-
1
-
-
18044373469
-
A genomic view of the complexity of mammalian proteolytic systems
-
Puente, X. S., Sánchez, L. M., Gutiérrez-Fernandez, A., Velasco, G., and López-Otín, C. (2005) A genomic view of the complexity of mammalian proteolytic systems. Biochem. Soc. Trans. 33, 331-334
-
(2005)
Biochem. Soc. Trans.
, vol.33
, pp. 331-334
-
-
Puente, X.S.1
Sánchez, L.M.2
Gutiérrez-Fernandez, A.3
Velasco, G.4
López-Otín, C.5
-
2
-
-
0036882394
-
Serine protease mechanism and specificity
-
Hedstrom, L. (2002) Serine protease mechanism and specificity. Chem. Rev. 102, 4501-4524
-
(2002)
Chem. Rev.
, vol.102
, pp. 4501-4524
-
-
Hedstrom, L.1
-
3
-
-
0028914722
-
Structural basis of substrate specificity in the serine proteases
-
Perona, J. J., and Craik, C. S. (1995) Structural basis of substrate specificity in the serine proteases. Protein Sci. 4, 337-360
-
(1995)
Protein Sci.
, vol.4
, pp. 337-360
-
-
Perona, J.J.1
Craik, C.S.2
-
4
-
-
42249095637
-
Engineering protease specificity made simple, but not simpler
-
Di Cera, E. (2008) Engineering protease specificity made simple, but not simpler. Nat. Chem. Biol. 4, 270-271
-
(2008)
Nat. Chem. Biol.
, vol.4
, pp. 270-271
-
-
Di Cera, E.1
-
5
-
-
42249109450
-
Serine peptidases: Classification, structure and function
-
Page, M. J., and Di Cera, E. (2008) Serine peptidases: classification, structure and function. Cell. Mol. Life Sci. 65, 1220-1236
-
(2008)
Cell. Mol. Life Sci.
, vol.65
, pp. 1220-1236
-
-
Page, M.J.1
Di Cera, E.2
-
6
-
-
0037231552
-
The dynamics of thrombin formation
-
Mann, K. G., Butenas, S., and Brummel, K. (2003) The dynamics of thrombin formation. Arterioscler. Thromb. Vasc. Biol. 23, 17-25
-
(2003)
Arterioscler. Thromb. Vasc. Biol.
, vol.23
, pp. 17-25
-
-
Mann, K.G.1
Butenas, S.2
Brummel, K.3
-
7
-
-
34548213567
-
Deciphering complement mechanisms: The contributions of structural biology
-
Arlaud, G. J., Barlow, P. N., Gaboriaud, C., Gros, P., and Narayana, S. V. (2007) Deciphering complement mechanisms: the contributions of structural biology. Mol. Immunol. 44, 3809-3822
-
(2007)
Mol. Immunol.
, vol.44
, pp. 3809-3822
-
-
Arlaud, G.J.1
Barlow, P.N.2
Gaboriaud, C.3
Gros, P.4
Narayana, S.V.5
-
8
-
-
79960541421
-
Allostery in trypsin-like proteases suggests new therapeutic strategies
-
Gohara, D. W., and Di Cera, E. (2011) Allostery in trypsin-like proteases suggests new therapeutic strategies. Trends Biotechnol. 29, 577-585
-
(2011)
Trends Biotechnol.
, vol.29
, pp. 577-585
-
-
Gohara, D.W.1
Di Cera, E.2
-
9
-
-
84865284711
-
Conformational selection in trypsin-like proteases
-
Pozzi, N., Vogt, A. D., Gohara, D. W., and Di Cera, E. (2012) Conformational selection in trypsin-like proteases. Curr. Opin. Struct. Biol. 22, 421-431
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 421-431
-
-
Pozzi, N.1
Vogt, A.D.2
Gohara, D.W.3
Di Cera, E.4
-
10
-
-
0016771378
-
The refined crystal structure of bovine β-trypsin at 1.8-Å resolution: I. Crystallization, data collection and application of patterson search technique
-
Fehlhammer, H., and Bode, W. (1975) The refined crystal structure of bovine β-trypsin at 1.8-Å resolution: I. crystallization, data collection and application of patterson search technique. J. Mol. Biol. 98, 683-692
-
(1975)
