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Contents |
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335 a.a.
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36 a.a.
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140 a.a.
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* Residue conservation analysis
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PDB id:
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Hydrolase/hydrolase inhibitor
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Title:
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Crystal structure of a serpin:protease complex
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Structure:
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Alpha-1-antitrypsin. Chain: a. Fragment: n-terminal fragment of proteolytic cleavage at met358- ser359. Engineered: yes. Alpha-1-antitrypsin. Chain: b. Fragment: c-terminal fragment of proteolytic cleavage at met358- ser359.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Expressed in: escherichia coli. Expression_system_taxid: 562. Bos taurus. Cattle. Organism_taxid: 9913.
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Biol. unit:
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Trimer (from
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Resolution:
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2.60Å
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R-factor:
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0.205
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R-free:
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0.239
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Authors:
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J.A.Huntington,R.W.Carrell
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Key ref:
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J.A.Huntington
et al.
(2000).
Structure of a serpin-protease complex shows inhibition by deformation.
Nature,
407,
923-926.
PubMed id:
DOI:
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Date:
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12-May-00
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Release date:
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25-Oct-00
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PROCHECK
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Headers
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References
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P01009
(A1AT_HUMAN) -
Alpha-1-antitrypsin from Homo sapiens
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Seq:
Struc:
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418 a.a.
335 a.a.
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Enzyme class:
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Chain C:
E.C.3.4.21.4
- trypsin.
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Reaction:
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Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
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DOI no:
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Nature
407:923-926
(2000)
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PubMed id:
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Structure of a serpin-protease complex shows inhibition by deformation.
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J.A.Huntington,
R.J.Read,
R.W.Carrell.
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ABSTRACT
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The serpins have evolved to be the predominant family of serine-protease
inhibitors in man. Their unique mechanism of inhibition involves a profound
change in conformation, although the nature and significance of this change has
been controversial. Here we report the crystallographic structure of a typical
serpin-protease complex and show the mechanism of inhibition. The conformational
change is initiated by reaction of the active serine of the protease with the
reactive centre of the serpin. This cleaves the reactive centre, which then
moves 71 A to the opposite pole of the serpin, taking the tethered protease with
it. The tight linkage of the two molecules and resulting overlap of their
structures does not affect the hyperstable serpin, but causes a surprising 37%
loss of structure in the protease. This is induced by the plucking of the serine
from its active site, together with breakage of interactions formed during
zymogen activation. The disruption of the catalytic site prevents the release of
the protease from the complex, and the structural disorder allows its
proteolytic destruction. It is this ability of the conformational mechanism to
crush as well as inhibit proteases that provides the serpins with their
selective advantage.
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Selected figure(s)
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Figure 1.
Figure 1: Formation of the complex. Ribbon depictions of
native  [1]-antitrypsin8
with trypsin aligned above it in the docking orientation (left),
and of the complex showing the 71 Å shift of the P1 methionine
of [1]-antitrypsin,
with full insertion of the cleaved reactive-centre loop into the
A-sheet (right). Regions of disordered structure in the
complexed trypsin are shown as interrupted coils projected from
the native structure of trypsin. Red, [1]-antitrypsin
 -sheet
A; yellow, reactive-centre loop; green ball-and-stick, P1 Met;
cyan, trypsin (with helices in magenta for orientation); red
ball-and-stick, active serine 195.
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Figure 2.
Figure 2: Proteolytic susceptibility of the complexed protease.
A stereo side view of the complex coloured according to C temperature
factors for trypsin ( [1]-antitrypsin,
coloured as in Fig. 1, retains the low B-factors of its isolated
cleaved form). The nine sites of proteolytic cleavage are shown
as balls and all occur in regions of crystallographic disorder
or high mobility. Cleavage sites: green, of trypsin, by
trypsin5; yellow, of chymotrypsin, by chymotrypsin 6; magenta,
of chymotrypsin, by neutrophil elastase^6. Temperature factors
from blue to red, going through green at 40 Å 2, yellow at 60 Å2
and red at 90 Å 2. When the full native trypsin structure is
superimposed on the ordered region of trypsin in the complex
there are no clashes with symmetry related molecules. The only
significant steric overlap is within the asymmetric unit between
the serpin and the disordered region of trypsin, as denoted here
by cyan balls.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
407,
923-926)
copyright 2000.
