SEARCH

SEARCH BY CITATION

REFERENCES

  • 1
    Puente, X. S.,Sanchez, L. M.,Gutierrez-Fernandez, A.,Velasco, G., and Lopez-Otin, C. ( 2005). A genomic view of the complexity of mammalian proteolytic systems. Biochem. Soc. Trans. 33, 331334.
  • 2
    Page, M. J. and Di Cera, E. ( 2008). Serine peptidases: classification, structure and function. Cell Mol. Life Sci. 65, 12201236.
  • 3
    Page, M.J. and Di Cera, E. ( 2008). Evolution of peptidase diversity. J. Biol. Chem. 283, 3001030014.
  • 4
    Hedstrom, L. ( 2002). Serine protease mechanism and specificity. Chem. Rev. 102, 45014524.
  • 5
    Perona, J.J. and Craik, C.S. ( 1995). Structural basis of substrate specificity in the serine proteases. Protein Sci. 4, 337360.
  • 6
    Di Cera, E. ( 2008). Engineering protease specificity made simple, but not simpler. Nat. Chem. Biol. 4, 270271.
  • 7
    Monod, J.,Wyman, J., and Changeux, J. P. ( 1965). On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88118.
  • 8
    Rawlings, N. D.,Morton, F. R.,Kok, C. Y.,Kong, J., and Barrett, A. J. ( 2008). MEROPS: the peptidase database. Nucleic Acids Res. 36, D320D325.
  • 9
    Blow, D. M.,Birktoft, J. J., and Hartley, B. S. ( 1969). Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221, 337340.
  • 10
    Ciechanover, A. and Iwai, K. ( 2004). The ubiquitin system: from basic mechanisms to the patient bed. IUBMB Life 56, 193201.
  • 11
    Gomis-Ruth, F. X. ( 2003). Structural aspects of the metzincin clan of metalloendopeptidases. Mol. Biotechnol. 24, 157202.
  • 12
    Rea, D. and Fulop, V. ( 2006). Structure-function properties of prolyl oligopeptidase family enzymes. Cell Biochem. Biophys. 44, 349365.
  • 13
    Schechter, I. and Berger, A. ( 1967). On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27, 157162.
  • 14
    Rothman, S. S. ( 1977). The digestive enzymes of the pancreas: a mixture of inconstant proportions. Annu. Rev. Physiol. 39, 373389.
  • 15
    Whitcomb, D. C. and Lowe, M. E. ( 2007). Human pancreatic digestive enzymes. Dig. Dis. Sci. 52, 117.
  • 16
    Steinhoff, M.,Vergnolle, N.,Young, S. H.,Tognetto, M.,Amadesi, S.,Ennes, H. S.,Trevisani, M.,Hollenberg, M. D.,Wallace, J. L.,Caughey, G. H.,Mitchell, S. E.,Williams, L. M.,Geppetti, P.,Mayer, E. A., and Bunnett, N. W. ( 2000). Agonists of proteinase-activated receptor 2 induce inflammation by a neurogenic mechanism. Nat. Med. 6, 151158.
  • 17
    Pereira, P. J.,Bergner, A.,Macedo-Ribeiro, S.,Huber, R.,Matschiner, G.,Fritz, H.,Sommerhoff, C. P., and Bode, W. ( 1998). Human β-tryptase is a ring-like tetramer with active sites facing a central pore. Nature 392, 306311.
  • 18
    Lin, C. Y.,Anders, J.,Johnson, M.,Sang, Q. A., and Dickson, R. B. ( 1999). Molecular cloning of cDNA for matriptase, a matrix-degrading serine protease with trypsin-like activity. J. Biol. Chem. 274, 1823118236.
  • 19
    Ramsay, A. J.,Reid, J. C.,Velasco, G.,Quigley, J. P., and Hooper, J. D. ( 2008). The type II transmembrane serine protease matriptase-2—identification, structural features, enzymology, expression pattern and potential roles. Front. Biosci. 13, 569579.