J. Mol. Biol.
, vol.98
, pp. 683-692
-
-
Fehlhammer, H.1
Bode, W.2
-
11
-
-
79960512113
-
Crystallographic and kinetic evidence of allostery in a trypsin-like protease
-
Niu, W., Chen, Z., Gandhi, P. S., Vogt, A. D., Pozzi, N., Pelc, L. A., Zapata, F., and Di Cera, E. (2011) Crystallographic and kinetic evidence of allostery in a trypsin-like protease. Biochemistry 50, 6301-6307
-
(2011)
Biochemistry
, vol.50
, pp. 6301-6307
-
-
Niu, W.1
Chen, Z.2
Gandhi, P.S.3
Vogt, A.D.4
Pozzi, N.5
Pelc, L.A.6
Zapata, F.7
Di Cera, E.8
-
12
-
-
77956279561
-
NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation
-
Lechtenberg, B. C., Johnson, D. J., Freund, S. M., and Huntington, J. A. (2010) NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation. Proc. Natl. Acad. Sci. U. S. A. 107, 14087-14092
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 14087-14092
-
-
Lechtenberg, B.C.1
Johnson, D.J.2
Freund, S.M.3
Huntington, J.A.4
-
13
-
-
0035967533
-
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
-
Peterson, F. C., Gordon, N. C., and Gettins, P. G. (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
-
(2001)
Biochemistry
, vol.40
, pp. 6275-6283
-
-
Peterson, F.C.1
Gordon, N.C.2
Gettins, P.G.3
-
14
-
-
84863499347
-
The dynamic structure of thrombin in solution
-
Fuglestad, B., Gasper, P. M., Tonelli, M., McCammon, J. A., Markwick, P. R., and Komives, E. A. (2012) The dynamic structure of thrombin in solution. Biophys. J. 103, 79-88
-
(2012)
Biophys. J.
, vol.103
, pp. 79-88
-
-
Fuglestad, B.1
Gasper, P.M.2
Tonelli, M.3
McCammon, J.A.4
Markwick, P.R.5
Komives, E.A.6
-
16
-
-
84864462749
-
Conformational selection or induced fit? A critical appraisal of the kinetic mechanism
-
Vogt, A. D., and Di Cera, E. (2012) Conformational selection or induced fit? a critical appraisal of the kinetic mechanism. Biochemistry 51, 5894-5902
-
(2012)
Biochemistry
, vol.51
, pp. 5894-5902
-
-
Vogt, A.D.1
Di Cera, E.2
-
17
-
-
0015223374
-
Equilibrium and rate constants for the interconversion of two conformations of -chymotrypsin: The existence of a catalytically inactive conformation at neutral pH
-
Fersht, A. R., and Requena, Y. (1971) Equilibrium and rate constants for the interconversion of two conformations of -chymotrypsin: the existence of a catalytically inactive conformation at neutral pH. J. Mol. Biol. 60, 279-290
-
(1971)
J. Mol. Biol.
, vol.60
, pp. 279-290
-
-
Fersht, A.R.1
Requena, Y.2
-
18
-
-
0027516679
-
Evidence for common structural changes in thrombin induced by active-site or exosite binding
-
Parry, M. A., Stone, S. R., Hofsteenge, J., and Jackman, M. P. (1993) Evidence for common structural changes in thrombin induced by active-site or exosite binding. Biochem. J. 290, 665-670
-
(1993)
Biochem. J.
, vol.290
, pp. 665-670
-
-
Parry, M.A.1
Stone, S.R.2
Hofsteenge, J.3
Jackman, M.P.4
-
19
-
-
0030810220
-
Kinetic pathway for the slow to fast transition of thrombin. Evidence of linked ligand binding at structurally distinct domains
-
Lai, M. T., Di Cera, E., and Shafer, J. A. (1997) Kinetic pathway for the slow to fast transition of thrombin. Evidence of linked ligand binding at structurally distinct domains. J. Biol. Chem. 272, 30275-30282
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 30275-30282
-
-
Lai, M.T.1
Di Cera, E.2
Shafer, J.A.3
-
20
-
-
33846031987
-
Rapid kinetics of Na+ binding to thrombin
-
Bah, A., Garvey, L. C., Ge, J., and Di Cera, E. (2006) Rapid kinetics of Na+ binding to thrombin. J. Biol. Chem. 281, 40049-40056
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 40049-40056
-
-
Bah, A.1
Garvey, L.C.2
Ge, J.3
Di Cera, E.4
-
21
-
-
65249128033
-
Autocatalytic activation of the furin zymogen requires removal of the emerging enzyme's N-terminus from the active site
-
Gawlik, K., Shiryaev, S. A., Zhu, W., Motamedchaboki, K., Desjardins, R., Day, R., Remacle, A. G., Stec, B., and Strongin, A. Y. (2009) Autocatalytic activation of the furin zymogen requires removal of the emerging enzyme's N-terminus from the active site. PLoS ONE 4, e5031
-
(2009)
PLoS ONE
, vol.4
, pp. e5031
-
-
Gawlik, K.1
Shiryaev, S.A.2
Zhu, W.3
Motamedchaboki, K.4
Desjardins, R.5
Day, R.6
Remacle, A.G.7
Stec, B.8
Strongin, A.Y.9
-
22
-
-
84855393059
-
Proprotein convertases in health and disease
-
Artenstein, A. W., and Opal, S. M. (2011) Proprotein convertases in health and disease. N. Engl. J. Med. 365, 2507-2518
-
(2011)
N. Engl. J. Med.
, vol.365
, pp. 2507-2518
-
-
Artenstein, A.W.1
Opal, S.M.2
-
23
-
-
34247892364
-
The crystal structure of PCSK9: A regulator of plasma LDL-cholesterol
-
Piper, D. E., Jackson, S., Liu, Q., Romanow, W. G., Shetterly, S., Thibault, S. T., Shan, B., and Walker, N. P. (2007) The crystal structure of PCSK9: a regulator of plasma LDL-cholesterol. Structure 15, 545-552
-
(2007)
Structure
, vol.15
, pp. 545-552
-
-
Piper, D.E.1
Jackson, S.2
Liu, Q.3
Romanow, W.G.4
Shetterly, S.5
Thibault, S.T.6
Shan, B.7
Walker, N.P.8
-
24
-
-
80054877888
-
Elucidation of crucial structures for a catechol-based inhibitor of plasma hyaluronan-binding protein (factor VII activating protease) autoactivation
-
Yamamoto, E., Kitano, Y., and Hasumi, K. (2011) Elucidation of crucial structures for a catechol-based inhibitor of plasma hyaluronan-binding protein (factor VII activating protease) autoactivation. Biosci. Biotechnol. Biochem. 75, 2070-2072
-
(2011)
Biosci. Biotechnol. Biochem.