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Figures were
selected
by the author.
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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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B.Krishnan,
and
L.M.Gierasch
(2011).
Dynamic local unfolding in the serpin α-1 antitrypsin provides a mechanism for loop insertion and polymerization.
|
| |
Nat Struct Mol Biol,
18,
222-226.
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|
|
|
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|
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B.Wladyka,
A.J.Kozik,
M.Bukowski,
A.Rojowska,
T.Kantyka,
G.Dubin,
and
A.Dubin
(2011).
α(1)-Antichymotrypsin inactivates staphylococcal cysteine protease in cross-class inhibition.
|
| |
Biochimie,
93,
948-953.
|
|
|
|
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|
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C.Klein
(2011).
Genetic defects in severe congenital neutropenia: emerging insights into life and death of human neutrophil granulocytes.
|
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Annu Rev Immunol,
29,
399-413.
|
|
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C.S.Craik,
M.J.Page,
and
E.L.Madison
(2011).
Proteases as therapeutics.
|
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Biochem J,
435,
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L.C.Thompson,
S.Goswami,
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D.E.Day,
I.M.Verhamme,
and
C.B.Peterson
(2011).
Metals affect the structure and activity of human plasminogen activator inhibitor-1. I. Modulation of stability and protease inhibition.
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| |
Protein Sci,
20,
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|
|
|
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|
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L.Meinert Niclasen,
J.G.Olsen,
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O.E.Sørensen,
and
B.B.Kragelund
(2011).
Streptococcal pyogenic exotoxin B (SpeB) boosts the contact system via binding of α-1 antitrypsin.
|
| |
Biochem J,
434,
123-132.
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|
|
|
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|
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N.Umasuthan,
I.Whang,
J.O.Kim,
M.J.Oh,
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C.Y.Choi,
S.Y.Yeo,
J.H.Lee,
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and
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(2011).
Rock bream (Oplegnathus fasciatus) serpin, protease nexin-1: transcriptional analysis and characterization of its antiprotease and anticoagulant activities.
|
| |
Dev Comp Immunol,
35,
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|
|
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|
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|
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T.Yamada,
T.Tomita,
L.M.Weiss,
and
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(2011).
Toxoplasma gondii inhibits granzyme B-mediated apoptosis by the inhibition of granzyme B function in host cells.
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| |
Int J Parasitol,
41,
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|
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A.Sirmaci,
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M.Huang,
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B.HiÅŸmi,
H.OzdaÄŸ,
B.Oztürk,
S.KulaksizoÄŸlu,
E.Yildirim,
H.Kokotas,
M.Grigoriadou,
M.B.Petersen,
H.Shahin,
M.Kanaan,
M.C.King,
Z.Y.Chen,
S.H.Blanton,
X.Z.Liu,
S.Zuchner,
N.Akar,
and
M.Tekin
(2010).
A truncating mutation in SERPINB6 is associated with autosomal-recessive nonsyndromic sensorineural hearing loss.
|
| |
Am J Hum Genet,
86,
797-804.
|
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|
|
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|
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D.Kaiserman,
and
P.I.Bird
(2010).
Control of granzymes by serpins.
|
| |
Cell Death Differ,
17,
586-595.
|
|
|
|
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|
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D.Lwalaba,
S.Weidlich,
K.H.Hoffmann,
and
J.Woodring
(2010).
Exogenous and endogenous protease inhibitors in the gut of the fall armyworm larvae, Spodoptera frugiperda.
|
| |
Arch Insect Biochem Physiol,
74,
114-126.