  • 20
    Netzel-Arnett, S.,Hooper, J. D.,Szabo, R.,Madison, E. L.,Quigley, J. P.,Bugge, T. H., and Antalis, T. M. ( 2003). Membrane anchored serine proteases: a rapidly expanding group of cell surface proteolytic enzymes with potential roles in cancer. Cancer Metastasis Rev. 22, 237258.
  • 21
    Diamandis, E. P.,Yousef, G. M.,Luo, L. Y.,Magklara, A., and Obiezu, C. V. ( 2000). The new human kallikrein gene family: implications in carcinogenesis. Trends Endocrinol. Metab. 11, 5460.
  • 22
    Proud, D. and Kaplan, A. P. ( 1988). Kinin formation: mechanisms and role in inflammatory disorders. Annu. Rev. Immunol. 6, 4983.
  • 23
    Barry, M. and Bleackley, R. C. ( 2002). Cytotoxic T lymphocytes: all roads lead to death. Nat. Rev. Immunol. 2, 401409.
  • 24
    Neurath, H. and Dixon, G. H. ( 1957). Structure and activation of trypsinogen and chymotrypsinogen. Fed. Proc. 16, 791801.
  • 25
    Fehlhammer, H. and Bode, W. ( 1975). The refined crystal structure of bovine β-trypsin at 1.8 A resolution. I. Crystallization, data collection and application of patterson search technique. J. Mol. Biol. 98, 683692.
  • 26
    Fehlhammer, H.,Bode, W., and Huber, R. ( 1977). Crystal structure of bovine trypsinogen at 1–8 A resolution. II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin. J. Mol. Biol. 111, 415438.
  • 27
    Renatus, M.,Engh, R. A.,Stubbs, M. T.,Huber, R.,Fischer, S.,Kohnert, U., and Bode, W. ( 1997). Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA. EMBO J. 16, 47974805.
  • 28
    Hartley, B. S. and Kilby, B. A. ( 1954). The reaction of p-nitrophenyl esters with chymotrypsin and insulin. Biochem J. 56, 288297.
  • 29
    Bobofchak, K. M.,Pineda, A. O.,Mathews, F. S., and Di Cera, E. ( 2005). Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. J. Biol. Chem. 280, 2564425650.
  • 30
    Hedstrom, L.,Szilagyi, L., and Rutter, W. J. ( 1992). Converting trypsin to chymotrypsin: the role of surface loops. Science 255, 12491253.
  • 31
    Venekei, I.,Szilagyi, L.,Graf, L., and Rutter, W. J. ( 1996). Attempts to convert chymotrypsin to trypsin. FEBS Lett. 383, 143147.
  • 32
    Hung, S. H. and Hedstrom, L. ( 1998). Converting trypsin to elastase: substitution of the S1 site and adjacent loops reconstitutes esterase specificity but not amidase activity. Protein Eng. 11, 669673.
  • 33
    Jelinek, B.,Antal, J.,Venekei, I., and Graf, L. ( 2004). Ala226 to Gly and Ser189 to Asp mutations convert rat chymotrypsin B to a trypsin-like protease. Protein Eng. Des. Sel. 17, 127131.
  • 34
    Varadarajan, N.,Rodriguez, S.,Hwang, B.-Y.,Georgiu, G., and Iverson, B. I. ( 2008). Engineering a family of highly active and selective endopeptidases with programmed substrate specificities. Nat. Chem. Biol. 4, 290294.
  • 35
    Di Cera, E. ( 2008). Thrombin. Mol. Aspects. Med. 29, 203254.
  • 36
    Bah, A.,Garvey, L. C.,Ge, J., and Di Cera, E. ( 2006). Rapid kinetics of Na+ binding to thrombin. J. Biol. Chem. 281, 4004940056.
  • 37
    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, 3184231853.
  • 38
    Kirby, A. J. and Hollfelder, F. ( 2008). Biochemistry: enzymes under the nanoscope. Nature 456, 4547.
