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Kinetics of the Interaction of Peptidases with Substrates and Modifiers

  • Antonio BaiciEmail author
  • Marko Novinec
  • Brigita Lenarčič
Chapter

Abstract

This chapter is dedicated to reviewing, commenting and illustrating with examples kinetic tools that are essential to the study of peptidases interacting with their substrates, inhibitors and activators. Kinetic characterization starts with the measurement of the kinetic parameters for substrates using graphical and mathematical methods because this information is essential for further characterizing the action of modifiers. The bulk of the chapter is dedicated to the description of the properties and mechanisms of classical, tight binding and slow onset reversible inhibition, as well as to enzyme inactivation. The reader may notice that some beloved, ‘classical’ kinetic methods are not mentioned in this chapter. With all due respect for the past, we believe that modern methods, such as numerical integration of differential equations and robust statistical approaches, can reasonably replace less powerful investigation tools.

Keywords

Progress Curve Reactive Center Loop Peptide Bond Hydrolysis Individual Rate Constant Active Site Concentration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Auld DS (2004) Catalytic mechanisms for metallopeptidases. In: Barrett AJ, Rawlings ND, Woessner JF Jr (eds) Aspartic and metallo peptidases, vol 1, Handbook of proteolytic enzymes. Elsevier, London, pp 268–289Google Scholar
  2. Baici A (1981) The specific velocity plot. A graphical method for determining inhibition parameters for both linear and hyperbolic enzyme inhibitors. Eur J Biochem 119:9–14PubMedCrossRefGoogle Scholar
  3. Baici A (1987) Graphical and statistical analysis of hyperbolic, tight-binding inhibition. Biochem J 244:793–796PubMedGoogle Scholar
  4. Baici A (1990) Interaction of human leukocyte elastase with soluble and insoluble protein substrates. A practical kinetic approach. Biochim Biophys Acta 1040:355–364PubMedCrossRefGoogle Scholar
  5. Baici A (1998) Inhibition of extracellular matrix-degrading endopeptidases: problems, comments, and hypotheses. Biol Chem 379:1007–1018PubMedGoogle Scholar
  6. Baici A, Knöpfel M, Fehr K, Skvaril F, Böni A (1980) Kinetics of the different susceptibility of the four human immunoglobulin G subclasses to proteolysis by human lysosomal elastase. Scand J Immunol 12:41–50PubMedCrossRefGoogle Scholar
  7. Baici A, Schenker P, Wächter M, Rüedi P (2009) 3-Fluoro-2,4-dioxa-3-phosphadecalins as inhibitors of acetylcholinesterase. A reappraisal of kinetic mechanisms and diagnostic methods. Chem Biodivers 6:261–282PubMedCrossRefGoogle Scholar
  8. Bartlett PA, Marlowe CK (1987) Possible role for water dissociation in the slow binding of phosphorus-containing transition-state-analogue inhibitors of thermolysin. Biochemistry 26:8553–8561PubMedCrossRefGoogle Scholar
  9. Botts J, Morales M (1953) Analytical description of the effects of modifiers and of enzyme multivalency upon the steady state catalyzed reaction rate. Trans Faraday Soc 49:696–707CrossRefGoogle Scholar
  10. Cha S (1976) Tight-binding inhibitors—III. A new approach for the determination of competition between tight-binding inhibitors and substrates. Inhibition of adenosine deaminase by coformycin. Biochem Pharmacol 25:2695–2702PubMedCrossRefGoogle Scholar
  11. Cha S (1980) Tight-binding inhibitors—VII. Extended interpretation of the rate equation. Experimental designs and statistical methods. Biochem Pharmacol 29:1779–1789PubMedCrossRefGoogle Scholar
  12. Chou T (1974) Relationships between inhibition constants and fractional inhibition in enzyme-catalyzed reactions with different numbers of reactants, different reaction mechanisms, and different types and mechanisms of inhibition. Mol Pharmacol 10:235–247PubMedGoogle Scholar
  13. Cleland WW (1963) The kinetics of enzyme-catalyzed reactions with two or more substrates or products. I. Nomenclature and rate equations. Biochim Biophys Acta 67:104–136PubMedCrossRefGoogle Scholar