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E.Karnaukhova
(2010).
Interactions of alpha1-proteinase inhibitor with small ligands of therapeutic potential: binding with retinoic acid.
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| |
Amino Acids,
38,
1011-1020.
|
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|
|
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|
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F.Turroni,
E.Foroni,
M.O'Connell Motherway,
F.Bottacini,
V.Giubellini,
A.Zomer,
A.Ferrarini,
M.Delledonne,
Z.Zhang,
D.van Sinderen,
and
M.Ventura
(2010).
Characterization of the serpin-encoding gene of Bifidobacterium breve 210B.
|
| |
Appl Environ Microbiol,
76,
3206-3219.
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|
|
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|
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J.A.Huntington,
and
J.C.Whisstock
(2010).
Molecular contortionism - on the physical limits of serpin 'loop-sheet' polymers.
|
| |
Biol Chem,
391,
973-982.
|
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|
|
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|
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J.E.Swedberg,
S.J.de Veer,
and
J.M.Harris
(2010).
Natural and engineered kallikrein inhibitors: an emerging pharmacopoeia.
|
| |
Biol Chem,
391,
357-374.
|
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|
|
|
|
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P.Goettig,
V.Magdolen,
and
H.Brandstetter
(2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
|
| |
Biochimie,
92,
1546-1567.
|
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|
|
|
|
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P.Przygodzka,
B.Ramstedt,
T.Tengel,
G.Larsson,
and
M.Wilczynska
(2010).
Bomapin is a redox-sensitive nuclear serpin that affects responsiveness of myeloid progenitor cells to growth environment.
|
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BMC Cell Biol,
11,
30.
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R.Wallis,
D.A.Mitchell,
R.Schmid,
W.J.Schwaeble,
and
A.H.Keeble
(2010).
Paths reunited: Initiation of the classical and lectin pathways of complement activation.
|
| |
Immunobiology,
215,
1.
|
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|
|
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|
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S.Ricagno,
M.Pezzullo,
A.Barbiroli,
M.Manno,
M.Levantino,
M.G.Santangelo,
F.Bonomi,
and
M.Bolognesi
(2010).
Two latent and two hyperstable polymeric forms of human neuroserpin.
|
| |
Biophys J,
99,
3402-3411.
|
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|
|
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|
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V.Stoka,
and
V.Turk
(2010).
A structural network associated with the kallikrein-kinin and renin-angiotensin systems.
|
| |
Biol Chem,
391,
443-454.
|
|
|
|
|
|
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W.J.Higgins,
D.M.Fox,
P.S.Kowalski,
J.E.Nielsen,
and
D.M.Worrall
(2010).
Heparin enhances serpin inhibition of the cysteine protease cathepsin L.
|
| |
J Biol Chem,
285,
3722-3729.
|
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|
|
|
|
|
A.S.Knaupp,
and
S.P.Bottomley
(2009).
Serpin polymerization and its role in disease--the molecular basis of alpha1-antitrypsin deficiency.
|
| |
IUBMB Life,
61,
1-5.
|
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|
|
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|
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B.Gooptu,
and
D.A.Lomas
(2009).
Conformational pathology of the serpins: themes, variations, and therapeutic strategies.
|
| |
Annu Rev Biochem,
78,
147-176.
|
|
|
|
|
|
|
B.Gooptu,
E.Miranda,
I.Nobeli,
M.Mallya,
A.Purkiss,
S.C.Brown,
C.Summers,
R.L.Phillips,
D.A.Lomas,
and
T.E.Barrett
(2009).
Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design.
|
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J Mol Biol,
387,
857-868.
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PDB codes:
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B.Richard,
R.Swanson,
and
S.T.Olson
(2009).
