|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains L, H:
E.C.3.4.21.5
- thrombin.
|
|
|
|
|
|
|
Reaction:
|
|
Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Embo J
8:3467-3475
(1989)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.
|
|
W.Bode,
I.Mayr,
U.Baumann,
R.Huber,
S.R.Stone,
J.Hofsteenge.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg
chloromethylketone was crystallized in an orthorhombic crystal form. Orientation
and position of a starting model derived from homologous modelling were
determined by Patterson search methods. The thrombin model was completed in a
cyclic modelling-crystallographic refinement procedure to a final R-value of
0.171 for X-ray data to 1.92 A. The structure is in full agreement with
published cDNA sequence data. The A-chain, ordered only in its central part, is
positioned along the molecular surface opposite to the active site. The B-chain
exhibits the characteristic polypeptide fold of trypsin-like proteinases.
Several extended insertions form, however, large protuberances; most important
for interaction with macromolecular substrates is the characteristic thrombin
loop around Tyr60A-Pro60B-Pro60C-Trp60D (chymotrypsinogen numbering) and the
enlarged loop around the unique Trp148. The former considerably restricts the
active site cleft and seems likely to be responsible for poor binding of most
natural proteinase inhibitors to thrombin. The exceptional specificity of
D-Phe-Pro-Arg chloromethylketone can be explained by a hydrophobic cage formed
by Ile174, Trp215, Leu99, His57, Tyr60A and Trp60D. The narrow active site
cleft, with a more polar base and hydrophobic rims, extends towards the
arginine-rich surface of loop Lys70-Glu80 that probably represents part of the
anionic binding region for hirudin and fibrinogen.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
M.W.Bunce,
R.Toso,
and
R.M.Camire
(2011).
Zymogen-like factor Xa variants restore thrombin generation and effectively bypass the intrinsic pathway in vitro.
|
| |
Blood,
117,
290-298.
|
|
|
|
|
|
|
T.Clausen,
M.Kaiser,
R.Huber,
and
M.Ehrmann
(2011).
HTRA proteases: regulated proteolysis in protein quality control.
|
| |
Nat Rev Mol Cell Biol,
12,
152-162.
|
|
|
|
|
|
|
A.R.Rezaie
(2010).
Regulation of the protein C anticoagulant and antiinflammatory pathways.
|
| |
Curr Med Chem,
17,
2059-2069.
|
|
|
|
|
|
|
C.Ribeiro,
R.C.Togawa,
I.A.Neshich,
I.Mazoni,
A.L.Mancini,
R.C.Minardi,
C.H.da Silveira,
J.G.Jardine,
M.M.Santoro,
and
G.Neshich
(2010).
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.
|
| |
BMC Struct Biol,
10,
36.
|
|
|
|
|
|
|
H.L.de Amorim,
P.A.Netz,
and
J.A.Guimarães
(2010).
Thrombin allosteric modulation revisited: a molecular dynamics study.
|
| |
J Mol Model,
16,
725-735.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
S.H.Qureshi,
and
A.R.Rezaie
(2010).
Inhibitory properties of the P1 Tyr variant of antithrombin.
|
| |
Biochemistry,
49,
2680-2686.
|
|
|
|
|
|
|
M.H.Bos,
and
R.M.Camire
(2010).
Procoagulant Adaptation of a Blood Coagulation Prothrombinase-like Enzyme Complex in Australian Elapid Venom.
|
| |
Toxins (Basel),
2,
1554-1567.
|
|
|
|
|
|
|
O.Lomas,
R.A.Argyle,
and
B.D.Prendergast
(2010).
Will direct thrombin inhibition change the boundaries of oral anti-coagulation?
|
| |
QJM,
103,
429-434.
|
|
|
|
|
|
|
T.Shiraishi,
S.Kadono,
M.Haramura,
H.Kodama,
Y.Ono,
H.Iikura,
T.Esaki,
T.Koga,
K.Hattori,
Y.Watanabe,
A.Sakamoto,
K.Yoshihashi,
T.Kitazawa,
K.Esaki,
M.Ohta,
H.Sato,
and
T.Kozono
(2010).
Design and synthesis of peptidomimetic factor VIIa inhibitors.
|
| |
Chem Pharm Bull (Tokyo),
58,
38-44.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.M.Kovach,
P.Kelley,
C.Eddy,
F.Jordan,
and
A.Baykal
(2009).
Proton bridging in the interactions of thrombin with small inhibitors.
|
| |
Biochemistry,
48,
7296-7304.
|
|
|
|
|
|
|
J.S.Bae,
and
A.R.Rezaie
(2009).
Thrombin inhibits nuclear factor kappaB and RhoA pathways in cytokine-stimulated vascular endothelial cells when EPCR is occupied by protein C.
|
| |
Thromb Haemost,
101,
513-520.
|
|
|
|
|
|
|
L.Yang,
M.F.Sun,
D.Gailani,
and
A.R.Rezaie
(2009).
Characterization of a heparin-binding site on the catalytic domain of factor XIa: mechanism of heparin acceleration of factor XIa inhibition by the serpins antithrombin and C1-inhibitor.
|
| |
Biochemistry,
48,
1517-1524.
|
|
|
|
|
|
|
M.I.Zavodszky,
A.Rohatgi,
J.R.Van Voorst,
H.Yan,
and
L.A.Kuhn
(2009).
Scoring ligand similarity in structure-based virtual screening.
|
| |
J Mol Recognit,
22,
280-292.
|
|
|
|
|
|
|
S.H.Qureshi,
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2009).
Membrane-dependent interaction of factor Xa and prothrombin with factor Va in the prothrombinase complex.
|
| |
Biochemistry,
48,
5034-5041.
|
|
|
|
|
|
|
S.H.Qureshi,
L.Yang,
C.Manithody,
A.V.Iakhiaev,
and
A.R.Rezaie
(2009).
Mutagenesis studies toward understanding allostery in thrombin.
|
| |
Biochemistry,
48,
8261-8270.
|
|
|
|
|
|
|
T.E.Adams,
W.Li,
and
J.A.Huntington
(2009).
Molecular basis of thrombomodulin activation of slow thrombin.
|
| |
J Thromb Haemost,
7,
1688-1695.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
A.Poyarkov,
X.Rocabayera,
S.Poyarkova,
and
V.Kukhar
(2008).
Influence of aromatic and aliphatic moieties on thrombin inhibitors potency.
|
| |
Open Biochem J,
2,
143-149.
|
|
|
|
|
|
|
A.Venceslá,
M.A.Corral-Rodríguez,
M.Baena,
M.Cornet,
M.Domènech,
M.Baiget,
P.Fuentes-Prior,
and
E.F.Tizzano
(2008).
Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites.
|
| |
Blood,
111,
3468-3478.
|
|
|
|
|
|
|
J.A.Huntington
(2008).
How Na+ activates thrombin--a review of the functional and structural data.
|
| |
Biol Chem,
389,
1025-1035.
|
|
|
|
|
|
|
J.S.Bae,
and
A.R.Rezaie
(2008).
Protease activated receptor 1 (PAR-1) activation by thrombin is protective in human pulmonary artery endothelial cells if endothelial protein C receptor is occupied by its natural ligand.
|
| |
Thromb Haemost,
100,
101-109.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
S.H.Qureshi,
and
A.R.Rezaie
(2008).
Factor Va alters the conformation of the Na+-binding loop of factor Xa in the prothrombinase complex.
|
| |
Biochemistry,
47,
5976-5985.
|
|
|
|
|
|
|
M.V.Kolodzeiskaya,
L.I.Sokolovskaya,
and
G.L.Volkov
(2008).
Role of A-chain in functioning of the active site of human alpha-thrombin.
|
| |
Biochemistry (Mosc),
73,
237-244.
|
|
|
|
|
|
|
P.Kamath,
and
S.Krishnaswamy
(2008).
Fate of Membrane-bound Reactants and Products during the Activation of Human Prothrombin by Prothrombinase.
|
| |
J Biol Chem,
283,
30164-30173.
|
|
|
|
|
|
|
R.Q.Monteiro,
A.R.Rezaie,
J.S.Bae,
E.Calvo,
J.F.Andersen,
and
I.M.Francischetti
(2008).
Ixolaris binding to factor X reveals a precursor state of factor Xa heparin-binding exosite.
|
| |
Protein Sci,
17,
146-153.
|
|
|
|
|
|
|
R.Toso,
H.Zhu,
and
R.M.Camire
(2008).
The conformational switch from the factor X zymogen to protease state mediates exosite expression and prothrombinase assembly.
|
| |
J Biol Chem,
283,
18627-18635.
|
|
|
|
|
|
|
S.H.Qureshi,
C.Manithody,
J.S.Bae,
L.Yang,
and
A.R.Rezaie
(2008).
Autolysis loop restricts the specificity of activated protein C: analysis by FRET and functional assays.
|
| |
Biophys Chem,
134,
239-245.
|
|
|
|
|
|
|
S.Macedo-Ribeiro,
C.Almeida,
B.M.Calisto,
T.Friedrich,
R.Mentele,
J.Stürzebecher,
P.Fuentes-Prior,
and
P.J.Pereira
(2008).
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
|
| |
PLoS ONE,
3,
e1624.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Li,
T.E.Adams,
J.Nangalia,
C.T.Esmon,
and
J.A.Huntington
(2008).
Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
|
| |
Proc Natl Acad Sci U S A,
105,
4661-4666.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Manithody,
L.Yang,
and
A.R.Rezaie
(2007).
Identification of a basic region on tissue factor that interacts with the first epidermal growth factor-like domain of factor X.
|
| |
Biochemistry,
46,
3193-3199.
|
|
|
|
|
|
|
D.Blomberg,
T.Fex,
Y.Xue,
K.Brickmann,
and
J.Kihlberg
(2007).
Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold.
|
| |
Org Biomol Chem,
5,
2599-2605.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Gailani,
A.Schmidt,
M.F.Sun,
P.H.Bolton-Maggs,
and
S.P.Bajaj
(2007).
A cross-reactive material positive variant of coagulation factor XI (FXIP520L) with a catalytic defect.
|
| |
J Thromb Haemost,
5,
781-787.
|
|
|
|
|
|
|
E.L.Wu,
Y.Mei,
K.Han,
and
J.Z.Zhang
(2007).
Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin.
|
| |
Biophys J,
92,
4244-4253.
|
|
|
|
|
|
|
J.S.Bae,
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2007).
Engineering a disulfide bond to stabilize the calcium-binding loop of activated protein C eliminates its anticoagulant but not its protective signaling properties.
|
| |
J Biol Chem,
282,
9251-9259.
|
|
|
|
|
|
|
J.S.Bae,
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2007).
The ligand occupancy of endothelial protein C receptor switches the protease-activated receptor 1-dependent signaling specificity of thrombin from a permeability-enhancing to a barrier-protective response in endothelial cells.
|
| |
Blood,
110,
3909-3916.
|
|
|
|
|
|
|
L.Yang,
J.S.Bae,
C.Manithody,
and
A.R.Rezaie
(2007).
Identification of a specific exosite on activated protein C for interaction with protease-activated receptor 1.
|
| |
J Biol Chem,
282,
25493-25500.
|
|
|
|
|
|
|
P.E.Bock,
P.Panizzi,
and
I.M.Verhamme
(2007).
Exosites in the substrate specificity of blood coagulation reactions.
|
| |
J Thromb Haemost,
5,
81-94.
|
|
|
|
|
|
|
Y.M.Fortenberry,
H.C.Whinna,
S.T.Cooper,
T.Myles,
L.L.Leung,
and
F.C.Church
(2007).
Essential thrombin residues for inhibition by protein C inhibitor with the cofactors heparin and thrombomodulin.
|
| |
J Thromb Haemost,
5,
1486-1492.
|
|
|
|
|
|
|
A.R.Rezaie
(2006).
Pentasaccharide enhances the inactivation of factor Xa by antithrombin by promoting the assembly of a Michaelis-type intermediate complex. Demonstration by rapid kinetic, surface plasmon resonance, and competitive binding studies.
|
| |
Biochemistry,
45,
5324-5329.
|
|
|
|
|
|
|
E.Schweizer,
A.Hoffmann-Röder,
J.A.Olsen,
P.Seiler,
U.Obst-Sander,
B.Wagner,
M.Kansy,
D.W.Banner,
and
F.Diederich
(2006).
Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors.
|
| |
Org Biomol Chem,
4,
2364-2375.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.Schweizer,
A.Hoffmann-Röder,
K.Schärer,
J.A.Olsen,
C.Fäh,
P.Seiler,
U.Obst-Sander,
B.Wagner,
M.Kansy,
and
F.Diederich
(2006).
A fluorine scan at the catalytic center of thrombin: C--F, C--OH, and C--OMe bioisosterism and fluorine effects on pKa and log D values.
|
| |
ChemMedChem,
1,
611-621.
|
|
|
|
|
|
|
E.Szepessy,
and
M.Sahin-Tóth
(2006).
Human mesotrypsin exhibits restricted S1' subsite specificity with a strong preference for small polar side chains.
|
| |
FEBS J,
273,
2942-2954.
|
|
|
|
|
|
|
K.Segers,
J.Rosing,
and
G.A.Nicolaes
(2006).
Structural models of the snake venom factor V activators from Daboia russelli and Daboia lebetina.
|
| |
Proteins,
64,
968-984.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2006).
Activation of protein C by the thrombin-thrombomodulin complex: cooperative roles of Arg-35 of thrombin and Arg-67 of protein C.
|
| |
Proc Natl Acad Sci U S A,
103,
879-884.
|
|
|
|
|
|
|
M.A.Bukys,
T.Orban,
P.Y.Kim,
D.O.Beck,
M.E.Nesheim,
and
M.Kalafatis
(2006).
The structural integrity of anion binding exosite I of thrombin is required and sufficient for timely cleavage and activation of factor V and factor VIII.
|
| |
J Biol Chem,
281,
18569-18580.
|
|
|
|
|
|
|
P.Panizzi,
R.Friedrich,
P.Fuentes-Prior,
H.K.Kroh,
J.Briggs,
G.Tans,
W.Bode,
and
P.E.Bock
(2006).
Novel fluorescent prothrombin analogs as probes of staphylocoagulase-prothrombin interactions.
|
| |
J Biol Chem,
281,
1169-1178.
|
|
|
|
|
|
|
P.Panizzi,
R.Friedrich,
P.Fuentes-Prior,
K.Richter,
P.E.Bock,
and
W.Bode
(2006).
Fibrinogen substrate recognition by staphylocoagulase.(pro)thrombin complexes.
|
| |
J Biol Chem,
281,
1179-1187.
|
|
|
|
|
|
|
R.Friedrich,
P.Panizzi,
S.Kawabata,
W.Bode,
P.E.Bock,
and
P.Fuentes-Prior
(2006).
Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation.
|
| |
J Biol Chem,
281,
1188-1195.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Toso,
and
R.M.Camire
(2006).
Role of Hirudin-like factor Va heavy chain sequences in prothrombinase function.
|
| |
J Biol Chem,
281,
8773-8779.
|
|
|
|
|
|
|
S.Rouy,
D.Vidaud,
J.L.Alessandri,
M.D.Dautzenberg,
L.Venisse,
M.C.Guillin,
and
A.Bezeaud
(2006).
Prothrombin Saint-Denis: a natural variant with a point mutation resulting in Asp to Glu substitution at position 552 in prothrombin.
|
| |
Br J Haematol,
132,
770-773.
|
|
|
|
|
|
|
W.L.Straube,
and
E.M.Tanaka
(2006).
Reversibility of the differentiated state: regeneration in amphibians.
|
| |
Artif Organs,
30,
743-755.
|
|
|
|
|
|
|
A.R.Rezaie,
C.Manithody,
and
L.Yang
(2005).
Identification of factor Xa residues critical for interaction with protein Z-dependent protease inhibitor: both active site and exosite interactions are required for inhibition.
|
| |
J Biol Chem,
280,
32722-32728.
|
|
|
|
|
|
|
C.Salvagnini,
C.Michaux,
J.Remiche,
J.Wouters,
P.Charlier,
and
J.Marchand-Brynaert
(2005).
Design, synthesis and evaluation of graftable thrombin inhibitors for the preparation of blood-compatible polymer materials.
|
| |
Org Biomol Chem,
3,
4209-4220.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.N.Gosalia,
C.M.Salisbury,
D.J.Maly,
J.A.Ellman,
and
S.L.Diamond
(2005).
Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays.
|
| |
Proteomics,
5,
1292-1298.
|
|
|
|
|
|
|
E.P.Bianchini,
S.J.Orcutt,
P.Panizzi,
P.E.Bock,
and
S.Krishnaswamy
(2005).
Ratcheting of the substrate from the zymogen to proteinase conformations directs the sequential cleavage of prothrombin by prothrombinase.
|
| |
Proc Natl Acad Sci U S A,
102,
10099-10104.
|
|
|
|
|
|
|
E.S.Istvan,
and
D.E.Goldberg
(2005).
Distal substrate interactions enhance plasmepsin activity.
|
| |
J Biol Chem,
280,
6890-6896.
|
|
|
|
|
|
|
E.Toyota,
H.Sekizaki,
Y.U.Takahashi,
K.Itoh,
and
K.Tanizawa
(2005).
Amidino-containing Schiff base copper(II) and iron(III) chelates as a thrombin inhibitor.
|
| |
Chem Pharm Bull (Tokyo),
53,
22-26.
|
|
|
|
|
|
|
J.A.Huntington
(2005).
Molecular recognition mechanisms of thrombin.
|
| |
J Thromb Haemost,
3,
1861-1872.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2005).
The functional significance of the autolysis loop in protein C and activated protein C.
|
| |
Thromb Haemost,
94,
60-68.
|
|
|
|
|
|
|
M.A.Bukys,
M.A.Blum,
P.Y.Kim,
N.Brufatto,
M.E.Nesheim,
and
M.Kalafatis
(2005).
Incorporation of factor Va into prothrombinase is required for coordinated cleavage of prothrombin by factor Xa.
|
| |
J Biol Chem,
280,
27393-27401.
|
|
|
|
|
|
|
M.Groll,
M.Bochtler,
H.Brandstetter,
T.Clausen,
and
R.Huber
(2005).
Molecular machines for protein degradation.
|
| |
Chembiochem,
6,
222-256.
|
|
|
|
|
|
|
S.Akhavan,
M.A.Miteva,
B.O.Villoutreix,
L.Venisse,
F.Peyvandi,
P.M.Mannucci,
M.C.Guillin,
and
A.Bezeaud
(2005).
A critical role for Gly25 in the B chain of human thrombin.
|
| |
J Thromb Haemost,
3,
139-145.
|
|
|
|
|
|
|
S.Kadono,
A.Sakamoto,
Y.Kikuchi,
M.Oh-Eda,
N.Yabuta,
T.Koga,
K.Hattori,
T.Shiraishi,
M.Haramura,
H.Kodama,
Y.Ono,
T.Esaki,
H.Sato,
Y.Watanabe,
S.Itoh,
M.Ohta,
and
T.Kozono
(2005).
Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
169-173.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Krishnaswamy
(2005).
