Abstract
The complexity of the physical interactions which govern macromolecules, along with natural selection processes, has driven the evolution of the subtly balanced biochemical systems seen in biology, and as part of this, protein behaviour ranging from surprising to mysterious. The balances of the complex enzymatic mixtures found in vivo enable sensitive and rapid triggering of biochemical response mechanisms, for example, while maintaining the stability and adaptability required for life. This combination of stability and subtlety is found among protein structures as well: a few amino acid types with unlimited variety in sequences; a few types of secondary structure but many globular folds; common folding scaffolds (predictable?) with hypervariability at functional segments.
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References
Abrahamson, M., Ritonja, A., Brown, M.A., Grubb, A., Machleidt, W. and Barrett, A.J., 1987, Identification of the probable inhibitory reactive sites of the cysteine proteinase inhibitors human cystatin C and chicken cystatin, J. Biol. Chem. 262: 9688–9694.
Anastasi, A., Brown, M.A., Kembhavi, A.A., Nicklin, M.J.H., Sayers, C.A., Sunter, D.C. and Barrett, A.J., 1983, Cystatin, a protein inhibitor of cysteine proteinases: Improved purification from egg-white, characterization, and detection in chicken serum, Biochem. J. 211: 129–138.
Arrowsmith, C., Pachter, R., Altman, R. and Jardetzky, O., 1991, The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution, Eur. J. Biochem. 202: 53–66.
Barrett, A.J., Rawlings, N.D., Davies, M.E., Machleidt, W., Salvesen, G. and Turk, V., 1986a, Cysteine proteinase inhibitors of the cystatin superfamily, in: “Proteinase Inhibitors”, A.J. Barrett and G. Salvesen, eds., Elsevier, Amsterdam, pp. 301–336.
Barrett, A.J., Fritz, H., Müller-Esterl, W., Grubb, A., Isemura, S., Järvinen, M., Katunuma, N., Machleidt, W., Sasaki, M. and Turk, V., 1986b, Nomenclature and classification of the proteins homologous with the cysteine proteinase inhibitor chicken cystatin, in: “Cysteine Proteinases and Their Inhibitors”, V. Turk, ed., Walter de Gruyter, Berlin, pp. 1–2.
Baumann, U., Huber, R., Bode, W., Grosse, D., Lesjak, M. and Laurell, C.-B., 1991, Crystal structure of cleaved α-1-antichymotrypsin at 2.7Å resolution and its comparison with other serpins, J. Mol. Biol. 218: 595–606.
Baumann, U., Bode, W., Huber, R., Travis, J. and Potempa, J., 1992, Crystal structure of cleaved equine leukocyte elastase inhibitor determined at 1.95Å resolution, J. Mol. Biol. 226: 1207–1218.
Birk, Y., 1985, The Bowman-Birk inhibitor: Trypsin-and chymotrypsin-inhibitor from soybeans, Int. J. Peptide Protein Res. 25: 113–131.
Blundell, T.L. and Humbel, R.E., 1980, Hormone families: pancreatic hormones and homologous growth factors, Nature 287: 781–787.
Bode, W., Engh, R., Musil, D., Laber, B., Stubbs, M., Huber, R. and Turk, V., 1990, Mechanism of interaction of cysteine proteinases and their protein inhibitors as compared to the serine proteinaseinhibitor interaction, Biol. Chem. Hoppe-Seyler 371S: 111–118.
Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikov, A., Brzin, J., Kos, J. and Turk, V., 1988, The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases, EMBO J. 7: 2593–2599.
Bode, W., Musil, D., Engh, R., Huber, R., Brzin, J., Kos, J. and Turk, V., 1989, The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its probable interaction with papain, in: “Intracellular Proteolysis: Mechanisms and Regulations,” N. Katanuma and E. Kominami, eds., Japan Scientific Societies Press, Tokyo, pp. 297–304.