  • 39
    Sigala, P. A.,Kraut, D. A.,Caaveiro, J. M.,Pybus, B.,Ruben, E. A.,Ringe, D.,Petsko, G. A., and Herschlag, D. ( 2008). Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J. Am. Chem. Soc. 130, 1369613708.
  • 40
    Pineda, A. O.,Chen, Z. W.,Bah, A.,Garvey, L. C.,Mathews, F. S., and Di Cera, E. ( 2006). Crystal structure of thrombin in a self-inhibited conformation. J. Biol. Chem. 281, 3292232928.
  • 41
    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 A? resolution. J. Mol. Biol. 185, 595624.
  • 42
    Reiling, K. K.,Krucinski, J.,Miercke, L. J.,Raymond, W. W.,Caughey, G. H., and Stroud, R. M. ( 2003). Structure of human pro-chymase: a model for the activating transition of granule-associated proteases. Biochemistry 42, 26162624.
  • 43
    Fersht, A. R. ( 1972). Conformational equilibria in -and -chymotrypsin. The energetics and importance of the salt bridge. J. Mol. Biol. 64, 497509.
  • 44
    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, 279290.
  • 45
    Gandhi, P. S.,Chen, Z.,Mathews, F. S., and Di Cera, E. ( 2008). Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc. Natl. Acad. Sci. USA 105, 18321837.
  • 46
    Rohr, K. B.,Selwood, T.,Marquardt, U.,Huber, R.,Schechter, N. M.,Bode, W., and Than, M. E. ( 2006). X-ray structures of free and leupeptin-complexed human alphaI-tryptase mutants: indication for an alpha[RIGHTWARDS ARROW]beta-tryptase transition. J. Mol. Biol. 357, 195209.
  • 47
    Rickert, K. W.,Kelley, P.,Byrne, N. J.,Diehl, R. E.,Hall, D. L.,Montalvo, A. M.,Reid, J. C.,Shipman, J. M.,Thomas, B. W.,Munshi, S. K.,Darke, P. L., and Su, H. P. ( 2008). Structure of human prostasin, a target for the regulation of hypertension. J. Biol. Chem. 283, 3486434872.
  • 48
    Krojer, T.,Garrido-Franco, M.,Huber, R.,Ehrmann, M., and Clausen, T. ( 2002). Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Nature 416, 455459.
  • 49
    Jing, H.,Babu, Y. S.,Moore, D.,Kilpatrick, J. M.,Liu, X. Y.,Volanakis, J. E., and Narayana, S.V. ( 1998). Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity. J. Mol. Biol. 282, 10611081.
  • 50
    Hink-Schauer, C.,Estebanez-Perpina, E.,Wilharm, E.,Fuentes-Prior, P.,Klinkert, W.,Bode, W., and Jenne, D. E. ( 2002). The 2.2-A crystal structure of human pro-granzyme K reveals a rigid zymogen with unusual features. J. Biol. Chem. 277, 5092350933.
  • 51
    Shia, S.,Stamos, J.,Kirchhofer, D.,Fan, B.,Wu, J.,Corpuz, R. T.,Santell, L.,Lazarus, R. A., and Eigenbrot, C. ( 2005). Conformational lability in serine protease active sites: structures of hepatocyte growth factor activator (HGFA) alone and with the inhibitory domain from HGFA inhibitor-1B. J. Mol. Biol. 346, 13351349.
  • 52
    Carvalho, A. L.,Sanz, L.,Barettino, D.,Romero, A.,Calvete, J. J., and Romao, M. J. ( 2002). Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: a homologue of human PSA. J. Mol. Biol. 322, 325337.
  • 53
    Ponnuraj, K.,Xu, Y.,Macon, K.,Moore, D.,Volanakis, J. E., and Narayana, S. V. ( 2004). Structural analysis of engineered Bb fragment of complement factor B: insights into the activation mechanism of the alternative pathway C3-convertase. Mol. Cell. 14, 1728.