Exosite-driven substrate specificity and function in coagulation.
|
| |
J Thromb Haemost,
3,
54-67.
|
|
|
|
|
|
|
S.Srivastava,
L.N.Goswami,
and
D.K.Dikshit
(2005).
Progress in the design of low molecular weight thrombin inhibitors.
|
| |
Med Res Rev,
25,
66-92.
|
|
|
|
|
|
|
T.Ogawa,
I.M.Verhamme,
M.F.Sun,
P.E.Bock,
and
D.Gailani
(2005).
Exosite-mediated substrate recognition of factor IX by factor XIa. The factor XIa heavy chain is required for initial recognition of factor IX.
|
| |
J Biol Chem,
280,
23523-23530.
|
|
|
|
|
|
|
W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
|
| |
J Thromb Haemost,
3,
2379-2388.
|
|
|
|
|
|
|
W.J.Carter,
E.Cama,
and
J.A.Huntington
(2005).
Crystal structure of thrombin bound to heparin.
|
| |
J Biol Chem,
280,
2745-2749.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.R.Rezaie,
and
F.S.Kittur
(2004).
The critical role of the 185-189-loop in the factor Xa interaction with Na+ and factor Va in the prothrombinase complex.
|
| |
J Biol Chem,
279,
48262-48269.
|
|
|
|
|
|
|
A.Zivelin,
T.Ogawa,
S.Bulvik,
M.Landau,
J.R.Toomey,
J.Lane,
U.Seligsohn,
and
D.Gailani
(2004).
Severe factor XI deficiency caused by a Gly555 to Glu mutation (factor XI-Glu555): a cross-reactive material positive variant defective in factor IX activation.
|
| |
J Thromb Haemost,
2,
1782-1789.
|
|
|
|
|
|
|
D.Gustafsson,
R.Bylund,
T.Antonsson,
I.Nilsson,
J.E.Nyström,
U.Eriksson,
U.Bredberg,
and
A.C.Teger-Nilsson
(2004).
A new oral anticoagulant: the 50-year challenge.
|
| |
Nat Rev Drug Discov,
3,
649-659.
|
|
|
|
|
|
|
D.S.Boskovic,
T.Troxler,
and
S.Krishnaswamy
(2004).
Active site-independent recognition of substrates and product by bovine prothrombinase: a fluorescence resonance energy transfer study.
|
| |
J Biol Chem,
279,
20786-20793.
|
|
|
|
|
|
|
F.S.Kittur,
C.Manithody,
and
A.R.Rezaie
(2004).
Role of the N-terminal epidermal growth factor-like domain of factor X/Xa.
|
| |
J Biol Chem,
279,
24189-24196.
|
|
|
|
|
|
|
I.Pechik,
J.Madrazo,
M.W.Mosesson,
I.Hernandez,
G.L.Gilliland,
and
L.Medved
(2004).
Crystal structure of the complex between thrombin and the central "E" region of fibrin.
|
| |
Proc Natl Acad Sci U S A,
101,
2718-2723.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Vanhoorelbeke,
H.Ulrichts,
R.A.Romijn,
E.G.Huizinga,
and
H.Deckmyn
(2004).
The GPIbalpha-thrombin interaction: far from crystal clear.
|
| |
Trends Mol Med,
10,
33-39.
|
|
|
|
|
|
|
L.Chen,
and
A.R.Rezaie
(2004).
Proexosite-1-dependent recognition and activation of prothrombin by taipan venom.
|
| |
J Biol Chem,
279,
17869-17874.
|
|
|
|
|
|
|
L.Chen,
C.Manithody,
L.Yang,
and
A.R.Rezaie
(2004).
Zymogenic and enzymatic properties of the 70-80 loop mutants of factor X/Xa.
|
| |
Protein Sci,
13,
431-442.
|
|
|
|
|
|
|
L.Yang,
S.Prasad,
E.Di Cera,
and
A.R.Rezaie
(2004).
The conformation of the activation peptide of protein C is influenced by Ca2+ and Na+ binding.
|
| |
J Biol Chem,
279,
38519-38524.
|
|
|
|
|
|
|
S.J.Orcutt,
and
S.Krishnaswamy
(2004).
Binding of substrate in two conformations to human prothrombinase drives consecutive cleavage at two sites in prothrombin.
|
| |
J Biol Chem,
279,
54927-54936.
|
|
|
|
|
|
|
S.Liu,
C.Zhang,
H.Zhou,
and
Y.Zhou
(2004).
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.
|
| |
Proteins,
56,
93.
|
|
|
|
|
|
|
S.M.Lima,
D.S.Peabody,
J.L.Silva,
and
A.C.de Oliveira
(2004).
Mutations in the hydrophobic core and in the protein-RNA interface affect the packing and stability of icosahedral viruses.
|
| |
Eur J Biochem,
271,
135-145.
|
|
|
|
|
|
|
S.Yegneswaran,
R.M.Mesters,
J.A.Fernández,
and
J.H.Griffin
(2004).
Prothrombin residues 473-487 contribute to factor Va binding in the prothrombinase complex.
|
| |
J Biol Chem,
279,
49019-49025.
|
|
|
|
|
|
|
W.J.Carter,
T.Myles,
C.S.Gibbs,
L.L.Leung,
and
J.A.Huntington
(2004).
Crystal structure of anticoagulant thrombin variant E217K provides insights into thrombin allostery.
|
| |
J Biol Chem,
279,
26387-26394.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Imokawa,
A.Simon,
and
J.P.Brockes
(2004).
A critical role for thrombin in vertebrate lens regeneration.
|
| |
Philos Trans R Soc Lond B Biol Sci,
359,
765-776.
|
|
|
|
|
|
|
A.R.Rezaie,
and
L.Yang
(2003).
Thrombomodulin allosterically modulates the activity of the anticoagulant thrombin.
|
| |
Proc Natl Acad Sci U S A,
100,
12051-12056.
|
|
|
|
|
|
|
J.A.Huntington,
and
T.P.Baglin
(2003).
Targeting thrombin--rational drug design from natural mechanisms.
|
| |
Trends Pharmacol Sci,
24,
589-595.
|
|
|
|
|
|
|
J.B.Lefkowitz,
A.Weller,
R.Nuss,
P.J.Santiago-Borrero,
D.L.Brown,
and
I.R.Ortiz
(2003).
A common mutation, Arg457-->Gln, links prothrombin deficiencies in the Puerto Rican population.
|
| |
J Thromb Haemost,
1,
2381-2388.
|
|
|
|
|
|
|
J.P.Ludeman,
R.N.Pike,
K.M.Bromfield,
P.J.Duggan,
J.Cianci,
B.Le Bonniec,
J.C.Whisstock,
and
S.P.Bottomley
(2003).
Determination of the P1', P2' and P3' subsite-specificity of factor Xa.
|
| |
Int J Biochem Cell Biol,
35,
221-225.
|
|
|
|
|
|
|
J.Rohlena,
J.A.Kolkman,
R.C.Boertjes,
K.Mertens,
and
P.J.Lenting
(2003).
Residues Phe342-Asn346 of activated coagulation factor IX contribute to the interaction with low density lipoprotein receptor-related protein.
|
| |
J Biol Chem,
278,
9394-9401.
|
|
|
|
|
|
|
K.L.Kaplan
(2003).
Direct thrombin inhibitors.
|
| |
Expert Opin Pharmacother,
4,
653-666.
|
|
|
|
|
|
|
L.Chen,
L.Yang,
and
A.R.Rezaie
(2003).
Proexosite-1 on prothrombin is a factor Va-dependent recognition site for the prothrombinase complex.
|
| |
J Biol Chem,
278,
27564-27569.
|
|
|
|
|
|
|
L.Yang,
and
A.R.Rezaie
(2003).
The fourth epidermal growth factor-like domain of thrombomodulin interacts with the basic exosite of protein C.
|
| |
J Biol Chem,
278,
10484-10490.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
S.T.Olson,
and
A.R.Rezaie
(2003).
Contribution of basic residues of the autolysis loop to the substrate and inhibitor specificity of factor IXa.
|
| |
J Biol Chem,
278,
25032-25038.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
T.D.Walston,
S.T.Cooper,
and
A.R.Rezaie
(2003).
Thrombomodulin enhances the reactivity of thrombin with protein C inhibitor by providing both a binding site for the serpin and allosterically modulating the activity of thrombin.
|
| |
J Biol Chem,
278,
37465-37470.
|
|
|
|
|
|
|
N.A.Raffler,
J.Schneider-Mergener,
and
M.Famulok
(2003).
A novel class of small functional peptides that bind and inhibit human alpha-thrombin isolated by mRNA display.
|
| |
Chem Biol,
10,
69-79.
|
|
|
|
|
|
|
N.Foeger,
E.M.Schmid,
and
T.Skern
(2003).
Human rhinovirus 2 2Apro recognition of eukaryotic initiation factor 4GI. Involvement of an exosite.
|
| |
J Biol Chem,
278,
33200-33207.
|
|
|
|
|
|
|
S.Bajusz
(2003).
Josef Rudinger Memorial Lecture 2002. Peptide related drug research.
|
| |
J Pept Sci,
9,
321-332.
|
|
|
|
|
|
|
S.Deam,
J.Uprichard,
J.T.Eaton,
S.J.Perkins,
and
G.Dolan
(2003).
Factor X Leicester: Ile411Phe associated with a low antigen level and a disproportionately low functional activity of factor X.
|
| |
J Thromb Haemost,
1,
603-605.
|
|
|
|
|
|
|
S.Yegneswaran,
R.M.Mesters,
and
J.H.Griffin
(2003).