Bode, W. and Huber, R., 1992, Natural protein proteinase inhibitors and their interaction with proteinases, Eur. J. Biochem 204: 433–451.
Björk, I., Nordling, K., Larsson, I. and Olson, S.T., 1992, Kinetic characterization of the substrate reaction between a complex of antithrombin with a synthetic reactive-bond loop tetradecapeptide and four target proteinases of the inhibitor, J. Biol. Chem. 267: 19047–19050.
Bürgi, H.B., Dunitz, J.D. and Shefter, E., 1973, Geometrical reaction coordinates: II. Nucleophilic addition to a carbonyl group, J. Am. Chem. Soc. 95: 5065–5067.
Carrell, R.W. and Travis, J., 1985, α-1-antitrypsin and the serpins: variation and countervariation, Trends Biochem. Sci. 10: 20–24.
Chazin, W.J., Hugli, T.E. and Wright, P.E., 1988, Biochemistry27: 9139–9148.
Chen, P., Rose, J., Love, R., Wei, C.H. and Wang, B., 1992, Reactive sites of an anticarcinogenic Bowman-Birk proteinase inhibitor are similar to other trypsin inhibitors, J. Biol. Chem. 267: 1990–1994.
Crystal, R. G., 1991, α-1-antitrypsin deficiency, emphysema, and liver disease, J. Clin. Invest. 85: 1343–1352.
Declerck, P.J., DeMol, M., Alessi, M.-C., Baudner, S., Paques, E.-P., Preissner, K.T., Müller-Berghaus, G. and Collen, D., 1988, Purification and characterization of a plasminogen activator inhibitor 1 binding protein from human plasma. Identification as a multimeric form of S protein (vitronectin), J. Biol. Chem. 263: 15454–15461.
Dieckmann, T., Mitschang, L., Hofmann, M., Kos, J., Turk, V., Auerswald, E.A., Jaenicke, R. and Oschkinat, H., 1994, The structures of native phosphorylated chicken cystatin and of a recombinant unphosphorylated variant in solution, J. Mol. Biol., in press.
Engh, R.A., Wright, H.T. and Huber, R., 1990, Modelling the intact form of the α-1-proteinase inhibitor, Protein Eng. 3: 469–477.
Engh, R.A., Dieckmann, T., Bode, W., Auerswald, E., Turk, V., Huber, R. and Oschkinat, H., 1994, Conformational variability of chicken cystatin: comparison of structures determined by X-ray diffraction and NMR spectroscopy, J. Mol. Biol., in press.
Engh, R.A., Löbermann, H., Schneider, M., Wiegand, G., Huber, R. and Laurell, C.-B., 1989, The S-variant of human α-1-antitrypsin, structure and implication for function and mutations, Prot. Eng. 2: 407–415.
Enghild, J.J., Valnickova, Z., Thogersen, I.B., Pizzo, S.V., and Salvesen, G., 1993, An examination of the inhibitory mechanism of serpins by analysing the interaction of trypsin and chymotrypsin with α2-antiplasmin, Biochem. J. 291: 933–938.
Evans, D.L.I, Marshall, C.J., Christey, P.B. and Carrell, R.W., 1992, Heparin binding site, conformational change, and activation of antithrombin, Biochemistry 31: 12629–12642.
Gettins, P., 1989, Absence of large scale conformational change upon limited proteolysis of ovalbumin, the prototypic serpin, J. Biol. Chem. 264: 3781–3785.
Hekman, C.M. and Loskutoff, D.J., 1985, Endothelial cells produce a latent inhibitor of plasminogen activators that can be activated by denaturation, J. Biol. Chem. 260: 11581–11587.
Herz, J., Clouthier, D.E. and Hammer, R.E., 1992, LDL-receptor related protein internalizes and degrades uPA-PAI-1 complexes and is essential for embryo implantation, Cell 71: 411–421.
