro,
and
R.A.Byrd
(1999).
Identification and dynamics of a heparin-binding site in hepatocyte growth factor.
|
| |
Biochemistry,
38,
14793-14802.
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M.Hricovíni,
M.Guerrini,
and
A.Bisio
(1999).
Structure of heparin-derived tetrasaccharide complexed to the plasma protein antithrombin derived from NOEs, J-couplings and chemical shifts.
|
| |
Eur J Biochem,
261,
789-801.
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B.O.Villoutreix,
Y.Härdig,
A.Wallqvist,
D.G.Covell,
P.García de Frutos,
and
B.Dahlbäck
(1998).
Structural investigation of C4b-binding protein by molecular modeling: localization of putative binding sites.
|
| |
Proteins,
31,
391-405.
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G.Waksman,
and
A.B.Herr
(1998).
New insights into heparin-induced FGF oligomerization.
|
| |
Nat Struct Biol,
5,
527-530.
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R.E.Hileman,
J.R.Fromm,
J.M.Weiler,
and
R.J.Linhardt
(1998).
Glycosaminoglycan-protein interactions: definition of consensus sites in glycosaminoglycan binding proteins.
|
| |
Bioessays,
20,
156-167.
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S.Faham,
R.J.Linhardt,
and
D.C.Rees
(1998).
Diversity does make a difference: fibroblast growth factor-heparin interactions.
|
| |
Curr Opin Struct Biol,
8,
578-586.
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|
W.J.Fairbrother,
M.A.Champe,
H.W.Christinger,
B.A.Keyt,
and
M.A.Starovasnik
(1998).
Solution structure of the heparin-binding domain of vascular endothelial growth factor.
|
| |
Structure,
6,
637-648.
|
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|
PDB codes:
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|
M.Hricovíni,
M.Guerrini,
G.Torri,
and
B.Casu
(1997).
Motional properties of E. coli polysaccharide K5 in aqueous solution analyzed by NMR relaxation measurements.
|
| |
Carbohydr Res,
300,
69-76.
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S.Cumberledge,
and
F.Reichsman
(1997).
Glycosaminoglycans and WNTs: just a spoonful of sugar helps the signal go down.
|
| |
Trends Genet,
13,
421-423.
|
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|
|
W.Iwasaki,
K.Nagata,
H.Hatanaka,
T.Inui,
T.Kimura,
T.Muramatsu,
K.Yoshida,
M.Tasumi,
and
F.Inagaki
(1997).
Solution structure of midkine, a new heparin-binding growth factor.
|
| |
EMBO J,
16,
6936-6946.
|
|
|
PDB codes:
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|
X.Jiang,
E.Myatt,
P.Lykos,
and
F.J.Stevens
(1997).
Interaction between glycosaminoglycans and immunoglobulin light chains.
|
| |
Biochemistry,
36,
13187-13194.
|
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|
|
B.Mulloy
(1996).
High-field NMR as a technique for the determination of polysaccharide structures.
|
| |
Mol Biotechnol,
6,
241-265.
|
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|
|
G.Venkataraman,
V.Sasisekharan,
A.B.Herr,
D.M.Ornitz,
G.Waksman,
C.L.Cooney,
R.Langer,
and
R.Sasisekharan
(1996).
Preferential self-association of basic fibroblast growth factor is stabilized by heparin during receptor dimerization and activation.
|
| |
Proc Natl Acad Sci U S A,
93,
845-850.
|
|
|
|
|
|
|
M.Hricovíni,
and
G.Torri
(1995).
Dynamics in aqueous solutions of the pentasaccharide corresponding to the binding site of heparin for antithrombin III studied by NMR relaxation measurements.
|
| |
Carbohydr Res,
268,
159-175.
|
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|
M.Hricovíni,
M.Guerrini,
G.Torri,
S.Piani,
and
F.Ungarelli
(1995).
Conformational analysis of heparin epoxide in aqueous solution. An NMR relaxation study.
|
| |
Carbohydr Res,
277,
11-23.
|
|
|
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|
|
P.D.Grootenhuis,
P.Westerduin,
D.Meuleman,
M.Petitou,
and
C.A.van Boeckel
(1995).
Rational design of synthetic heparin analogues with tailor-made coagulation factor inhibitory activity.
|
| |
Nat Struct Biol,
2,
736-739.
|
|
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|
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|
|
S.Ernst,
R.Langer,
C.L.Cooney,
and
R.Sasisekharan
(1995).
Enzymatic degradation of glycosaminoglycans.
|
| |
Crit Rev Biochem Mol Biol,
30,
387-444.
|
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|
|
|
|
G.Venkataraman,
V.Sasisekharan,
C.L.Cooney,
R.Langer,
and
R.Sasisekharan
(1994).
A stereochemical approach to pyranose ring flexibility: its implications for the conformation of dermatan sulfate.
|
| |
Proc Natl Acad Sci U S A,
91,
6171-6175.
|
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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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