, vol.75
, pp. 2070-2072
-
-
Yamamoto, E.1
Kitano, Y.2
Hasumi, K.3
-
25
-
-
0036382842
-
Crystal structures of uninhibited factor VIIa link its cofactor and substrate-assisted activation to specific interactions
-
Sichler, K., Banner, D. W., D'Arcy, A., Hopfner, K. P., Huber, R., Bode, W., Kresse, G. B., Kopetzki, E., and Brandstetter, H. (2002) Crystal structures of uninhibited factor VIIa link its cofactor and substrate-assisted activation to specific interactions. J. Mol. Biol. 322, 591-603
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 591-603
-
-
Sichler, K.1
Banner, D.W.2
D'Arcy, A.3
Hopfner, K.P.4
Huber, R.5
Bode, W.6
Kresse, G.B.7
Kopetzki, E.8
Brandstetter, H.9
-
26
-
-
10144246566
-
Hereditary pancreatitis is caused by a mutation in the cationic trypsinogen gene
-
Whitcomb, D. C., Gorry, M. C., Preston, R. A., Furey, W., Sossenheimer, M. J., Ulrich, C. D., Martin, S. P., Gates, L. K., Jr., Amann, S. T., Toskes, P. P., Liddle, R., McGrath, K., Uomo, G., Post, J. C., and Ehrlich, G. D. (1996) Hereditary pancreatitis is caused by a mutation in the cationic trypsinogen gene. Nat. Genet. 14, 141-145
-
(1996)
Nat. Genet.
, vol.14
, pp. 141-145
-
-
Whitcomb, D.C.1
Gorry, M.C.2
Preston, R.A.3
Furey, W.4
Sossenheimer, M.J.5
Ulrich, C.D.6
Martin, S.P.7
Gates, L.K.8
Amann, S.T.9
Toskes, P.P.10
Liddle, R.11
McGrath, K.12
Uomo, G.13
Post, J.C.14
Ehrlich, G.D.15
-
27
-
-
77955496853
-
Proteolytic processing of the serine protease matriptase-2: Identification of the cleavage sites required for its autocatalytic release from the cell surface
-
Stirnberg, M., Maurer, E., Horstmeyer, A., Kolp, S., Frank, S., Bald, T., Arenz, K., Janzer, A., Prager, K., Wunderlich, P., Walter, J., and Gütschow, M. (2010) Proteolytic processing of the serine protease matriptase-2: identification of the cleavage sites required for its autocatalytic release from the cell surface. Biochem. J. 430, 87-95
-
(2010)
Biochem. J.
, vol.430
, pp. 87-95
-
-
Stirnberg, M.1
Maurer, E.2
Horstmeyer, A.3
Kolp, S.4
Frank, S.5
Bald, T.6
Arenz, K.7
Janzer, A.8
Prager, K.9
Wunderlich, P.10
Walter, J.11
Gütschow, M.12
-
28
-
-
84876558747
-
Autoactivation of thrombin precursors
-
Pozzi, N., Chen, Z., Zapata, F., Niu, W., Barranco-Medina, S., Pelc, L. A., and Di Cera, E. (2013) Autoactivation of thrombin precursors. J. Biol. Chem. 288, 11601-11610
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 11601-11610
-
-
Pozzi, N.1
Chen, Z.2
Zapata, F.3
Niu, W.4
Barranco-Medina, S.5
Pelc, L.A.6
Di Cera, E.7
-
29
-
-
84864123309
-
Exposure of R169 controls protein C activation and autoactivation
-
Pozzi, N., Barranco-Medina, S., Chen, Z., and Di Cera, E. (2012) Exposure of R169 controls protein C activation and autoactivation. Blood 120, 664-670
-
(2012)
Blood
, vol.120
, pp. 664-670
-
-
Pozzi, N.1
Barranco-Medina, S.2
Chen, Z.3
Di Cera, E.4
-
30
-
-
37049178293
-
Evolution of proteolytic enzymes
-
Neurath, H. (1984) Evolution of proteolytic enzymes. Science 224, 350-357
-
(1984)
Science
, vol.224
, pp. 350-357
-
-
Neurath, H.1
-
31
-
-
11744288074
-
Structure and activation of trypsinogen and chymotrypsinogen
-
Neurath, H., and Dixon, G. H. (1957) Structure and activation of trypsinogen and chymotrypsinogen. Fed. Proc. 16, 791-801
-
(1957)
Fed. Proc.