Huber, R., Kukla, D., Bode, W., Schwager, P., Bartels, K., Deisenhofer, J. and Steigemann, W., 1974, Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9Å resolution, J. Mol. Biol. 89: 73–101.
Huber, R. and Bode, W., 1978, Structural basis of the activation and action of trypsin, Acc. Chem. Res. 11: 114–122.
Huber, R. and Carrell. R.W., 1989, Implications of the three-dimensional structure of α-1-antitrypsin for structure and function of serpins, Biochemistry 28: 8951–8966.
Huber, R., Scholze, H., Pâques, E.P., and Deisenhofer, J., 1980, Crystal structure analysis and molecular model of human C3a anaphylatoxin, Hoppe-Seyler’s Z. Physiol Chem. 361: 1389–1399.
Hunt L.T. and Dayhoff, M.O., 1980, A surprising new protein superfamily containing ovalbumin, antithrombin III and alpha-1-proteinase inhibitor, Biochem. Biophys. Res. Commun. 95: 864–871.
Ikenaka, T. and Norioka, S., 1986, Bowman-Birk family serine proteinase inhibitors, in: “Proteinase Inhibitors”, A. J. Barrett and G. Salvesen, eds., Elsevier, Amsterdam, pp. 361–374.
Imber, M.J. and Pizzo, S.V., 1981, Clearance and binding of two electrophoretic “fast” forms of human α-2-macroglobulin, J. Biol. Chem. 256: 8134–8139.
Joslin, G., Fallon, R.J., Bullock, J., Adams, S. and Perlmutter, D.H., 1991, The SEC-receptor recognizes a pentapeptide neodomain of α-1-antitrypsin-proteinase complex, J. Biol. Chem. 266: 11282–11288.
Joslin, G., Griffin, G.L., August, A.M., Adams, S., Fallon, R.J., Senior, R.M. and Perlmutter, D.H., 1992, The serpin-enzyme complex (SEC) receptor mediates the neutrophil chemotactic effect of α-1-antitrypsin-elastase complex and amyloid b peptide, J. Clin. Invest. 90: 1150–1154.
Joslin, G., Wittwer, A., Adams, S., Tollefsen, D.M., August, A. Perlmutter, D.H., 1993, Cross competition for binding of α-1-antitrypsin (alAT)-elastase complexes to serpin-enzyme complex receptor by other serpin enzyme complexes and by proteolytically modified α-1-AT*, J. Biol. Chem. 268: 1886–1893.
Laskowski, J.M. and Kato, I., 1980, Protein inhibitors of proteinases, Ann. Rev. Biochem. 49: 593–626.
Laskowski, M., Jr., Kato, I., Ardelt, W., Cook, J., Denton, A. Empie, M.W., Kohr, W.J., Park, S.J., Parks, K., Schatzley, B.L. Schoenberger, O.L., Tashiro, M., Vichot, G., Whatley, H.E. Wieczorek, A. and Wieczorek, M., 1987, Ovomucoid Third Domains from 100 Avian Species: Isolation, Sequences, and Hypervariability of Enzyme-Inhibitor Contact Residues, Biochemistry 26: 202–221.
Lawson, C.L., Zhang, R., Schevitz, R.W., Otwinowski, Z., Joachimiak, A. and Sigler, P.B., 1988, Flexibility of the DNA-binding domains of tip repressor, Proteins: Str., Fun., and Gen. 3: 18–31.
Lin. G., Bode, W., Huber, R. Chi, C. and Engh, R.A., 1993, The 0.25-nm X-ray structure of the Bowman-Birk type inhibitor from mung bean in ternary complex with porcine trypsin, Eur. J. Biochem. 212: 549–555.
Löbermann, H., Tokuoka, R., Deisenhofer, J. and Huber, R., 1984, Human α-1 Proteinase inhibitor. Crystal structure analysis of two modifications. Molecular model and preliminary analysis of the implications for function, J. Mol. Biol. 177: 531–556.