  • 54
    Barrette-Ng, I. H.,Ng, K. K.,Mark, B. L.,Van Aken, D.,Cherney, M. M.,Garen, C.,Kolodenko, Y.,Gorbalenya, A. E.,Snijder, E. J., and James, M. N. ( 2002). Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole. J. Biol. Chem. 277, 3996039966.
  • 55
    Friedrich, R.,Panizzi, P.,Fuentes-Prior, P.,Richter, K.,Verhamme, I.,Anderson, P. J.,Kawabata, S.,Huber, R.,Bode, W., and Bock, P. E. ( 2003). Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation. Nature 425, 535539.
  • 56
    Perutz, M. F. ( 1970). Stereochemistry of cooperative effects in haemoglobin. Nature 228, 726739.
  • 57
    Kantrowicz, E. R. and Lipscomb, W. M. ( 1990). Escherichia coli aspartate transcarbamylase: the molecular basis for a concerted allosteric transition. Trends Biochem Sci. 15, 5359.
  • 58
    Changeux, J. P. and Edelstein, S. J. ( 2006). Allosteric mechanisms of signal transduction. Science 308, 14241428.
  • 59
    Xu, Z.,Horwich, A. L., and Sigler, P. B. ( 1997). The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 388, 741750.
  • 60
    Frieden, C. ( 1970). Kinetic aspects of regulation of metabolic processes. The hysteretic enzyme concept. J. Biol. Chem. 245, 57885799.
  • 61
    Botts, J. and Morales, M. ( 1953). Analytical description of the effects of modifiers and of multivalency upon the steady state catalyzed reaction rate. Trans. Faraday Soc. 49, 696707.
  • 62
    Ainslie, G. R.,Jr.,Shill, J. P., and Neet, K. E. ( 1972). Transients and cooperativity. A slow transition model for relating transients and cooperative kinetics of enzymes. J. Biol. Chem. 247, 70887096.
  • 63
    Goodey, N. M. and Benkovic, S. J. ( 2008). Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 4, 474482.
  • 64
    Hedstrom, L. ( 1996). Trypsin: a case study in the structural determinants of enzyme specificity. Biol. Chem. 377, 465470.
  • 65
    Di Cera, E. ( 2006). A structural perspective on enzymes activated by monovalent cations. J. Biol. Chem. 281, 13051308.
  • 66
    Eisenmesser, E. Z.,Bosco, D. A.,Akke, M., and Kern, D. ( 2002). Enzyme dynamics during catalysis. Science 295, 15201523.
  • 67
    Lu, H. P.,Xun, L., and Xie, X. S. ( 1998). Single-molecule enzymatic dynamics. Science 282, 18771882.
  • 68
    Sytina, O. A.,Heyes, D. J.,Hunter, C. N.,Alexandre, M. T.,van Stokkum, I. H.,van Grondelle, R., and Groot, M. L. ( 2008). Conformational changes in an ultrafast light-driven enzyme determine catalytic activity. Nature 456, 10011004.
  • 69
    Cantwell, A. M. and Di Cera, E. ( 2000). Rational design of a potent anticoagulant thrombin. J. Biol. Chem. 275, 3982739830.
  • 70
    Gibbs, C. S.,Coutre, S. E.,Tsiang, M.,Li, W. X.,Jain, A. K.,Dunn, K. E.,Law, V. S.,Mao, C. T.,Matsumura, S. Y.,Mejza, S. J.,Paborsky, L. R., and Leung, L. L. K. ( 1995). Conversion of thrombin into an anticoagulant by protein engineering. Nature 378, 413416.
  • 71
    Carter, W. J.,Myles, T.,Gibbs, C. S.,Leung, L. L., and Huntington, J. A. ( 2004). Crystal structure of anticoagulant thrombin variant E217K provides insights into thrombin allostery. J. Biol. Chem. 279, 2638726394.
  • 72
    Pineda, A. O.,Chen, Z. W.,Caccia, S.,Cantwell, A. M.,Savvides, S. N.,Waksman, G.,Mathews, F. S., and Di Cera, E. ( 2004). The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. J. Biol. Chem. 279, 3982439828.