  14. Cornish-Bowden A (2004) Fundamentals of enzyme kinetics. Portland Press, LondonGoogle Scholar
  15. Cornish-Bowden A, Eisenthal R (1974) Statistical considerations in the estimation of enzyme kinetic parameters by the direct linear plot and other methods. Biochem J 139:721–730PubMedGoogle Scholar
  16. Cornish-Bowden A, Eisenthal R (1978) Estimation of Michaelis constants and maximum velocity from the direct linear plot. Biochim Biophys Acta 523:268–272PubMedCrossRefGoogle Scholar
  17. Cornish-Bowden A, Porter WR, Trager WF (1978) Evaluation of distribution-free confidence limits for enzyme kinetic parameters. J Theor Biol 74:163–175PubMedCrossRefGoogle Scholar
  18. Cortés A, Cascante M, Cárdenas ML, Cornish-Bowden A (2001) Relationships between inhibition constants, inhibitor concentrations for 50% inhibition and types of inhibition: new ways of analysing data. Biochem J 357:263–268PubMedCrossRefGoogle Scholar
  19. Duggleby RG, Attwood PV, Wallace JC, Keech DB (1982) Avidin is a slow-binding inhibitor of pyruvate carboxylase. Biochemistry 21:3364–3370PubMedCrossRefGoogle Scholar
  20. Eisenthal R, Cornish-Bowden A (1974) The direct linear plot. A new graphical procedure for estimating enzyme kinetic parameters. Biochem J 139:715–720PubMedGoogle Scholar
  21. Eisenthal R, Danson MJ, Hough DW (2007) Catalytic efficiency and k cat/K M: a useful comparator? Trends Biotechnol 25:247–249PubMedCrossRefGoogle Scholar
  22. Fenner G (1931) Das Genauigkeitsmass von Summen, Differenzen, Produkten und Quotienten der Beobachtungsreihen. Naturwissenschaften 19:310CrossRefGoogle Scholar
  23. Fersht A (1977) Enzyme structure and mechanism. Freeman, New YorkGoogle Scholar
  24. Fontes R, Ribeiro JM, Sillero A (2000) Inhibition and activation of enzymes. The effect of a modifier on the reaction rate and on kinetic parameters. Acta Biochim Pol 47:233–257PubMedGoogle Scholar
  25. Frieden C (1970) Kinetic aspects of regulation of metabolic processes. The hysteretic enzyme concept. J Biol Chem 245:5788–5799PubMedGoogle Scholar
  26. Hopkins PCR, Carrell RW, Stone SR (1993) Effects of mutations in the hinge region of serpins. Biochemistry 32:7650–7657PubMedCrossRefGoogle Scholar
  27. International Union of Biochemistry (1979) Units of enzyme activity. Eur J Biochem 97:319–320CrossRefGoogle Scholar
  28. International Union of Biochemistry (1982) Symbolism and terminology in enzyme kinetics. Recommendations 1981. Eur J Biochem 128:281–291Google Scholar
  29. James MNG (2004) Catalytic pathway of aspartic peptidases. In: Barrett AJ, Rawlings ND, Woessner JF Jr (eds) Aspartic and metallo peptidases, vol 1, Handbook of proteolytic enzymes. Elsevier, London, pp 12–19Google Scholar
  30. Johansen G, Lumry R (1961) Statistical analysis of enzymic steady-state rate data. C R Trav Lab Carlsberg 32:185–214PubMedGoogle Scholar
  31. Johnson KA (2009) Fitting enzyme kinetic data with Kintek Global Kinetic Explorer. Methods Enzymol 467:601–626PubMedGoogle Scholar
  32. Johnson KA, Simpson ZB, Blom T (2009a) FitSpace Explorer: an algorithm to evaluate multidimensional parameter space in fitting kinetic data. Anal Biochem 387:30–41PubMedCrossRefGoogle Scholar
  33. Johnson KA, Simpson ZB, Blom T (2009b) Global Kinetic Explorer: a new computer program for dynamic simulation and fitting of kinetic data. Anal Biochem 387:20–29PubMedCrossRefGoogle Scholar
  34. Komiyama T, Ray CA, Pickup DJ, Howard AD, Thornberry NA, Peterson EP, Salvesen G (1994) Inhibition of interleukin-1-β converting-enzyme by the cowpox virus serpin Crma. An example of cross-class inhibition. J Biol Chem 269:19331–19337PubMedGoogle Scholar
  35. Koshland DE (2002) The application and usefulness of the ratio k cat/K m. Bioorg Chem 30:211–213PubMedCrossRefGoogle Scholar
  36. Kuzmič P (2008) A steady state mathematical model for stepwise “slow-binding” reversible enzyme inhibition. Anal Biochem 380:5–12PubMedCrossRefGoogle Scholar
  37. Meh P, Pavšič M, Turk V, Baici A, Lenarčič B (2005) Dual concentration-dependent activity of thyroglobulin type-1 domain of testican: specific inhibitor and substrate of cathepsin L. Biol Chem 386:75–83PubMedCrossRefGoogle Scholar