Machleidt, M., Thiele, U., Laber, B., Assfalg-Machleidt, I., Esteri, A., Wiegand, G., Kos, J., Turk, V. and Bode, W., 1989, Mechanism of inhibition of papain by chicken egg white cystatin. Inhibition constants of N-terminally truncated forms and cyanogen bromide fragments of the inhibitor FEBS Lett. 243: 234–238.
Marquardt, M., Walter, J., Deisenhofer, J., Bode, W. and Huber, R., 1983, The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen, and its complexes with inhibitors, Acta Crystallogr. B39: 480–490.
Mast, A.E., Enghild, J.J. and Pizzo, S.V., 1991, Analysis of the plasma elimination kinetics and conformational stabilities ornative, proteinase complexed and reactive site cleaved serpins: comparison of α-1-proteinase inhibitor, α1-antichymotrypsin, antithrombin III, α-2-antiplasmin, angiotensinogen and ovalbumin. Biochemistry 30: 1225–1230.
Mast, A.E., Enghild, J.J. and Salvesen, G., 1992, Conformation of the reactive site loop of α-1-Proteinase Inhibitor probed by limited proteolysis, Biochemistry 31: 2720–2728.
Mimuro, J. and Loskutoff, D.J., 1989a, Binding of type 1 plasminogen activator inhibitor to the extracellular matrix of cultured bovine endothelial cells, J. Biol. Chem. 264: 5058–5063.
Mimuro, J. and Loskutoff, D.J., 1989b, Purification of a protein from bovine plasma that binds to type 1 plasminogen-activator inhibitor and prevents its interaction with extracellular-matrix-evidence that the protein is vitronectin, J. Biol. Chem. 264: 936–939.
Mottonen, J., Strand, A., Symersky, J., Sweet, R.M., Danley, D.E., Geoghehan, K.F., Gerard, R.D. and Goldsmith, E.J., 1992, Structural basis of latency in plasminogen activator inhibitor-1, Nature 355: 270–273.
Murzin, A.G., 1993, Sweet-tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors, J. Mol. Biol. 230: 689–694.
Nykjaer, A., Petersen, CM., Moller, J., Jensen, P.H., Moestrup, S.K., Holtet, T.L., Etzrodt, M., Thogersen, H.C., Munch, M., Andreasen, P.A. and Gliemann, J., 1992, Purified α-2Macroglobulin receptor/LDL receptor-related protein binds urokinase-plasminogen activator inhibitor type-1 complexes, J. Biol. Chem. 267: 14543–14546.
Odani, S. and Ikenaka, T., 1973, Studies on soybean trypsin inhibitors: VIII. Disulfide bridges in soybean Bowman-Birk inhibitor, J. Biochem. 74: 697–715.
Owen, M.C., Brennan, S.O., Lewis, J.H. and Carrell, R.W., 1983, Mutation of antitrypsin to antithrombin. Antitrypsin Pittsburgh (358Met-Arg), a fatal bleeding disorder, N. Engl. J. Med. 309: 694–698.
Pizzo, S.V., 1989, Serpin receptor 1. a hepatic receptor that mediates the clearance of antithrombin III-proteinase complexes, Amer. J. Med. 87 3B: 10S–13S.
Podack, E-R., Dahlböck, B. and Griffin, J.H., 1986, Interaction of S-protein of complement with thrombin and antithrombin III during coagulation. Protection of thrombin by S-protein from antithrombin III inactivation, J. Biol. Chem. 261: 7387–7392.
Potempa, J., Shieh, B.-H. and Travis, J., 1988, Alpha-2-antiplasmin: A serpin with two separate but overlapping reactive sites, Science 241: 699–700.
Pratt, C.W. and Church, C., 1992, Heparin binding to protein C inhibitor, J. Biol. Chem. 267: 8783–8794.