Identification of distinct sequences in human blood coagulation factor Xa and prothrombin essential for substrate and cofactor recognition in the prothrombinase complex.
|
| |
J Biol Chem,
278,
33312-33318.
|
|
|
|
|
|
|
T.H.Yun,
F.A.Baglia,
T.Myles,
D.Navaneetham,
J.A.López,
P.N.Walsh,
and
L.L.Leung
(2003).
Thrombin activation of factor XI on activated platelets requires the interaction of factor XI and platelet glycoprotein Ib alpha with thrombin anion-binding exosites I and II, respectively.
|
| |
J Biol Chem,
278,
48112-48119.
|
|
|
|
|
|
|
Y.Imokawa,
and
J.P.Brockes
(2003).
Selective activation of thrombin is a critical determinant for vertebrate lens regeneration.
|
| |
Curr Biol,
13,
877-881.
|
|
|
|
|
|
|
C.Manithody,
L.Yang,
and
A.R.Rezaie
(2002).
Role of basic residues of the autolysis loop in the catalytic function of factor Xa.
|
| |
Biochemistry,
41,
6780-6788.
|
|
|
|
|
|
|
H.Brandstetter,
J.S.Kim,
M.Groll,
P.Göttig,
and
R.Huber
(2002).
Structural basis for the processive protein degradation by tricorn protease.
|
| |
Biol Chem,
383,
1157-1165.
|
|
|
|
|
|
|
K.Soejima,
M.Yuguchi,
J.Mizuguchi,
K.Tomokiyo,
T.Nakashima,
T.Nakagaki,
and
S.Iwanaga
(2002).
The 99 and 170 loop-modified factor VIIa mutants show enhanced catalytic activity without tissue factor.
|
| |
J Biol Chem,
277,
49027-49035.
|
|
|
|
|
|
|
L.Jiang,
Y.Gao,
F.Mao,
Z.Liu,
and
L.Lai
(2002).
Potential of mean force for protein-protein interaction studies.
|
| |
Proteins,
46,
190-196.
|
|
|
|
|
|
|
L.Yang,
C.Manithody,
and
A.R.Rezaie
(2002).
Localization of the heparin binding exosite of factor IXa.
|
| |
J Biol Chem,
277,
50756-50760.
|
|
|
|
|
|
|
M.Wilkens,
and
S.Krishnaswamy
(2002).
The contribution of factor Xa to exosite-dependent substrate recognition by prothrombinase.
|
| |
J Biol Chem,
277,
9366-9374.
|
|
|
|
|
|
|
P.Goettig,
M.Groll,
J.S.Kim,
R.Huber,
and
H.Brandstetter
(2002).
Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism.
|
| |
EMBO J,
21,
5343-5352.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.M.Camire
(2002).
Prothrombinase assembly and S1 site occupation restore the catalytic activity of FXa impaired by mutation at the sodium-binding site.
|
| |
J Biol Chem,
277,
37863-37870.
|
|
|
|
|
|
|
S.J.Orcutt,
C.Pietropaolo,
and
S.Krishnaswamy
(2002).
Extended interactions with prothrombinase enforce affinity and specificity for its macromolecular substrate.
|
| |
J Biol Chem,
277,
46191-46196.
|
|
|
|
|
|
|
S.K.Buddai,
L.Toulokhonova,
P.W.Bergum,
G.P.Vlasuk,
and
S.Krishnaswamy
(2002).
Nematode anticoagulant protein c2 reveals a site on factor Xa that is important for macromolecular substrate binding to human prothrombinase.
|
| |
J Biol Chem,
277,
26689-26698.
|
|
|
|
|
|
|
F.C.Peterson,
N.C.Gordon,
and
P.G.Gettins
(2001).
High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Application to the study of trypsin-inhibitor complexes and trypsinogen activation by NMR spectroscopy.
|
| |
Biochemistry,
40,
6275-6283.
|
|
|
|
|
|
|
F.Lian,
L.He,
N.S.Colwell,
P.Lollar,
and
D.M.Tollefsen
(2001).
Anticoagulant activities of a monoclonal antibody that binds to exosite II of thrombin.
|
| |
Biochemistry,
40,
8508-8513.
|
|
|
|
|
|
|
J.Chao,
R.Q.Miao,
V.Chen,
L.M.Chen,
and
L.Chao
(2001).
Novel roles of kallistatin, a specific tissue kallikrein inhibitor, in vascular remodeling.
|
| |
Biol Chem,
382,
15-21.
|
|
|
|
|
|
|
N.Majeux,
M.Scarsi,
and
A.Caflisch
(2001).
Efficient electrostatic solvation model for protein-fragment docking.
|
| |
Proteins,
42,
256-268.
|
|
|
|
|
|
|
A.R.Rezaie
(2000).
Identification of basic residues in the heparin-binding exosite of factor Xa critical for heparin and factor Va binding.
|
| |
J Biol Chem,
275,
3320-3327.
|
|
|
|
|
|
|
A.R.Rezaie,
and
S.T.Olson
(2000).
Calcium enhances heparin catalysis of the antithrombin-factor Xa reaction by promoting the assembly of an intermediate heparin-antithrombin-factor Xa bridging complex. Demonstration by rapid kinetics studies.
|
| |
Biochemistry,
39,
12083-12090.
|
|
|
|
|
|
|
A.R.Rezaie,
and
X.He
(2000).
Sodium binding site of factor Xa: role of sodium in the prothrombinase complex.
|
| |
Biochemistry,
39,
1817-1825.
|
|
|
|
|
|
|
J.J.Slon-Usakiewicz,
J.Sivaraman,
Y.Li,
M.Cygler,
and
Y.Konishi
(2000).
Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures.
|
| |
Biochemistry,
39,
2384-2391.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.L.Richardson,
B.Kröger,
W.Hoeffken,
J.E.Sadler,
P.Pereira,
R.Huber,
W.Bode,
and
P.Fuentes-Prior
(2000).
Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor.
|
| |
EMBO J,
19,
5650-5660.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Y.Chirgadze,
D.J.Sall,
S.L.Briggs,
D.K.Clawson,
M.Zhang,
G.F.Smith,
and
R.W.Schevitz
(2000).
The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors.
|
| |
Protein Sci,
9,
29-36.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Recacha,
M.J.Costanzo,
B.E.Maryanoff,
M.Carson,
L.DeLucas,
and
D.Chattopadhyay
(2000).
Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1395-1400.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Braud,
C.Bon,
and
A.Wisner
(2000).
Snake venom proteins acting on hemostasis.
|
| |
Biochimie,
82,
851-859.
|
|
|
|
|
|
|
S.Sperl,
U.Jacob,
N.Arroyo de Prada,
J.Stürzebecher,
O.G.Wilhelm,
W.Bode,
V.Magdolen,
R.Huber,
and
L.Moroder
(2000).
(4-aminomethyl)phenylguanidine derivatives as nonpeptidic highly selective inhibitors of human urokinase.
|
| |
Proc Natl Acad Sci U S A,
97,
5113-5118.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.L.Nienaber,
D.Davidson,
R.Edalji,
V.L.Giranda,
V.Klinghofer,
J.Henkin,
P.Magdalinos,
R.Mantei,
S.Merrick,
J.M.Severin,
R.A.Smith,
K.Stewart,
K.Walter,
J.Wang,
M.Wendt,
M.Weitzberg,
X.Zhao,
and
T.Rockway
(2000).
Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite.
|
| |
Structure,
8,
553-563.
|
|
|
|
|
|
|
V.Nienaber,
J.Wang,
D.Davidson,
and
J.Henkin
(2000).
Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite.
|
| |
J Biol Chem,
275,
7239-7248.
|
|
|
|
|
|
|
A.Lombardi,
G.De Simone,
F.Nastri,
S.Galdiero,
R.Della Morte,
N.Staiano,
C.Pedone,
M.Bolognesi,
and
V.Pavone
(1999).
The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.
|
| |
Protein Sci,
8,
91-95.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Lombardi,
G.De Simone,
S.Galdiero,
N.Staiano,
F.Nastri,
and
V.Pavone
(1999).
From natural to synthetic multisite thrombin inhibitors.
|
| |
Biopolymers,
51,
19-39.
|
|
|
|
|
|
|
A.R.Rezaie
(1999).
Role of exosites 1 and 2 in thrombin reaction with plasminogen activator inhibitor-1 in the absence and presence of cofactors.
|
| |
Biochemistry,
38,
14592-14599.
|
|
|
|
|
|
|
E.M.Tanaka,
D.N.Drechsel,
and
J.P.Brockes
(1999).
Thrombin regulates S-phase re-entry by cultured newt myotubes.
|
| |
Curr Biol,
9,
792-799.
|
|
|
|
|
|
|
G.P.Samokhin,
M.R.Jirousek,
D.K.Ways,
and
R.A.Henriksen
(1999).
Effects of protein kinase C inhibitors on thromboxane production by thrombin-stimulated platelets.
|
| |
Eur J Pharmacol,
386,
297-303.
|
|
|
|
|
|
|
H.Jhoti,
A.Cleasby,
S.Reid,
P.J.Thomas,
M.Weir,
and
A.Wonacott
(1999).
Crystal structures of thrombin complexed to a novel series of synthetic inhibitors containing a 5,5-trans-lactone template.
|
| |
Biochemistry,
38,
7969-7977.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Jing,
K.J.Macon,
D.Moore,
L.J.DeLucas,
J.E.Volanakis,
and
S.V.Narayana
(1999).
Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.
|
| |
EMBO J,
18,
804-814.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.E.Knobe,
A.Berntsdotter,
L.Shen,
J.Morser,
B.Dahlbäck,
and
B.O.Villoutreix
(1999).