  38. Morrison JF (1982) The slow-binding and slow, tight-binding inhibition of enzyme-catalysed reactions. Trends Biochem Sci 7:102–105CrossRefGoogle Scholar
  39. Nakajima K, Powers JC, Ashe BM, Zimmerman M (1979) Mapping the extended substrate binding site of cathepsin G and human leukocyte elastase. Studies with peptide substrates related to the α1-protease inhibitor reactive site. J Biol Chem 254:4027–4032PubMedGoogle Scholar
  40. Naqui A (1983) What does I50 mean? Biochem J 215:429–430PubMedGoogle Scholar
  41. Novinec M, Grass RN, Stark WJ, Turk V, Baici A, Lenarčič B (2007) Interaction between human cathepsins K, L and S and elastins: mechanism of elastinolysis and inhibition by macromolecular inhibitors. J Biol Chem 282:7893–7902PubMedCrossRefGoogle Scholar
  42. Novinec M, Kovačič L, Lenarčič B, Baici A (2010) Conformational flexibility and allosteric regulation of cathepsin K. Biochem J 429:379–389PubMedCrossRefGoogle Scholar
  43. Orsi BA, Tipton KF (1979) Kinetic analysis of progress curves. Methods Enzymol 63:159–183PubMedGoogle Scholar
  44. Polgár L (2004a) Catalytic mechanisms of cysteine peptidases. In: Barrett AJ, Rawlings ND, Woessner JF Jr (eds) Cysteine, serine and threonine peptidases, vol 2, Handbook of proteolytic enzymes. Elsevier, London, pp 1072–1079Google Scholar
  45. Polgár L (2004b) Catalytic mechanisms of serine and threonine peptidases. In: Barrett AJ, Rawlings ND, Woessner JF Jr (eds) Cysteine, serine and threonine peptidases, vol 2, Handbook of proteolytic enzymes. Elsevier, London, pp 1440–1448Google Scholar
  46. Rawlings ND, Barrett AJ, Bateman A (2010) MEROPS: the peptidase database. Nucleic Acids Res 38:D227–D233PubMedCentralPubMedCrossRefGoogle Scholar
  47. Schechter I, Berger A (1967) On the size of the active sites in proteases. I. Papain. Biochem Biophys Res Commun 27:157–162PubMedCrossRefGoogle Scholar
  48. Schenker P, Baici A (2009) Simultaneous interaction of enzymes with two modifiers: reappraisal of kinetic models and new paradigms. J Theor Biol 261:318–329PubMedCrossRefGoogle Scholar
  49. Schultz RM, Varma-Nelson P, Ortiz R, Kozlowski KA, Orawski AT, Pagast P, Frankfater A (1989) Active and inactive forms of the transition-state analog protease inhibitor leupeptin: explanation of the observed slow binding of leupeptin to cathepsin B and papain. J Biol Chem 264:1497–1507PubMedGoogle Scholar
  50. Schweizer A, Roschitzki-Voser H, Amstutz P, Briand C, Gulotti-Georgieva M, Prenosil E, Binz HK, Capitani G, Baici A, Plückthun A, Grütter MG (2007) Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism. Structure 15:625–636PubMedCrossRefGoogle Scholar
  51. Segel IH (1975) Enzyme kinetics. Behavior and analysis of rapid equilibrium and steady-state enzyme systems. Wiley, New YorkGoogle Scholar
  52. Selwyn MJ (1965) A simple test for inactivation of an enzyme during assay. Biochim Biophys Acta 105:193–195PubMedGoogle Scholar
  53. Szedlacsek SE, Ostafe V, Serban M, Vlad MO (1988) A re-evaluation of the kinetic equations for hyperbolic tight-binding inhibition. Biochem J 254:311–312PubMedGoogle Scholar
  54. Tallant C, Marrero A, Gomis-Ruth FX (2010) Matrix metalloproteinases: fold and function of their catalytic domains. Biochim Biophys Acta 1803:20–28PubMedCrossRefGoogle Scholar
  55. Topham CM (1990) A generalized theoretical treatment of the kinetics of an enzyme-catalysed reaction in the presence of an unstable irreversible modifier. J Theor Biol 145:547–572PubMedCrossRefGoogle Scholar
  56. Williams JW, Morrison JF, Duggleby RG (1979) Methotrexate, a high-affinity pseudosubstrate of dihydrofolate reductase. Biochemistry 18:2567–2573PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Antonio Baici
    • 1
    Email author
  • Marko Novinec
    • 2
  • Brigita Lenarčič
    • 2
  1. 1.Department of BiochemistryUniversity of ZurichZurichSwitzerland
  2. 2.Department of Chemistry and BiochemistryUniversity of LjubljanaLjubljanaSlovenia

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