Pratt, C.W., Whinna, H.C. and Church, C., 1992, A comparison of the heparin binding serine proteinase inhibitors, J. Biol. Chem. 267: 8795–8801.
Preissner, K.T., Wassmuth, R. and Müller-Berghaus, G., 1985, Physicochemical characterisation of human S-protein and its function in the blood coagulation system, Biochem. J. 231: 349–355.
Preissner, K.T., 1991, Structure and biological role of vitronectin, Annu. Rev. Cell Biol. 7: 275–310.
Priestle, J.P., 1988, Ribbon: A stereo cartoon drawing program for proteins, J. Appl. Cryst. 21: 572–576.
Rawlings, N.D. and Barrett, A.J., 1990, Evolution of proteins of the cystatin superfamily, J. Mol. Evol. 30: 60–71.
Read, R. and James, M.N.G., 1986, Introduction to the protein inhibitors: X-ray crystallography, in: “Proteinase Inhibitors”, A. J. Barrett and G. Salvesen, eds., Elsevier, Amsterdam, pp. 301–336.
Richardson, J.S., 1981, The Anatomy and Taxonomy of Protein Structure, Adv. Protein Chem. 34: 167–339.
Rühlmann, A., Kukla, D., Schwager, P., Bartels, K. and Huber, R., 1973, Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor: Crystal structure determination and stereochemistry of the contact region, J. Mol. Biol. 77: 417–436.
Saitoh, E., Isemura, S., Sanada, K. and Ohnishi, K., 1991, Cystatins of family II are harboring two domains which retain inhibitory activities against the proteinases, Biochem. Biophys. Res. Comm. 175: 1070–1075.
Salonen, E.-M., Vaheri, A., Pöllänen, J., Stephens, R. and Andreasen, P., 1989, Interaction of plasminogen activator inhibitor (PAI-1) with vitronectin, J. Biol. Chem. 264: 6339–6343.
Schapira, M. and Patston, P.A., 1991, Serine protease inhibitors (Serpins), Trends Card. Med. 1: 146–151.
Schevitz, R.W., Otwinowski, Z., Joachimiak, A., Lawson, C.L. and Sigler, P.B., 1985, The three-dimensional structure of trp repressor, Nature 317: 782–786.
Schreuder, H., deBoer, H., Pronk, S., Hol., W., Dijkema, R., Moulders, J. and Theunissen, H., 1993, Crystallization and preliminary X-ray analysis of human antithrombin III, J. Mol. Biol. 229: 249–250.
Schulze, A.J., Baumann, U., Knof, S., Jäger, E., Huber, R. and Laurell, C.-B., 1990, Structural transition of α-1-antitrypsin by a peptide sequentially similar to β-strand s4A, Eur. J. Biochem. 194: 51–56.
Schulze A. J., Huber, R., Degryse, E., Speck, D. and Bischoff, R., 1991, Inhibitory activity and conformational changes in α-1-proteinase inhibitor variants, Eur. J. Biochem. 202: 1147–1155.
Schulze, A.J., Frohnert, P.W., Engh, R.A. and Huber, R., 1992, Evidence for the extent of insertion of the active site loop of intact α-1-Proteinase Inhibitor in β-sheet A., Biochemistry 31: 7560–7565.
Schulze, A. J., 1993, Untersuchungen zur Struktur und Funktion von Serinproteinase Inhibitoren und Serinproteinasen, PhD Thesis, Technische Universität München.
Seiffert, D. and Loskutoff, D.J., 1991, Kinetic analysis of the interaction between type-1 plasminogen activator inhibitor and vitronectin and evidence that the bovine inhibitor binds to a thrombinderived aminoterminal fragment of bovine vitronectin, Biochem. Biophys. Acta 1078: 2223–2230.
Skriver, K., Wikoff, W.R., Patson, P.A., Tausk, F., Schapira, M., Kaplan, A.P., and Bock, C.S., 1991, Substrate properties of C1 inhibitor Ma (alanine 434→glutamic acid), J. Biol. Chem. 266: 9216–9221.