Probing the activation of protein C by the thrombin-thrombomodulin complex using structural analysis, site-directed mutagenesis, and computer modeling.
|
| |
Proteins,
35,
218-234.
|
|
|
|
|
|
|
K.L.Hayes,
and
P.B.Tracy
(1999).
The platelet high affinity binding site for thrombin mimics hirudin, modulates thrombin-induced platelet activation, and is distinct from the glycoprotein Ib-IX-V complex.
|
| |
J Biol Chem,
274,
972-980.
|
|
|
|
|
|
|
M.C.Maurer,
J.Y.Trosset,
C.C.Lester,
E.E.DiBella,
and
H.A.Scheraga
(1999).
New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program.
|
| |
Proteins,
34,
29-48.
|
|
|
|
|
|
|
M.Scarsi,
N.Majeux,
and
A.Caflisch
(1999).
Hydrophobicity at the surface of proteins.
|
| |
Proteins,
37,
565-575.
|
|
|
|
|
|
|
N.Majeux,
M.Scarsi,
J.Apostolakis,
C.Ehrhardt,
and
A.Caflisch
(1999).
Exhaustive docking of molecular fragments with electrostatic solvation.
|
| |
Proteins,
37,
88.
|
|
|
|
|
|
|
T.Kishi,
M.Kato,
T.Shimizu,
K.Kato,
K.Matsumoto,
S.Yoshida,
S.Shiosaka,
and
T.Hakoshima
(1999).
Crystal structure of neuropsin, a hippocampal protease involved in kindling epileptogenesis.
|
| |
J Biol Chem,
274,
4220-4224.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
X.He,
and
A.R.Rezaie
(1999).
Identification and characterization of the sodium-binding site of activated protein C.
|
| |
J Biol Chem,
274,
4970-4976.
|
|
|
|
|
|
|
Y.Zhou,
and
M.E.Johnson
(1999).
Comparative molecular modeling analysis of-5-amidinoindole and benzamidine binding to thrombin and trypsin: specific H-bond formation contributes to high 5-amidinoindole potency and selectivity for thrombin and factor Xa.
|
| |
J Mol Recognit,
12,
235-241.
|
|
|
|
|
|
|
A.Betz,
and
S.Krishnaswamy
(1998).
Regions remote from the site of cleavage determine macromolecular substrate recognition by the prothrombinase complex.
|
| |
J Biol Chem,
273,
10709-10718.
|
|
|
|
|
|
|
A.R.Rezaie
(1998).
Calcium enhances heparin catalysis of the antithrombin-factor Xa reaction by a template mechanism. Evidence that calcium alleviates Gla domain antagonism of heparin binding to factor Xa.
|
| |
J Biol Chem,
273,
16824-16827.
|
|
|
|
|
|
|
A.R.Rezaie
(1998).
Elucidation of the structural basis for the slow reactivity of thrombin with plasminogen activator inhibitor-1.
|
| |
Biochemistry,
37,
13138-13142.
|
|
|
|
|
|
|
A.R.Rezaie
(1998).
Reactivities of the S2 and S3 subsite residues of thrombin with the native and heparin-induced conformers of antithrombin.
|
| |
Protein Sci,
7,
349-357.
|
|
|
|
|
|
|
C.L.Strickland,
J.M.Fevig,
R.A.Galemmo,
B.L.Wells,
C.A.Kettner,
and
P.C.Weber
(1998).
Biochemical and crystallographic characterization of homologous non-peptidic thrombin inhibitors having alternate binding modes.
|
| |
Acta Crystallogr D Biol Crystallogr,
54,
1207-1215.
|
|
|
|
|
|
|
E.Skordalakes,
S.Elgendy,
C.A.Goodwin,
D.Green,
M.F.Scully,
V.V.Kakkar,
J.M.Freyssinet,
G.Dodson,
and
J.J.Deadman
(1998).
Bifunctional peptide boronate inhibitors of thrombin: crystallographic analysis of inhibition enhanced by linkage to an exosite 1 binding peptide.
|
| |
Biochemistry,
37,
14420-14427.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.De Simone,
A.Lombardi,
S.Galdiero,
F.Nastri,
R.Della Morte,
N.Staiano,
C.Pedone,
M.Bolognesi,
and
V.Pavone
(1998).
Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
|
| |
Protein Sci,
7,
243-253.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Kubinyi
(1998).
[Molecular similarity. 2. The structural basis of drug design]
|
| |
Pharm Unserer Zeit,
27,
158-172.
|
|
|
|
|
|
|
I.Massova,
P.Martin,
A.Bulychev,
R.Kocz,
M.Doyle,
B.F.Edwards,
and
S.Mobashery
(1998).
Templates for design of inhibitors for serine proteases: application of the program DOCK to the discovery of novel inhibitors for thrombin.
|
| |
Bioorg Med Chem Lett,
8,
2463-2466.
|
|
|
|
|
|
|
J.H.Han,
and
D.M.Tollefsen
(1998).
Ligand binding to thrombin exosite II induces dissociation of the thrombin-heparin cofactor II(L444R) complex.
|
| |
Biochemistry,
37,
3203-3209.
|
|
|
|
|
|
|
J.Y.Trosset,
and
H.A.Scheraga
(1998).
Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines.
|
| |
Proc Natl Acad Sci U S A,
95,
8011-8015.
|
|
|
|
|
|
|
K.P.Hopfner,
E.Kopetzki,
G.B.Kresse,
W.Bode,
R.Huber,
and
R.A.Engh
(1998).
New enzyme lineages by subdomain shuffling.
|
| |
Proc Natl Acad Sci U S A,
95,
9813-9818.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.A.Harker
(1998).
Therapeutic inhibition of thrombin activities, receptors, and production.
|
| |
Hematol Oncol Clin North Am,
12,
1211-1230.
|
|
|
|
|
|
|
M.M.Rooney,
J.L.Mullin,
and
S.T.Lord
(1998).
Substitution of tyrosine for phenylalanine in fibrinopeptide A results in preferential thrombin cleavage of fibrinopeptide B from fibrinogen.
|
| |
Biochemistry,
37,
13704-13709.
|
|
|
|
|
|
|
M.P.Weir,
S.S.Bethell,
A.Cleasby,
C.J.Campbell,
R.J.Dennis,
C.J.Dix,
H.Finch,
H.Jhoti,
C.J.Mooney,
S.Patel,
C.M.Tang,
M.Ward,
A.J.Wonacott,
and
C.W.Wharton
(1998).
Novel natural product 5,5-trans-lactone inhibitors of human alpha-thrombin: mechanism of action and structural studies.
|
| |
Biochemistry,
37,
6645-6657.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
N.S.Colwell,
M.A.Blinder,
M.Tsiang,
C.S.Gibbs,
P.E.Bock,
and
D.M.Tollefsen
(1998).
Allosteric effects of a monoclonal antibody against thrombin exosite II.
|
| |
Biochemistry,
37,
15057-15065.
|
|
|
|
|
|
|
S.D.Lewis,
B.J.Lucas,
S.F.Brady,
J.T.Sisko,
K.J.Cutrona,
P.E.Sanderson,
R.M.Freidinger,
S.S.Mao,
S.J.Gardell,
and
J.A.Shafer
(1998).
Characterization of the two-step pathway for inhibition of thrombin by alpha-ketoamide transition state analogs.
|
| |
J Biol Chem,
273,
4843-4854.
|
|
|
|
|
|
|
S.R.Presnell,
G.S.Patil,
C.Mura,
K.M.Jude,
J.M.Conley,
J.A.Bertrand,
C.M.Kam,
J.C.Powers,
and
L.D.Williams
(1998).
Oxyanion-mediated inhibition of serine proteases.
|
| |
Biochemistry,
37,
17068-17081.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Myles,
F.C.Church,
H.C.Whinna,
D.Monard,
and
S.R.Stone
(1998).
Role of thrombin anion-binding exosite-I in the formation of thrombin-serpin complexes.
|
| |
J Biol Chem,
273,
31203-31208.
|
|
|
|
|
|
|
Y.A.Muller,
R.F.Kelley,
and
A.M.de Vos
(1998).
Hinge bending within the cytokine receptor superfamily revealed by the 2.4 A crystal structure of the extracellular domain of rabbit tissue factor.
|
| |
Protein Sci,
7,
1106-1115.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.R.Rezaie,
and
S.T.Olson
(1997).
Contribution of lysine 60f to S1' specificity of thrombin.
|
| |
Biochemistry,
36,
1026-1033.
|
|
|
|
|
|
|
A.V.Ciaccia,
A.J.Willemze,
and
F.C.Church
(1997).
Heparin promotes proteolytic inactivation by thrombin of a reactive site mutant (L444R) of recombinant heparin cofactor II.
|
| |
J Biol Chem,
272,
888-893.
|
|
|
|
|
|
|
A.van de Locht,
W.Bode,
R.Huber,
B.F.Le Bonniec,
S.R.Stone,
C.T.Esmon,
and
M.T.Stubbs
(1997).
The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.
|
| |
EMBO J,
16,
2977-2984.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.E.Timm
(1997).
The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme).
|
| |
Protein Sci,
6,
1418-1425.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.J.Enyedy,
and
I.M.Kovach
(1997).
Modulation of human alpha-thrombin activity with phosphonate ester inhibitors.
|
| |
Bioorg Med Chem,
5,
1531-1541.
|
|
|
|
|
|
|
G.M.Vath,
C.A.Earhart,
J.V.Rago,
M.H.Kim,
G.A.Bohach,
P.M.Schlievert,
and
D.H.Ohlendorf
(1997).