, vol.16
, pp. 791-801
-
-
Neurath, H.1
Dixon, G.H.2
-
33
-
-
0037438708
-
Dissecting substrate recognition by thrombin using the inactive mutant S195A
-
Krem, M. M., and Di Cera, E. (2003) Dissecting substrate recognition by thrombin using the inactive mutant S195A. Biophys. Chem. 100, 315-323
-
(2003)
Biophys. Chem.
, vol.100
, pp. 315-323
-
-
Krem, M.M.1
Di Cera, E.2
-
34
-
-
0029090336
-
The Na+ binding site of thrombin
-
Di Cera, E., Guinto, E. R., Vindigni, A., Dang, Q. D., Ayala, Y. M., Wuyi, M., and Tulinsky, A. (1995) The Na+ binding site of thrombin. J. Biol. Chem. 270, 22089-22092
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 22089-22092
-
-
Di Cera, E.1
Guinto, E.R.2
Vindigni, A.3
Dang, Q.D.4
Ayala, Y.M.5
Wuyi, M.6
Tulinsky, A.7
-
35
-
-
0028586082
-
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: Changes accompanying activation and exosite binding to thrombin
-
Vijayalakshmi, J., Padmanabhan, K. P., Mann, K. G., and Tulinsky, A. (1994) The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin. Protein Sci. 3, 2254-2271
-
(1994)
Protein Sci.
, vol.3
, pp. 2254-2271
-
-
Vijayalakshmi, J.1
Padmanabhan, K.P.2
Mann, K.G.3
Tulinsky, A.4
-
36
-
-
0018907213
-
The role of phospholipids and factor Va in the prothrombinase complex
-
Rosing, J., Tans, G., Govers-Riemslag, J. W., Zwaal, R. F., and Hemker, H. C. (1980) The role of phospholipids and factor Va in the prothrombinase complex. J. Biol. Chem. 255, 274-283
-
(1980)
J. Biol. Chem.
, vol.255
, pp. 274-283
-
-
Rosing, J.1
Tans, G.2
Govers-Riemslag, J.W.3
Zwaal, R.F.4
Hemker, H.C.5
-
37
-
-
84869015264
-
Prothrombin activation by platelet-associated prothrombinase proceeds through the prethrombin-2 pathway via a concerted mechanism
-
Haynes, L. M., Bouchard, B. A., Tracy, P. B., and Mann, K. G. (2012) Prothrombin activation by platelet-associated prothrombinase proceeds through the prethrombin-2 pathway via a concerted mechanism. J. Biol. Chem. 287, 38647-38655
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 38647-38655
-
-
Haynes, L.M.1
Bouchard, B.A.2
Tracy, P.B.3
Mann, K.G.4
-
38
-
-
3843133006
-
Molecular dissection of Na+ binding to thrombin
-
Pineda, A. O., Carrell, C. J., Bush, L. A., Prasad, S., Caccia, S., Chen, Z. W., Mathews, F. S., and Di Cera, E. (2004) Molecular dissection of Na+ binding to thrombin. J. Biol. Chem. 279, 31842-31853
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 31842-31853
-
-
Pineda, A.O.1
Carrell, C.J.2
Bush, L.A.3
Prasad, S.4
Caccia, S.5
Chen, Z.W.6
Mathews, F.S.7
Di Cera, E.8
-
39
-
-
81855199864
-
Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation
-
Pozzi, N., Chen, Z., Zapata, F., Pelc, L. A., Barranco-Medina, S., and Di Cera, E. (2011) Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation. Biochemistry 50, 10195-10202
-
(2011)
Biochemistry
, vol.50
, pp. 10195-10202
-
-
Pozzi, N.1
Chen, Z.2
Zapata, F.3
Pelc, L.A.4
Barranco-Medina, S.5
Di Cera, E.6
-
40
-
-
0027050807
-
The refined 1.9-Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships
-
Bode, W., Turk, D., and Karshikov, A. (1992) The refined 1.9-Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci. 1, 426-471
-
(1992)
Protein Sci.
, vol.1
, pp. 426-471
-
-
Bode, W.1
Turk, D.2
Karshikov, A.3
-
41
-
-
0014280059
-
New looks and outlooks in physical enzymology
-
Eigen, M. (1968) New looks and outlooks in physical enzymology. Q. Rev. Biophys. 1, 3-33
-
(1968)
Q. Rev. Biophys.
, vol.1
, pp. 3-33
-
-
Eigen, M.1
-
42
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland, D. E. (1958) Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. U. S. A. 44, 98-104
-
(1958)
Proc. Natl. Acad. Sci. U. S. A.
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
43
-
-
44049103958
-
Residence time of receptorligand complexes and its effect on biological function
-
Tummino, P. J., and Copeland, R. A. (2008) Residence time of receptorligand complexes and its effect on biological function. Biochemistry 47, 5481-5492
-
(2008)
Biochemistry
, vol.47
, pp. 5481-5492
-
-
Tummino, P.J.1
Copeland, R.A.2
-
44
-
-
84883213263
-
Conformational selection is a dominant mechanism of ligand binding
-
Vogt, A. D., and Di Cera, E. (2013) Conformational selection is a dominant mechanism of ligand binding. Biochemistry 52, 5723-5729
-
(2013)
Biochemistry
, vol.52
, pp. 5723-5729
-
-
Vogt, A.D.1
Di Cera, E.2
-
45
-
-
84894262099
-
Essential role of conformational selection in ligand binding
-
Vogt, A. D., Pozzi, N., Chen, Z., and Di Cera, E. (2014) Essential role of conformational selection in ligand binding. Biophys. Chem. 186, 13-21
-
(2014)
Biophys. Chem.