The signature 3-O-sulfo group of the anticoagulant heparin sequence is critical for heparin binding to antithrombin but is not required for allosteric activation.
|
| |
J Biol Chem,
284,
27054-27064.
|
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|
|
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C.Boudier,
A.S.Klymchenko,
Y.Mely,
and
A.Follenius-Wund
(2009).
Local environment perturbations in alpha(1)-antitrypsin monitored by a ratiometric fluorescent label.
|
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Photochem Photobiol Sci,
8,
814-821.
|
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C.W.Ko,
Z.Wei,
R.J.Marsh,
D.A.Armoogum,
N.Nicolaou,
A.J.Bain,
A.Zhou,
and
L.Ying
(2009).
Probing nanosecond motions of plasminogen activator inhibitor-1 by time-resolved fluorescence anisotropy.
|
| |
Mol Biosyst,
5,
1025-1031.
|
|
|
|
|
|
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D.C.Rijken,
and
H.R.Lijnen
(2009).
New insights into the molecular mechanisms of the fibrinolytic system.
|
| |
J Thromb Haemost,
7,
4.
|
|
|
|
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G.Izaguirre,
A.R.Rezaie,
and
S.T.Olson
(2009).
Engineering functional antithrombin exosites in alpha1-proteinase inhibitor that specifically promote the inhibition of factor Xa and factor IXa.
|
| |
J Biol Chem,
284,
1550-1558.
|
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|
|
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H.Kroeger,
E.Miranda,
I.MacLeod,
J.Pérez,
D.C.Crowther,
S.J.Marciniak,
and
D.A.Lomas
(2009).
Endoplasmic reticulum-associated degradation (ERAD) and autophagy cooperate to degrade polymerogenic mutant serpins.
|
| |
J Biol Chem,
284,
22793-22802.
|
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|
|
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|
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J.A.Huntington,
T.J.Sendall,
and
M.Yamasaki
(2009).
New insight into serpin polymerization and aggregation.
|
| |
Prion,
3,
12-14.
|
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J.H.Baek,
W.S.Yang,
C.Lee,
and
M.H.Yu
(2009).
Functional unfolding of alpha1-antitrypsin probed by hydrogen-deuterium exchange coupled with mass spectrometry.
|
| |
Mol Cell Proteomics,
8,
1072-1081.
|
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|
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J.K.Jensen,
K.Dolmer,
and
P.G.Gettins
(2009).
Specificity of Binding of the Low Density Lipoprotein Receptor-related Protein to Different Conformational States of the Clade E Serpins Plasminogen Activator Inhibitor-1 and Proteinase Nexin-1.
|
| |
J Biol Chem,
284,
17989-17997.
|
|
|
|
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J.Langdown,
K.J.Belzar,
W.J.Savory,
T.P.Baglin,
and
J.A.Huntington
(2009).
The critical role of hinge-region expulsion in the induced-fit heparin binding mechanism of antithrombin.
|
| |
J Mol Biol,
386,
1278-1289.
|
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PDB code:
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J.W.Ahn,
B.J.Atwell,
and
T.H.Roberts
(2009).
Serpin genes AtSRP2 and AtSRP3 are required for normal growth sensitivity to a DNA alkylating agent in Arabidopsis.
|
| |
BMC Plant Biol,
9,
52.
|
|
|
|
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|
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K.A.Tanaka,
N.S.Key,
and
J.H.Levy
(2009).
Blood coagulation: hemostasis and thrombin regulation.
|
| |
Anesth Analg,
108,
1433-1446.
|
|
|
|
|
|
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L.Yang,
S.H.Qureshi,
C.Manithody,
and
A.R.Rezaie
(2009).
Role of P2 glycine in determining the specificity of antithrombin reaction with coagulation proteases.
|
| |
Biochem Biophys Res Commun,
389,
162-167.
|
|
|
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|
|
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M.Cugno,
A.Zanichelli,
F.Foieni,
S.Caccia,
and
M.Cicardi
(2009).