The structure of the superantigen exfoliative toxin A suggests a novel regulation as a serine protease.
|
| |
Biochemistry,
36,
1559-1566.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.A.Malikayil,
J.P.Burkhart,
H.A.Schreuder,
R.J.Broersma,
C.Tardif,
L.W.Kutcher,
S.Mehdi,
G.L.Schatzman,
B.Neises,
and
N.P.Peet
(1997).
Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety.
|
| |
Biochemistry,
36,
1034-1040.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.J.Perona,
and
C.S.Craik
(1997).
Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold.
|
| |
J Biol Chem,
272,
29987-29990.
|
|
|
|
|
|
|
J.J.Slon-Usakiewicz,
E.Purisima,
Y.Tsuda,
T.Sulea,
A.Pedyczak,
J.Féthière,
M.Cygler,
and
Y.Konishi
(1997).
Nonpolar interactions of thrombin S' subsites with its bivalent inhibitor: methyl scan of the inhibitor linker.
|
| |
Biochemistry,
36,
13494-13502.
|
|
|
|
|
|
|
K.P.Hopfner,
H.Brandstetter,
A.Karcher,
E.Kopetzki,
R.Huber,
R.A.Engh,
and
W.Bode
(1997).
Converting blood coagulation factor IXa into factor Xa: dramatic increase in amidolytic activity identifies important active site determinants.
|
| |
EMBO J,
16,
6626-6635.
|
|
|
|
|
|
|
M.G.Malkowski,
P.D.Martin,
J.C.Guzik,
and
B.F.Edwards
(1997).
The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding.
|
| |
Protein Sci,
6,
1438-1448.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Renatus,
M.T.Stubbs,
R.Huber,
P.Bringmann,
P.Donner,
W.D.Schleuning,
and
W.Bode
(1997).
Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
|
| |
Biochemistry,
36,
13483-13493.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Renatus,
W.Bode,
R.Huber,
J.Stürzebecher,
D.Prasa,
S.Fischer,
U.Kohnert,
and
M.T.Stubbs
(1997).
Structural mapping of the active site specificity determinants of human tissue-type plasminogen activator. Implications for the design of low molecular weight substrates and inhibitors.
|
| |
J Biol Chem,
272,
21713-21719.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Fuentes-Prior,
C.Noeske-Jungblut,
P.Donner,
W.D.Schleuning,
R.Huber,
and
W.Bode
(1997).
Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
|
| |
Proc Natl Acad Sci U S A,
94,
11845-11850.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Morenweiser,
E.A.Auerswald,
A.van de Locht,
H.Fritz,
J.Stürzebecher,
and
M.T.Stubbs
(1997).
Structure-based design of a potent chimeric thrombin inhibitor.
|
| |
J Biol Chem,
272,
19938-19942.
|
|
|
|
|
|
|
U.Obst,
D.W.Banner,
L.Weber,
and
F.Diederich
(1997).
Molecular recognition at the thrombin active site: structure-based design and synthesis of potent and selective thrombin inhibitors and the X-ray crystal structures of two thrombin-inhibitor complexes.
|
| |
Chem Biol,
4,
287-295.
|
|
|
|
|
|
|
X.He,
J.Ye,
C.T.Esmon,
and
A.R.Rezaie
(1997).
Influence of Arginines 93, 97, and 101 of thrombin to its functional specificity.
|
| |
Biochemistry,
36,
8969-8976.
|
|
|
|
|
|
|
A.Caflisch
(1996).
Computational combinatorial ligand design: application to human alpha-thrombin.
|
| |
J Comput Aided Mol Des,
10,
372-396.
|
|
|
|
|
|
|
A.R.Rezaie
(1996).
Role of residue 99 at the S2 subsite of factor Xa and activated protein C in enzyme specificity.
|
| |
J Biol Chem,
271,
23807-23814.
|
|
|
|
|
|
|
A.R.Rezaie
(1996).
Tryptophan 60-D in the B-insertion loop of thrombin modulates the thrombin-antithrombin reaction.
|
| |
Biochemistry,
35,
1918-1924.
|
|
|
|
|
|
|
A.R.Rezaie,
and
C.T.Esmon
(1996).
Molecular basis of residue 192 participation in determination of coagulation protease specificity.
|
| |
Eur J Biochem,
242,
477-484.
|
|
|
|
|
|
|
A.van de Locht,
M.T.Stubbs,
M.Bauer,
and
W.Bode
(1996).
Crystallographic evidence that the F2 kringle catalytic domain linker of prothrombin does not cover the fibrinogen recognition exosite.
|
| |
J Biol Chem,
271,
3413-3416.
|
|
|
|
|
|
|
A.van de Locht,
M.T.Stubbs,
W.Bode,
T.Friedrich,
C.Bollschweiler,
W.Höffken,
and
R.Huber
(1996).
The ornithodorin-thrombin crystal structure, a key to the TAP enigma?
|
| |
EMBO J,
15,
6011-6017.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.O.Villoutreix,
H.Lilja,
K.Pettersson,
T.Lövgren,
and
O.Teleman
(1996).
Structural investigation of the alpha-1-antichymotrypsin: prostate-specific antigen complex by comparative model building.
|
| |
Protein Sci,
5,
836-851.
|
|
|
|
|
|
|
C.D.Dickinson,
C.R.Kelly,
and
W.Ruf
(1996).
Identification of surface residues mediating tissue factor binding and catalytic function of the serine protease factor VIIa.
|
| |
Proc Natl Acad Sci U S A,
93,
14379-14384.
|
|
|
|
|
|
|
E.E.DiBella,
and
H.A.Scheraga
(1996).
The role of the insertion loop around tryptophan 148 in tthe activity of thrombin.
|
| |
Biochemistry,
35,
4427-4433.
|
|
|
|
|
|
|
H.M.Tucker,
and
R.D.Gerard
(1996).
Sequence requirements in the reactive-center loop of plasminogen-activator inhibitor-1 for recognition of plasminogen activators.
|
| |
Eur J Biochem,
237,
180-187.
|
|
|
|
|
|
|
J.A.Bertrand,
J.Oleksyszyn,
C.M.Kam,
B.Boduszek,
S.Presnell,
R.R.Plaskon,
F.L.Suddath,
J.C.Powers,
and
L.D.Williams
(1996).
Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models.
|
| |
Biochemistry,
35,
3147-3155.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Anagli,
E.M.Vilei,
M.Molinari,
S.Calderara,
and
E.Carafoli
(1996).
Purification of active calpain by affinity chromatography on an immobilized peptide inhibitor.
|
| |
Eur J Biochem,
241,
948-954.
|
|
|
|
|
|
|
J.Féthière,
Y.Tsuda,
R.Coulombe,
Y.Konishi,
and
M.Cygler
(1996).
Crystal structure of two new bifunctional nonsubstrate type thrombin inhibitors complexed with human alpha-thrombin.
|
| |
Protein Sci,
5,
1174-1183.
|
|
|
|
|
|
|
M.Z.Djie,
B.F.Le Bonniec,
P.C.Hopkins,
K.Hipler,
and
S.R.Stone
(1996).
Role of the P2 residue in determining the specificity of serpins.
|
| |
Biochemistry,
35,
11461-11469.
|
|
|
|
|
|
|
P.D.Grootenhuis,
and
M.Karplus
(1996).
Functionality map analysis of the active site cleft of human thrombin.
|
| |
J Comput Aided Mol Des,
10,
1.
|
|
|
|
|
|
|
P.D.Martin,
M.G.Malkowski,
J.DiMaio,
Y.Konishi,
F.Ni,
and
B.F.Edwards
(1996).
Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues.
|
| |
Biochemistry,
35,
13030-13039.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.A.Engh,
H.Brandstetter,
G.Sucher,
A.Eichinger,
U.Baumann,
W.Bode,
R.Huber,
T.Poll,
R.Rudolph,
and
W.von der Saal
(1996).
Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design.
|
| |
Structure,
4,
1353-1362.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Krishnan,
A.Tulinsky,
G.P.Vlasuk,
D.Pearson,
P.Vallar,
P.Bergum,
T.K.Brunck,
and
W.C.Ripka
(1996).
Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic.
|
| |
Protein Sci,
5,
422-433.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.T.Lord,
E.Strickland,
and
E.Jayjock
(1996).
Strategy for recombinant multichain protein synthesis: fibrinogen B beta-chain variants as thrombin substrates.
|
| |
Biochemistry,
35,
2342-2348.
|
|
|
|
|
|
|
T.Mather,
V.Oganessyan,
P.Hof,
R.Huber,
S.Foundling,
C.Esmon,
and
W.Bode
(1996).
The 2.8 A crystal structure of Gla-domainless activated protein C.
|
| |
EMBO J,
15,
6822-6831.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Ganesh,
A.Y.Lee,
J.Clardy,
and
A.Tulinsky
(1996).
Comparison of the structures of the cyclotheonamide A complexes of human alpha-thrombin and bovine beta-trypsin.
|
| |
Protein Sci,
5,
825-835.
|
|
|
|
|
|
|
V.L.Nienaber,
L.J.Mersinger,
and
C.A.Kettner
(1996).
Structure-based understanding of ligand affinity using human thrombin as a model system.
|
| |
Biochemistry,
35,
9690-9699.
|
|
|
|
|
|
|
W.Markland,
A.C.Ley,
and
R.C.Ladner
(1996).
Iterative optimization of high-affinity protease inhibitors using phage display. 2. Plasma kallikrein and thrombin.
|
| |
Biochemistry,
35,
8058-8067.
|
|
|
|
|
|
|
Y.Cheng,
J.J.Slon-Usakiewicz,
J.Wang,
E.O.Purisima,
and
Y.Konishi
(1996).
Nonpolar interactions of thrombin and its inhibitors at the fibrinogen recognition exosite: thermodynamic analysis.
|
| |
Biochemistry,
35,
13021-13029.
|
|
|
|
|
|
|
A.R.Rezaie,
S.T.Cooper,
F.C.Church,
and
C.T.Esmon
(1995).