, vol.186
, pp. 13-21
-
-
Vogt, A.D.1
Pozzi, N.2
Chen, Z.3
Di Cera, E.4
-
46
-
-
0015152607
-
Escherichia coli alkaline phosphatase: An analysis of transient kinetics
-
Halford, S. E. (1971) Escherichia coli alkaline phosphatase: an analysis of transient kinetics. Biochem. J. 125, 319-327
-
(1971)
Biochem. J.
, vol.125
, pp. 319-327
-
-
Halford, S.E.1
-
47
-
-
0015298504
-
Escherichia coli alkaline phosphatase: Relaxation spectra of ligand binding
-
Halford, S. E. (1972) Escherichia coli alkaline phosphatase: relaxation spectra of ligand binding. Biochem. J. 126, 727-738
-
(1972)
Biochem. J.
, vol.126
, pp. 727-738
-
-
Halford, S.E.1
-
48
-
-
0019821957
-
Binding of high affinity heparin to antithrombin III: Stopped flow kinetic studies of the binding interaction
-
Olson, S. T., Srinivasan, K. R., Björk, I., and Shore, J. D. (1981) Binding of high affinity heparin to antithrombin III: stopped flow kinetic studies of the binding interaction. J. Biol. Chem. 256, 11073-11079
-
(1981)
J. Biol. Chem.
, vol.256
, pp. 11073-11079
-
-
Olson, S.T.1
Srinivasan, K.R.2
Björk, I.3
Shore, J.D.4
-
49
-
-
24044468582
-
Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding: Analysis of stopped-flow kinetic experiments
-
Galletto, R., Jezewska, M. J., and Bujalowski, W. (2005) Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding: analysis of stopped-flow kinetic experiments. Cell. Biochem. Biophys. 42, 121-144
-
(2005)
Cell. Biochem. Biophys.
, vol.42
, pp. 121-144
-
-
Galletto, R.1
Jezewska, M.J.2
Bujalowski, W.3
-
50
-
-
84898953700
-
Distinguishing induced fit from conformational selection
-
Gianni, S., Dogan, J., and Jemth, P. (2014) Distinguishing induced fit from conformational selection. Biophys. Chem. 189, 33-39
-
(2014)
Biophys. Chem.
, vol.189
, pp. 33-39
-
-
Gianni, S.1
Dogan, J.2
Jemth, P.3
-
51
-
-
0004244695
-
-
University Science Books, Mill Valley, CA
-
Wyman, J., and Gill, S. J. (1990) Binding and Linkage, University Science Books, Mill Valley, CA
-
(1990)
Binding and Linkage
-
-
Wyman, J.1
Gill, S.J.2
-
52
-
-
84894256162
-
Exploring the role of receptor flexibility in structure-based drug discovery
-
Feixas, F., Lindert, S., Sinko, W., and McCammon, J. A. (2014) Exploring the role of receptor flexibility in structure-based drug discovery. Biophys. Chem. 186, 31-45
-
(2014)
Biophys. Chem.
, vol.186
, pp. 31-45
-
-
Feixas, F.1
Lindert, S.2
Sinko, W.3
McCammon, J.A.4
-
53
-
-
84927610134
-
Sulfated low molecular weight lignins, allosteric inhibitors of coagulation proteinases via the heparin binding site, significantly alter the active site of thrombin and factor Xa compared to heparin
-
Henry, B. L., and Desai, U. R. (2014) Sulfated low molecular weight lignins, allosteric inhibitors of coagulation proteinases via the heparin binding site, significantly alter the active site of thrombin and factor Xa compared to heparin. Thromb. Res. 134, 1123-1129
-
(2014)
Thromb. Res.