Stein, P.E. and Chothia, C., 1991, Serpin tertiary structure transformation, J. Mol. Biol. 221: 615–621.
Stein, P.E., Tewkesbury, C. and Carrell., R.W., 1989, Ovalbumin and angiotensinogen lack serpin S-R conformational change, Biochem. J. 262: 103–107.
Stein, P.E., Leslie, A.J., Finch, J.T., Turnell, W.G., McLaughlin, P.J. and Carrell, R.W., 1990, Crystal structure of ovalbumin as a model for the reactive centre of serpins, Nature 347: 99–102.
Stubbs, M. T., Laber, B., Bode, W., Huber, R., Jerala, R., Lenarcic, B., Turk, V., 1990, The refined 2.4 Å X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction, EMBO J. 9, 1939–1947.
Sweet, R.M., Wright, H.T., Janin, J., Chothia, C.H. and Blow, D.M., 1974, Crystal structure of the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6 Å resolution, Biochemistry 13: 4212–4228.
Suzuki, A., Tsunogae, Y., Tanaka, I., Yamane, T., Ashida, T., Norioka, S., Hara, S. and Ikenaka, T., 1987, The structure of Bowman-Birk type protease inhibitor A-II from peanut (Arachis hypogaea) at 3.3 Å resolution, J. Biochem. 101: 267–274.
Travis, A.J. and Salvesen, G., 1983, Plasma proteinase inhibitors, Annu. Rev. Biochem. 52: 655–709.
Tsunogae, Y., Tanaka, I., Yamane, T., Kikkawa, J., Ashida, T., Ishikawa, C. and Takahashi, K., 1986, Structure of the trypsin-binding domain of Bowman-Birk type protease inhibitor and its interaction with trypsin, J. Biochem. 100: 1637–1646.
Turk, V. and Bode, W., 1991, The cystatins: protein inhibitors of cysteine proteinases, FEBS Lett. 285: 213–219.
Turk, V., Brzin, J., Lenarcic, B., Locnikar, P., Popovic, T., Ritonja, A., Babnik, J., Bode, W. and Machleidt, W., 1985, in: “Intracellular Protein Catabolism V,” E. Khairallah and J. Bond, eds., Alan R. Liss, New York, pp. 91–103.
Wardell, M.R., Abrahams, J.-P., Bruce, D., Skinner, R. and Leslie, A.G.W., 1993, Crystallization and Preliminary X-ray Diffraction Analysis of Two Conformations of Intact Human Antithrombin, J. Mol. Biol., in press.
Werner, M.H. and Wemmer, D.E., 1992, Three-dimensional structure of soybean trypsin/chymotrypsin Bowman-Birk inhibitor in solution, Biochemistry 31: 999–1010.
Wei, A., Rubin, H., Cooperman, B.S., Schechter, N. and Christianson, D.W., 1992, Crystallization, activity assay and preliminary X-ray diffraction analysis of the uncleaved serpin antichymotrypsin, J. Mol. Biol. 226: 273–276.
Wiman, B., Almquist, A., Sigurdardottir, O. and Lindahl, T., 1988, Plasminogen activator inhibitor 1 (PAI-1) is bound to vitronectin in plasma, FEBS Lett. 242: 125–128.
Wright, T., Qian, H.-X. and Huber, R., 1990, Crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin. Its relationship to the structure of cleaved alpha-1-antitrypsin, J. Mol. Biol. 213: 513–528.
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Engh, R.A., Huber, R., Bode, W. (1994). Multiple Conformations of Cystatin, Mung Bean Inhibitor, and Serpins. In: Doniach, S. (eds) Statistical Mechanics, Protein Structure, and Protein Substrate Interactions. NATO ASI Series, vol 325. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1349-4_30
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