Protein C inhibitor is a potent inhibitor of the thrombin-thrombomodulin complex.
|
| |
J Biol Chem,
270,
25336-25339.
|
|
|
|
|
|
|
A.van de Locht,
D.Lamba,
M.Bauer,
R.Huber,
T.Friedrich,
B.Kröger,
W.Höffken,
and
W.Bode
(1995).
Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
|
| |
EMBO J,
14,
5149-5157.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.E.Maryanoff,
H.C.Zhang,
M.N.Greco,
K.A.Glover,
J.A.Kauffman,
and
P.Andrade-Gordon
(1995).
Cyclotheonamide derivatives: synthesis and thrombin inhibition. Exploration of specific structure-function issues.
|
| |
Bioorg Med Chem,
3,
1025-1038.
|
|
|
|
|
|
|
D.R.St Laurent,
N.Balasubramanian,
W.T.Han,
A.Trehan,
M.E.Federici,
N.A.Meanwell,
J.J.Wright,
and
S.M.Seiler
(1995).
Active site-directed thrombin inhibitors--II. Studies related to arginine/guanidine bioisosteres.
|
| |
Bioorg Med Chem,
3,
1145-1156.
|
|
|
|
|
|
|
E.Casale,
C.Collyer,
P.Ascenzi,
G.Balliano,
P.Milla,
F.Viola,
M.Fasano,
E.Menegatti,
and
M.Bolognesi
(1995).
Inhibition of bovine beta-trypsin, human alpha-thrombin and porcine pancreatic beta-kallikrein-B by 4',6-diamidino-2-phenylindole, 6-amidinoindole and benzamidine: a comparative thermodynamic and X-ray structural study.
|
| |
Biophys Chem,
54,
75-81.
|
|
|
|
|
|
|
E.Di Cera,
E.R.Guinto,
A.Vindigni,
Q.D.Dang,
Y.M.Ayala,
M.Wuyi,
and
A.Tulinsky
(1995).
The Na+ binding site of thrombin.
|
| |
J Biol Chem,
270,
22089-22092.
|
|
|
|
|
|
|
E.E.DiBella,
M.C.Maurer,
and
H.A.Scheraga
(1995).
Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin.
|
| |
J Biol Chem,
270,
163-169.
|
|
|
|
|
|
|
G.De Nanteuil,
P.Gloanec,
C.Lila,
B.Portevin,
A.Boudon,
A.Rupin,
and
T.J.Verbeuren
(1995).
New tripeptidic thrombin inhibitors. Influence of P2 and P3 residues on activity and selectivity.
|
| |
Bioorg Med Chem,
3,
1019-1024.
|
|
|
|
|
|
|
G.Spraggon,
C.Phillips,
U.K.Nowak,
C.P.Ponting,
D.Saunders,
C.M.Dobson,
D.I.Stuart,
and
E.Y.Jones
(1995).
The crystal structure of the catalytic domain of human urokinase-type plasminogen activator.
|
| |
Structure,
3,
681-691.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Brandstetter,
M.Bauer,
R.Huber,
P.Lollar,
and
W.Bode
(1995).
X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.
|
| |
Proc Natl Acad Sci U S A,
92,
9796-9800.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.R.Lijnen,
S.Wnendt,
J.Schneider,
E.Janocha,
B.Van Hoef,
D.Collen,
and
G.J.Steffens
(1995).
Functional properties of a recombinant chimeric protein with combined thrombin inhibitory and plasminogen-activating potential.
|
| |
Eur J Biochem,
234,
350-357.
|
|
|
|
|
|
|
J.J.Perona,
and
C.S.Craik
(1995).
Structural basis of substrate specificity in the serine proteases.
|
| |
Protein Sci,
4,
337-360.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Håkansson,
A.Tulinsky,
M.M.Abelman,
T.A.Miller,
G.P.Vlasuk,
P.W.Bergum,
M.S.Lim-Wilby,
and
T.K.Brunck
(1995).
Crystallographic structure of a peptidyl keto acid inhibitor and human alpha-thrombin.
|
| |
Bioorg Med Chem,
3,
1009-1017.
|
|
|
|
|
|
|
M.C.Bouton,
J.L.Plantier,
M.Dembak,
M.C.Guillin,
M.J.Rabiet,
and
M.Jandrot-Perrus
(1995).
Role of the thrombin insertion loop 144-155. Study of thrombin mutations W148G, K154E and a thrombin-based synthetic peptide.
|
| |
Eur J Biochem,
229,
526-532.
|
|
|
|
|
|
|
M.T.Stubbs,
and
W.Bode
(1995).
The clot thickens: clues provided by thrombin structure.
|
| |
Trends Biochem Sci,
20,
23-28.
|
|
|
|
|
|
|
M.Tsiang,
A.K.Jain,
K.E.Dunn,
M.E.Rojas,
L.L.Leung,
and
C.S.Gibbs
(1995).
Functional mapping of the surface residues of human thrombin.
|
| |
J Biol Chem,
270,
16854-16863.
|
|
|
|
|
|
|
P.Ascenzi,
G.Amiconi,
W.Bode,
M.Bolognesi,
M.Coletta,
and
E.Menegatti
(1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
|
| |
Mol Aspects Med,
16,
215-313.
|
|
|
|
|
|
|
P.C.Hopkins,
D.C.Crowther,
R.W.Carrell,
and
S.R.Stone
(1995).
Development of a novel recombinant serpin with potential antithrombotic properties.
|
| |
J Biol Chem,
270,
11866-11871.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
P.M.Sherman,
D.A.Lawrence,
I.M.Verhamme,
D.Paielli,
J.D.Shore,
and
D.Ginsburg
(1995).
Identification of tissue-type plasminogen activator-specific plasminogen activator inhibitor-1 mutants. Evidence that second sites of interaction contribute to target specificity.
|
| |
J Biol Chem,
270,
9301-9306.
|
|
|
|
|
|
|
S.Mosimann,
R.Meleshko,
and
M.N.James
(1995).
A critical assessment of comparative molecular modeling of tertiary structures of proteins.
|
| |
Proteins,
23,
301-317.
|
|
|
|
|
|
|
S.T.Olson,
A.W.Stephens,
C.H.Hirs,
P.E.Bock,
and
I.Björk
(1995).
Kinetic characterization of the proteinase binding defect in a reactive site variant of the serpin, antithrombin. Role of the P1' residue in transition-state stabilization of antithrombin-proteinase complex formation.
|
| |
J Biol Chem,
270,
9717-9724.
|
|
|
|
|
|
|
W.F.Lau,
L.Tabernero,
J.S.Sack,
and
E.J.Iwanowicz
(1995).
Molecular modeling studies of novel retro-binding tripeptide active-site inhibitors of thrombin.
|
| |
Bioorg Med Chem,
3,
1039-1048.
|
|
|
|
|
|
|
W.T.Han,
A.K.Trehan,
J.J.Wright,
M.E.Federici,
S.M.Seiler,
and
N.A.Meanwell
(1995).
Azetidin-2-one derivatives as inhibitors of thrombin.
|
| |
Bioorg Med Chem,
3,
1123-1143.
|
|
|
|
|
|
|
C.L.Fisher,
J.S.Greengard,
and
J.H.Griffin
(1994).
Models of the serine protease domain of the human antithrombotic plasma factor activated protein C and its zymogen.
|
| |
Protein Sci,
3,
588-599.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.Fitzgerald
(1994).
Specific thrombin inhibitors in vivo.
|
| |
Ann N Y Acad Sci,
714,
41-52.
|
|
|
|
|
|
|
H.A.Schreuder,
B.de Boer,
R.Dijkema,
J.Mulders,
H.J.Theunissen,
P.D.Grootenhuis,
and
W.G.Hol
(1994).
The intact and cleaved human antithrombin III complex as a model for serpin-proteinase interactions.
|
| |
Nat Struct Biol,
1,
48-54.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.S.Greengard,
C.L.Fisher,
B.Villoutreix,
and
J.H.Griffin
(1994).
Structural basis for type I and type II deficiencies of antithrombotic plasma protein C: patterns revealed by three-dimensional molecular modelling of mutations of the protease domain.
|
| |
Proteins,
18,
367-380.
|
|
|
|
|
|
|
J.Vijayalakshmi,
K.P.Padmanabhan,
K.G.Mann,
and
A.Tulinsky
(1994).
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
|
| |
Protein Sci,
3,
2254-2271.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.E.McGrath,
T.Erpel,
C.Bystroff,
and
R.J.Fletterick
(1994).
Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex.
|
| |
EMBO J,
13,
1502-1507.
|
|
|
|
|
|
|
M.T.Stubbs,
and
W.Bode
(1994).
Coagulation factors and their inhibitors.
|
| |
Curr Opin Struct Biol,
4,
823-832.
|
|
|
|
|
|
|
P.D.Edwards,
and
P.R.Bernstein
(1994).
Synthetic inhibitors of elastase.
|
| |
Med Res Rev,
14,
127-194.
|
|
|
|
|
|
|
U.Egner,
G.A.Hoyer,
and
W.D.Schleuning
(1994).
Rational design of hirulog-type inhibitors of thrombin.
|
| |
J Comput Aided Mol Des,
8,
479-490.
|
|
|
|
|
|
|
A.Kumar,
and
D.S.Fair
(1993).
Specific molecular interaction sites on factor VII involved in factor X activation.
|
| |
Eur J Biochem,
217,
509-518.
|
|
|
|
|
|
|
A.Zdanov,
S.Wu,
J.DiMaio,
Y.Konishi,
Y.Li,
X.Wu,
B.F.Edwards,
P.D.Martin,
and
M.Cygler
(1993).