, vol.134
, pp. 1123-1129
-
-
Henry, B.L.1
Desai, U.R.2
-
54
-
-
0026003287
-
The region of the thrombin receptor resembling hirudin binds to thrombin and alters enzyme specificity
-
Liu, L. W., Vu, T. K., Esmon, C. T., and Coughlin, S. R. (1991) The region of the thrombin receptor resembling hirudin binds to thrombin and alters enzyme specificity. J. Biol. Chem. 266, 16977-16980
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 16977-16980
-
-
Liu, L.W.1
Vu, T.K.2
Esmon, C.T.3
Coughlin, S.R.4
-
55
-
-
0025900393
-
Allosteric changes in thrombin's activity produced by peptides corresponding to segments of natural inhibitors and substrates
-
Hortin, G. L., and Trimpe, B. L. (1991) Allosteric changes in thrombin's activity produced by peptides corresponding to segments of natural inhibitors and substrates. J. Biol. Chem. 266, 6866-6871
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 6866-6871
-
-
Hortin, G.L.1
Trimpe, B.L.2
-
56
-
-
0030948651
-
Energetics of thrombin-thrombomodulin interaction
-
Vindigni, A., White, C. E., Komives, E. A., and Di Cera, E. (1997) Energetics of thrombin-thrombomodulin interaction. Biochemistry 36, 6674-6681
-
(1997)
Biochemistry
, vol.36
, pp. 6674-6681
-
-
Vindigni, A.1
White, C.E.2
Komives, E.A.3
Di Cera, E.4
-
57
-
-
0034732094
-
Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex
-
Fuentes-Prior, P., Iwanaga, Y., Huber, R., Pagila, R., Rumennik, G., Seto, M., Morser, J., Light, D. R., and Bode, W. (2000) Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex. Nature 404, 518-525
-
(2000)
Nature
, vol.404
, pp. 518-525
-
-
Fuentes-Prior, P.1
Iwanaga, Y.2
Huber, R.3
Pagila, R.4
Rumennik, G.5
Seto, M.6
Morser, J.7
Light, D.R.8
Bode, W.9
-
58
-
-
0026476381
-
Thrombin is a Na+-activated enzyme
-
Wells, C. M., and Di Cera, E. (1992) Thrombin is a Na+-activated enzyme. Biochemistry 31, 11721-11730
-
(1992)
Biochemistry
, vol.31
, pp. 11721-11730
-
-
Wells, C.M.1
Di Cera, E.2
-
59
-
-
0024558370
-
The roles of protein C and thrombomodulin in the regulation of blood coagulation
-
Esmon, C. T. (1989) The roles of protein C and thrombomodulin in the regulation of blood coagulation. J. Biol. Chem. 264, 4743-4746
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 4743-4746
-
-
Esmon, C.T.1
-
60
-
-
0026351350
-
The active site of thrombin is altered upon binding to thrombomodulin: Two distinct structural changes are detected by fluorescence, but only one correlates with protein C activation
-
Ye, J., Esmon, N. L., Esmon, C. T., and Johnson, A. E. (1991) The active site of thrombin is altered upon binding to thrombomodulin: two distinct structural changes are detected by fluorescence, but only one correlates with protein C activation. J. Biol. Chem. 266, 23016-23021
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 23016-23021
-
-
Ye, J.1
Esmon, N.L.2
Esmon, C.T.3
Johnson, A.E.4
-
61
-
-
0030959346
-
The thrombin E192Q-BPTI complex reveals gross structural rearrangements: Implications for the interaction with antithrombin and thrombomodulin
-
van de Locht, A., Bode, W., Huber, R., Le Bonniec, B. F., Stone, S. R., Esmon, C. T., and Stubbs, M. T. (1997) The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin. EMBO J. 16, 2977-2984
-
(1997)
EMBO J.
, vol.16
, pp. 2977-2984
-
-
Van De Locht, A.1
Bode, W.2
Huber, R.3
Le Bonniec, B.F.4
Stone, S.R.5
Esmon, C.T.6
Stubbs, M.T.7
-
62
-
-
0025203764
-
Further localization of binding sites for thrombin and protein C in human thrombomodulin
-
Hayashi, T., Zushi, M., Yamamoto, S., and Suzuki, K. (1990) Further localization of binding sites for thrombin and protein C in human thrombomodulin. J. Biol. Chem. 265, 20156-20159
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 20156-20159
-
-
Hayashi, T.1
Zushi, M.2
Yamamoto, S.3
Suzuki, K.4
-
63
-
-
0142091399
-
Thrombomodulin allosterically modulates the activity of the anticoagulant thrombin
-
Rezaie, A. R., and Yang, L. (2003) Thrombomodulin allosterically modulates the activity of the anticoagulant thrombin. Proc. Natl. Acad. Sci. U. S. A. 100, 12051-12056
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 12051-12056
-
-
Rezaie, A.R.1
Yang, L.2
-
64
-
-
32244444849
-
Activation of protein C by the thrombin-thrombomodulin complex: Cooperative roles of Arg-35 of thrombin and Arg-67 of protein C
-
Yang, L., Manithody, C., and Rezaie, A. R. (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
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 879-884
-
-
Yang, L.1
Manithody, C.2
Rezaie, A.R.3
-
65
-
-
4644224910
-
The conformation of the activation peptide of protein C is influenced by Ca2+ and Na+ binding
-
Yang, L., Prasad, S., Di Cera, E., and Rezaie, A. R. (2004) The conformation of the activation peptide of protein C is influenced by Ca2+ and Na+ binding. J. Biol. Chem. 279, 38519-38524
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 38519-38524
-
-
Yang, L.1
Prasad, S.2
Di Cera, E.3
Rezaie, A.R.4
-
66
-
-
84923370191
-
Why Ser and not Thr brokers catalysis in the trypsin fold
-
Pelc, L. A., Chen, Z., Gohara, D. W., Vogt, A. D., Pozzi, N., and Di Cera, E. (2015) Why Ser and not Thr brokers catalysis in the trypsin fold. Biochemistry 54, 1457-1464
-
(2015)
Biochemistry
, vol.54
, pp. 1457-1464
-
-
Pelc, L.A.1
Chen, Z.2
Gohara, D.W.3
Vogt, A.D.4
Pozzi, N.5
Di Cera, E.6
-
67
-
-
0022521744
-
Kinetics of the inhibition of thrombin by hirudin
-
Stone, S. R., and Hofsteenge, J. (1986) Kinetics of the inhibition of thrombin by hirudin. Biochemistry 25, 4622-4628
-
(1986)
Biochemistry
, vol.25
, pp. 4622-4628
-
-
Stone, S.R.1
Hofsteenge, J.2
-
68
-
-
0029785840
-
Residue 225 determines the Na+-induced allosteric regulation of catalytic activity in serine proteases
-
Dang, Q. D., and Di Cera, E. (1996) Residue 225 determines the Na+-induced allosteric regulation of catalytic activity in serine proteases. Proc. Natl. Acad. Sci. U. S. A. 93, 10653-10656
-
(1996)
Proc. Natl. Acad. Sci. U. S. A.