C1-inhibitor deficiency and angioedema: molecular mechanisms and clinical progress.
|
| |
Trends Mol Med,
15,
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|
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|
|
|
M.Garrett,
A.Fullaondo,
L.Troxler,
G.Micklem,
and
D.Gubb
(2009).
Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes.
|
| |
BMC Genomics,
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489.
|
|
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|
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P.C.Ong,
S.J.Golding,
M.C.Pearce,
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S.A.Grigoryev,
D.Pike,
C.G.Langendorf,
T.A.Bashtannyk-Puhalovich,
S.P.Bottomley,
J.C.Whisstock,
R.N.Pike,
and
S.McGowan
(2009).
Conformational change in the chromatin remodelling protein MENT.
|
| |
PLoS ONE,
4,
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|
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R.Bass,
L.Wagstaff,
L.Ravenhill,
and
V.Ellis
(2009).
Binding of extracellular maspin to beta1 integrins inhibits vascular smooth muscle cell migration.
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| |
J Biol Chem,
284,
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|
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|
S.F.Soukup,
J.Culi,
and
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(2009).
Uptake of the necrotic serpin in Drosophila melanogaster via the lipophorin receptor-1.
|
| |
PLoS Genet,
5,
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|
|
|
|
|
|
|
T.K.Huang,
M.A.Plesha,
B.W.Falk,
A.M.Dandekar,
and
K.A.McDonald
(2009).
Bioreactor strategies for improving production yield and functionality of a recombinant human protein in transgenic tobacco cell cultures.
|
| |
Biotechnol Bioeng,
102,
508-520.
|
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|
T.Zögg,
and
H.Brandstetter
(2009).
Structural basis of the cofactor- and substrate-assisted activation of human coagulation factor IXa.
|
| |
Structure,
17,
1669-1678.
|
|
|
PDB codes:
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|
|
|
|
|
|
U.I.Ekeowa,
B.Gooptu,
D.Belorgey,
P.Hägglöf,
S.Karlsson-Li,
E.Miranda,
J.Pérez,
I.MacLeod,
H.Kroger,
S.J.Marciniak,
D.C.Crowther,
and
D.A.Lomas
(2009).
alpha1-Antitrypsin deficiency, chronic obstructive pulmonary disease and the serpinopathies.
|
| |
Clin Sci (Lond),
116,
837-850.
|
|
|
|
|
|
|
Y.P.Chang,
R.Mahadeva,
W.S.Chang,
S.C.Lin,
and
Y.H.Chu
(2009).
Small-molecule peptides inhibit Z alpha1-antitrypsin polymerization.
|
| |
J Cell Mol Med,
13,
2304-2316.
|
|
|
|
|
|
|
Z.Li,
S.Alam,
J.Wang,
C.S.Sandstrom,
S.Janciauskiene,
and
R.Mahadeva
(2009).
Oxidized {alpha}1-antitrypsin stimulates the release of monocyte chemotactic protein-1 from lung epithelial cells: potential role in emphysema.
|
| |
Am J Physiol Lung Cell Mol Physiol,
297,
L388-L400.
|
|
|
|
|
|
|
Z.Volovyk,
D.M.Monroe,
Y.Qi,
R.Becker,
and
M.Hoffman
(2009).
A rationally designed heparin, M118, has anticoagulant activity similar to unfractionated heparin and different from Lovenox in a cell-based model of thrombin generation.
|
| |
J Thromb Thrombolysis,
28,
132-139.
|
|
|
|
|
|
|
Z.Zou,
Z.Picheng,
H.Weng,
K.Mita,
and
H.Jiang
(2009).
A comparative analysis of serpin genes in the silkworm genome.
|
| |
Genomics,
93,
367-375.
|
|
|
|
|
|
|
A.Eissa,
and
E.P.Diamandis
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PDB code:
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PDB code:
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PDB code:
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PDB codes:
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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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