Crystal structure of the complex of human alpha-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6.
|
| |
Proteins,
17,
252-265.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.E.Maryanoff,
X.Qiu,
K.P.Padmanabhan,
A.Tulinsky,
H.R.Almond,
P.Andrade-Gordon,
M.N.Greco,
J.A.Kauffman,
K.C.Nicolaou,
and
A.Liu
(1993).
Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide A.
|
| |
Proc Natl Acad Sci U S A,
90,
8048-8052.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.Wilhelm,
and
W.Siess
(1993).
Activation of the cloned platelet thrombin receptor decreases the pertussis-toxin-dependent ADP-ribosylation of the membrane and soluble inhibitory guanine-nucleotide-binding-alpha proteins. Inhibition by the prostacyclin analog, iloprost.
|
| |
Eur J Biochem,
216,
81-88.
|
|
|
|
|
|
|
C.Tapparelli,
R.Metternich,
C.Ehrhardt,
and
N.S.Cook
(1993).
Synthetic low-molecular weight thrombin inhibitors: molecular design and pharmacological profile.
|
| |
Trends Pharmacol Sci,
14,
366-376.
|
|
|
|
|
|
|
G.Marchetti,
P.Patracchini,
D.Gemmati,
G.Castaman,
F.Rodeghiero,
A.Wacey,
D.N.Cooper,
E.G.Tuddenham,
and
F.Bernardi
(1993).
Symptomatic type II protein C deficiency caused by a missense mutation (Gly 381-->Ser) in the substrate-binding pocket.
|
| |
Br J Haematol,
84,
285-289.
|
|
|
|
|
|
|
H.C.Whinna,
and
F.C.Church
(1993).
Interaction of thrombin with antithrombin, heparin cofactor II, and protein C inhibitor.
|
| |
J Protein Chem,
12,
677-688.
|
|
|
|
|
|
|
J.P.Priestle,
J.Rahuel,
H.Rink,
M.Tones,
and
M.G.Grütter
(1993).
Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms.
|
| |
Protein Sci,
2,
1630-1642.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.C.Bouton,
M.Jandrot-Perrus,
A.Bezeaud,
and
M.C.Guillin
(1993).
Late-fibrin(ogen) fragment E modulates human alpha-thrombin specificity.
|
| |
Eur J Biochem,
215,
143-149.
|
|
|
|
|
|
|
R.A.Wiley,
and
D.H.Rich
(1993).
Peptidomimetics derived from natural products.
|
| |
Med Res Rev,
13,
327-384.
|
|
|
|
|
|
|
A.B.Kelly,
J.M.Maraganore,
P.Bourdon,
S.R.Hanson,
and
L.A.Harker
(1992).
Antithrombotic effects of synthetic peptides targeting various functional domains of thrombin.
|
| |
Proc Natl Acad Sci U S A,
89,
6040-6044.
|
|
|
|
|
|
|
A.Karshikov,
W.Bode,
A.Tulinsky,
and
S.R.Stone
(1992).
Electrostatic interactions in the association of proteins: an analysis of the thrombin-hirudin complex.
|
| |
Protein Sci,
1,
727-735.
|
|
|
|
|
|
|
D.K.Banfield,
and
R.T.MacGillivray
(1992).
Partial characterization of vertebrate prothrombin cDNAs: amplification and sequence analysis of the B chain of thrombin from nine different species.
|
| |
Proc Natl Acad Sci U S A,
89,
2779-2783.
|
|
|
|
|
|
|
D.T.Hung,
T.K.Vu,
V.I.Wheaton,
I.F.Charo,
N.A.Nelken,
N.Esmon,
C.T.Esmon,
and
S.R.Coughlin
(1992).
"Mirror image" antagonists of thrombin-induced platelet activation based on thrombin receptor structure.
|
| |
J Clin Invest,
89,
444-450.
|
|
|
|
|
|
|
E.Meyer
(1992).
Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.
|
| |
Protein Sci,
1,
1543-1562.
|
|
|
|
|
|
|
H.Nakanishi,
R.A.Chrusciel,
R.Shen,
S.Bertenshaw,
M.E.Johnson,
T.J.Rydel,
A.Tulinsky,
and
M.Kahn
(1992).
Peptide mimetics of the thrombin-bound structure of fibrinopeptide A.
|
| |
Proc Natl Acad Sci U S A,
89,
1705-1709.
|
|
|
|
|
|
|
M.D.Walkinshaw
(1992).
Protein targets for structure-based drug design.
|
| |
Med Res Rev,
12,
317-372.
|
|
|
|
|
|
|
M.T.Stubbs,
H.Oschkinat,
I.Mayr,
R.Huber,
H.Angliker,
S.R.Stone,
and
W.Bode
(1992).
The interaction of thrombin with fibrinogen. A structural basis for its specificity.
|
| |
Eur J Biochem,
206,
187-195.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.D.Lewis,
D.V.Brezniak,
J.W.Fenton,
and
J.A.Shafer
(1992).
Catalytically competent human and bovine zeta-thrombin and chimeras generated from unfolded polypeptide chains.
|
| |
Protein Sci,
1,
998.
|
|
|
|
|
|
|
S.Onesti,
D.J.Matthews,
P.Aducci,
G.Amiconi,
M.Bolognesi,
E.Menegatti,
and
P.Ascenzi
(1992).
Binding of the Kunitz-type trypsin inhibitor DE-3 from Erythrina caffra seeds to serine proteinases: a comparative study.
|
| |
J Mol Recognit,
5,
105-114.
|
|
|
|
|
|
|
S.P.Bajaj,
A.K.Sabharwal,
J.Gorka,
and
J.J.Birktoft
(1992).
Antibody-probed conformational transitions in the protease domain of human factor IX upon calcium binding and zymogen activation: putative high-affinity Ca(2+)-binding site in the protease domain.
|
| |
Proc Natl Acad Sci U S A,
89,
152-156.
|
|
|
|
|
|
|
S.R.Coughlin,
T.K.Vu,
D.T.Hung,
and
V.I.Wheaton
(1992).
Characterization of a functional thrombin receptor. Issues and opportunities.
|
| |
J Clin Invest,
89,
351-355.
|
|
|
|
|
|
|
W.Bode,
D.Turk,
and
A.Karshikov
(1992).
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
|
| |
Protein Sci,
1,
426-471.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
|
| |
Eur J Biochem,
204,
433-451.
|
|
|
|
|
|
|
B.F.Le Bonniec,
and
C.T.Esmon
(1991).
Glu-192----Gln substitution in thrombin mimics the catalytic switch induced by thrombomodulin.
|
| |
Proc Natl Acad Sci U S A,
88,
7371-7375.
|
|
|
|
|
|
|
J.Stenflo,
A.K.Ohlin,
E.Persson,
C.Valcarce,
J.Astermark,
T.Drakenberg,
M.Selander,
S.Linse,
and
I.Björk
(1991).
Epidermal growth factor-like domains in the vitamin K-dependent clotting factors. Some structure-function relationships.
|
| |
Ann N Y Acad Sci,
614,
11-29.
|
|
|
|
|
|
|
Q.Y.Wu,
J.P.Sheehan,
M.Tsiang,
S.R.Lentz,
J.J.Birktoft,
and
J.E.Sadler
(1991).
Single amino acid substitutions dissociate fibrinogen-clotting and thrombomodulin-binding activities of human thrombin.
|
| |
Proc Natl Acad Sci U S A,
88,
6775-6779.
|
|
|
|
|
|
|
R.Bar-Shavit,
V.Sabbah,
M.G.Lampugnani,
P.C.Marchisio,
J.W.Fenton,
I.Vlodavsky,
and
E.Dejana
(1991).
An Arg-Gly-Asp sequence within thrombin promotes endothelial cell adhesion.
|
| |
J Cell Biol,
112,
335-344.
|
|
|
|
|
|
|
T.Schmitz,
M.Rothe,
and
J.Dodt
(1991).
Mechanism of the inhibition of alpha-thrombin by hirudin-derived fragments hirudin(1-47) and hirudin(45-65).
|
| |
Eur J Biochem,
195,
251-256.
|
|
|
|
|
|
|
E.Bender,
R.Vogel,
K.P.Koller,
and
J.Engels
(1990).
Synthesis and secretion of hirudin by Streptomyces lividans.
|
| |
Appl Microbiol Biotechnol,
34,
203-207.
|
|
|
|
|
|
|
E.L.Madison,
E.J.Goldsmith,
R.D.Gerard,
M.J.Gething,
J.F.Sambrook,
and
R.S.Bassel-Duby
(1990).
Amino acid residues that affect interaction of tissue-type plasminogen activator with plasminogen activator inhibitor 1.
|
| |
Proc Natl Acad Sci U S A,
87,
3530-3533.
|
|
|
|
|
|
|
M.G.Grütter,
J.P.Priestle,
J.Rahuel,
H.Grossenbacher,
W.Bode,
J.Hofsteenge,
and
S.R.Stone
(1990).
Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.
|
| |
EMBO J,
9,
2361-2365.
|
|
|
|
|
|
|
R.Huber,
J.Römisch,
and
E.P.Paques
(1990).
The crystal and molecular structure of human annexin V, an anticoagulant protein that binds to calcium and membranes.
|
| |
EMBO J,
9,
3867-3874.
|
|
|
|
|
|
|
W.Bode,
D.Turk,
and
J.Stürzebecher
(1990).
Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin.
|
| |
Eur J Biochem,
193,
175-182.
|
|
|
PDB code:
|
|
|
|
|
|
|
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
code is
shown on the right.
|
 |
Links