, vol.93
, pp. 10653-10656
-
-
Dang, Q.D.1
Di Cera, E.2
-
69
-
-
0026520387
-
Converting trypsin to chymotrypsin: The role of surface loops
-
Hedstrom, L., Szilagyi, L., and Rutter, W. J. (1992) Converting trypsin to chymotrypsin: the role of surface loops. Science 255, 1249-1253
-
(1992)
Science
, vol.255
, pp. 1249-1253
-
-
Hedstrom, L.1
Szilagyi, L.2
Rutter, W.J.3
-
70
-
-
80052323661
-
Rigidification of the autolysis loop enhances Na+ binding to thrombin
-
Pozzi, N., Chen, R., Chen, Z., Bah, A., and Di Cera, E. (2011) Rigidification of the autolysis loop enhances Na+ binding to thrombin. Biophys. Chem. 159, 6-13
-
(2011)
Biophys. Chem.
, vol.159
, pp. 6-13
-
-
Pozzi, N.1
Chen, R.2
Chen, Z.3
Bah, A.4
Di Cera, E.5
-
71
-
-
0017348682
-
Crystal structure of bovine trypsinogen at 1-8 Å resolution: II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin
-
Fehlhammer, H., Bode, W., and Huber, R. (1977) Crystal structure of bovine trypsinogen at 1-8 Å resolution: II. crystallographic refinement, refined crystal structure and comparison with bovine trypsin. J. Mol. Biol. 111, 415-438
-
(1977)
J. Mol. Biol.
, vol.111
, pp. 415-438
-
-
Fehlhammer, H.1
Bode, W.2
Huber, R.3
-
72
-
-
0017618454
-
Structure of bovine trypsinogen at 1.9-Å resolution
-
Kossiakoff, A. A., Chambers, J. L., Kay, L. M., and Stroud, R. M. (1977) Structure of bovine trypsinogen at 1.9-Å resolution. Biochemistry 16, 654-664
-
(1977)
Biochemistry
, vol.16
, pp. 654-664
-
-
Kossiakoff, A.A.1
Chambers, J.L.2
Kay, L.M.3
Stroud, R.M.4
-
73
-
-
25844471033
-
A true autoactivating enzyme. Structural insight into mannose-binding lectinassociated serine protease-2 activations
-
Gál, P., Harmat, V., Kocsis, A., Bián, T., Barna, L., Ambrus, G., Végh, B., Balczer, J., Sim, R. B., Náray-Szabó, G., and Závodszky, P. (2005) A true autoactivating enzyme. Structural insight into mannose-binding lectinassociated serine protease-2 activations. J. Biol. Chem. 280, 33435-33444
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 33435-33444
-
-
Gál, P.1
Harmat, V.2
Kocsis, A.3
Bián, T.4
Barna, L.5
Ambrus, G.6
Végh, B.7
Balczer, J.8
Sim, R.B.9
Náray-Szabó, G.10
Závodszky, P.11
-
74
-
-
0021930156
-
Bovine chymotrypsinogen A x-ray crystal structure analysis and refinement of a new crystal form at 1.8-Å resolution
-
Wang, D., Bode, W., and Huber, R. (1985) Bovine chymotrypsinogen A x-ray crystal structure analysis and refinement of a new crystal form at 1.8-Å resolution. J. Mol. Biol. 185, 595-624
-
(1985)
J. Mol. Biol.
, vol.185
, pp. 595-624
-
-
Wang, D.1
Bode, W.2
Huber, R.3
-
75
-
-
33744927154
-
Crystal structure of the factor XI zymogen reveals a pathway for transactivation
-
Papagrigoriou, E., McEwan, P. A., Walsh, P. N., and Emsley, J. (2006) Crystal structure of the factor XI zymogen reveals a pathway for transactivation. Nat. Struct. Mol. Biol. 13, 557-558
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, pp. 557-558
-
-
Papagrigoriou, E.1
McEwan, P.A.2
Walsh, P.N.3
Emsley, J.4
-
76
-
-
33847651701
-
Factor B structure provides insights into activation of the central protease of the complement system
-
Milder, F. J., Gomes, L., Schouten, A., Janssen, B. J., Huizinga, E. G., Romijn, R. A., Hemrika, W., Roos, A., Daha, M. R., and Gros, P. (2007) Factor B structure provides insights into activation of the central protease of the complement system. Nat. Struct. Mol. Biol. 14, 224-228
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 224-228
-
-
Milder, F.J.1
Gomes, L.2
Schouten, A.3
Janssen, B.J.4
Huizinga, E.G.5
Romijn, R.A.6
Hemrika, W.7
Roos, A.8
Daha, M.R.9
Gros, P.10
-
77
-
-
0025866812
-
Refined structure of the hirudin-thrombin complex
-
Rydel, T. J., Tulinsky, A., Bode, W., and Huber, R. (1991) Refined structure of the hirudin-thrombin complex. J. Mol. Biol. 221, 583-601
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 583-601
-
-
Rydel, T.J.1
Tulinsky, A.2
Bode, W.3
Huber, R.4
-
78
-
-
22844449689
-
Hirudin binding reveals key determinants of thrombin allostery
-
Mengwasser, K. E., Bush, L. A., Shih, P., Cantwell, A. M., and Di Cera, E. (2005) Hirudin binding reveals key determinants of thrombin allostery. J. Biol. Chem. 280, 26997-27003
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 26997-27003
-
-
Mengwasser, K.E.1
Bush, L.A.2
Shih, P.3
Cantwell, A.M.4
Di Cera, E.5
-
79
-
-
0028084791
-
Molecular recognition by thrombin: Role of the slow-fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components
-
Ayala, Y., and Di Cera, E. (1994) Molecular recognition by thrombin: role of the slow-fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components. J. Mol. Biol. 235, 733-746
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 733-746
-
-
Ayala, Y.1
Di Cera, E.2
-
80
-
-
0033515039
-
Unexpected crucial role of residue 225 in serine proteases
-
Guinto, E. R., Caccia, S., Rose, T., Fütterer, K., Waksman, G., and Di Cera, E. (1999) Unexpected crucial role of residue 225 in serine proteases. Proc. Natl. Acad. Sci. U. S. A. 96, 1852-1857
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, pp. 1852-1857
-
-
Guinto, E.R.1
Caccia, S.2
Rose, T.3
Fütterer, K.4
Waksman, G.5
Di Cera, E.6
-
81
-
-
67849094264
-
Slow thrombin is zymogen-like
-
Huntington, J. A. (2009) Slow thrombin is zymogen-like. J. Thromb. Haemost. 7, 159-164
-
(2009)
J. Thromb. Haemost.
, vol.7
, pp. 159-164
-
-
Huntington, J.A.1
-
82
-
-
77956544191
-
Ligand binding shuttles thrombin along a continuum of zymogen-like and proteinaselike states
-
Kamath, P., Huntington, J. A., and Krishnaswamy, S. (2010) Ligand binding shuttles thrombin along a continuum of zymogen-like and proteinaselike states. J. Biol. Chem. 285, 28651-28658
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 28651-28658
-
-
Kamath, P.1
Huntington, J.A.2
Krishnaswamy, S.3
-
84
-
-
84886671844
-
Correlated motions and residual frustration in thrombin
-
Fuglestad, B., Gasper, P. M., McCammon, J. A., Markwick, P. R., and Komives, E. A. (2013) Correlated motions and residual frustration in thrombin. J. Phys. Chem. B 117, 12857-12863
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 12857-12863
-
-
Fuglestad, B.1
Gasper, P.M.2
McCammon, J.A.3
Markwick, P.R.4
Komives, E.A.5
-
85
-
-
84986563426
-
Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
-
Plattner, N., and Noé, F. (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun. 6, 7653
-
(2015)
Nat. Commun.
, vol.6
, pp. 7653
-
-
Plattner, N.1
Noé, F.2
-
86
-
-
84890346744
-
Histone H4 promotes prothrombin autoactivation
-
Barranco-Medina, S., Pozzi, N., Vogt, A. D., and Di Cera, E. (2013) Histone H4 promotes prothrombin autoactivation. J. Biol. Chem. 288, 35749-35757
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 35749-35757
-
-
Barranco-Medina, S.1
Pozzi, N.2
Vogt, A.D.3
Di Cera, E.4
-
87
-
-
0017850232
-
Crystal structure analysis and refinement of two variants of trigonal trypsinogen: Trigonal trypsin and PEG (polyethylene glycol) trypsinogen and their comparison with orthorhombic trypsin and trigonal trypsinogen
-
Bode, W., and Huber, R. (1978) Crystal structure analysis and refinement of two variants of trigonal trypsinogen: trigonal trypsin and PEG (polyethylene glycol) trypsinogen and their comparison with orthorhombic trypsin and trigonal trypsinogen. FEBS Lett. 90, 265-269
-
(1978)
FEBS Lett.
, vol.90
, pp. 265-269
-
-
Bode, W.1
Huber, R.2
-
88
-
-
0017893796
-
The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding: The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9-Å resolution
-
Bode, W., Schwager, P., and Huber, R. (1978) The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding: the refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9-Å resolution. J. Mol. Biol. 118, 99-112
-
(1978)
J. Mol. Biol.
, vol.118
, pp. 99-112
-
-
Bode, W.1
Schwager, P.2
Huber, R.3
|