Skip to main content

Chemical Reaction Engineering to Understand Applied Kinetics in Free Enzyme Homogeneous Reactors

  • Protocol
  • First Online:
Enzyme Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2397))

Abstract

Chemical reaction engineering is interested in elucidating the reaction kinetics through the determination of the fundamental influencing variables. The understanding of enzyme kinetics is needed to implement the potential of enzymes to satisfy determined production targets and for the design of the reactor. The quantification of the enzyme kinetics is implemented by the elucidation and building of the kinetic model (it includes one or more kinetic equations). In the context of process development, the kinetic model is not only useful to identify feasibility and for optimizing reaction conditions but also, at an early stage of development it is very useful to anticipate implementation bottlenecks, and so guide reactor setup. In this chapter we describe theoretical and practical considerations to illustrate the methodological framework of kinetic analysis. We take as study cases four archetypal kinetic cases by using as example the hydrolysis of cellobiose catalyzed by a beta-glucosidase. We show the different experimental data that can be obtained by the monitoring of enzymatic reactions in different configuration of free enzyme homogeneous ideal reactors; we show step-by-step the visualization, treatment, and analysis of data to elucidate kinetic models and the procedure for the quantification of kinetic constants. Finally, the performance of different reactors is compared in the interplay with the enzyme kinetics. This book chapter aims at being useful for a broad multidisciplinary audience and different levels of academic development.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Sheldon RA, Woodley JM (2018) Role of biocatalysis in sustainable chemistry. Chem Rev 118:801–838

    Article  CAS  Google Scholar 

  2. Sheldon RA, Brady D (2019) Broadening the scope of biocatalysis in sustainable organic synthesis. ChemSusChem 12:2859–2881

    Article  CAS  Google Scholar 

  3. Woodley JM (2020) New frontiers in biocatalysis for sustainable synthesis. Curr Opin Green Sustain Chem 21:22–26

    Article  Google Scholar 

  4. Illanes A (2008) Enzyme biocatalysis. Principles and applications. Springer, Dordrecht

    Book  Google Scholar 

  5. Illanes A, Wilson L, Vera C (2013) Problem solving in enzyme biocatalysis. Willey

    Book  Google Scholar 

  6. Guisan JM, Lopez-Gallego F, Bolivar JM, Rocha-Martin J, Fernandez-Lorente G (2020) The science of enzyme immobilization. Methods Mol Biol 2100:1–26

    Article  CAS  Google Scholar 

  7. Sheldon RAA, Brady D, Bode MLL (2020) The Hitchhiker’s guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. Chem Sci 11:2587–2605

    Article  Google Scholar 

  8. Bornscheuer UT (2018) The fourth wave of biocatalysis is approaching. Philos Trans R Soc A Math Phys Eng Sci 376:7

    Google Scholar 

  9. Illanes A, Wilson L, Vera C (2018) Technical biocatalysis. In: Williams G, Hall M (eds) Modern biocatalysis: advances towards synthetic biological systems, vol 32. RSC Catalysis Series, pp 475–515

    Google Scholar 

  10. Buchholz K, Kasche V, Bornscheuer UT (2012) Biocatalysts and enzyme technology. Wiley

    Google Scholar 

  11. Basso A, Serban S (2020) Overview of immobilized enzymes’ applications in pharmaceutical, chemical, and food industry. Methods Mol Biol 2100:27–63

    Article  CAS  Google Scholar 

  12. Levenspiel O (1999) Chemical reaction engineering. Ind Eng Chem Res 38(11):4140–4143

    Article  CAS  Google Scholar 

  13. Woodley JM (2019) Reaction engineering for the industrial implementation of biocatalysis. Top Catal 62(17–20):1202–1207. https://doi.org/10.1007/s11244-019-01154-5

    Article  CAS  Google Scholar 

  14. Illanes A, Cauerhff A, Wilson L, Castro GR (2012) Recent trends in biocatalysis engineering. Bioresour Technol 115:48–57. https://doi.org/10.1016/j.biortech.2011.12.050

    Article  CAS  PubMed  Google Scholar 

  15. Doran PM (2013) Chapter 12—homogeneous reactions. In: Bioprocess engineering principles, 2nd edn. Academic, pp 599–703

    Chapter  Google Scholar 

  16. Al-Haque N, Santacoloma PA, Neto W, Tufvesson P, Gani R, Woodley JM (2012) A robust methodology for kinetic model parameter estimation for biocatalytic reactions. Biotechnol Prog 28(5):1186–1196. https://doi.org/10.1002/btpr.1588

    Article  CAS  PubMed  Google Scholar 

  17. Dias Gomes M, Woodley JM (2019) Considerations when measuring biocatalyst performance. Molecules 24(19). https://doi.org/10.3390/molecules24193573

  18. Nordblad M, Gomes MD, Meissner MP, Ramesh H, Woodley JM (2018) Scoping biocatalyst performance using reaction trajectory analysis. Org Process Res Dev 22(9):1101–1114. https://doi.org/10.1021/acs.oprd.8b00119

    Article  CAS  Google Scholar 

  19. Blackmond DG (2005) Reaction progress kinetic analysis: a powerful methodology for mechanistic studies of complex catalytic reactions. Angew Chem Int Ed Engl 44(28):4302–4320. https://doi.org/10.1002/anie.200462544

    Article  CAS  PubMed  Google Scholar 

  20. Sin G, Woodley JA, Gernaey KV (2009) Application of modeling and simulation tools for the evaluation of biocatalytic processes: a future perspective. Biotechnol Prog 25(6):1529–1538. https://doi.org/10.1002/btpr.276

    Article  CAS  PubMed  Google Scholar 

  21. Dunn IJ, Heinzle E, Ingham J, Prenosil JE (2003) Biological reaction engineering. Wiley

    Book  Google Scholar 

  22. Fernandes RL, Bodla VK, Carlquist M, Heins A-L, Lantz AE, Sin G, Gernaey KV (2013) Applying mechanistic models in bioprocess development. In: Mandenius CF, TitchenerHooker NJ (eds) Measurement, monitoring, modelling and control of bioprocesses, Advances in biochemical engineering-biotechnology, vol 132. Springer, pp 137–166

    Chapter  Google Scholar 

  23. Halling PJ (2020) Estimation of initial rate from discontinuous progress data. Biocatal Biotransformation 38(5):325–342. https://doi.org/10.1080/10242422.2020.1746771

    Article  CAS  Google Scholar 

  24. Duggleby RG (2001) Quantitative analysis of the time courses of enzyme-catalyzed reactions. Methods 24(2):168–174. https://doi.org/10.1006/meth.2001.1177

    Article  CAS  PubMed  Google Scholar 

  25. Zavrel M, Kochanowski K, Spiess AC (2010) Comparison of different approaches and computer programs for progress curve analysis of enzyme kinetics. Eng Life Sci 10(3):191–200. https://doi.org/10.1002/elsc.200900083

    Article  CAS  Google Scholar 

  26. Illanes A, Altamirano C, Wilson L (2008) Homogeneous enzyme kinetics. In: Enzyme biocatalysis. Springer, pp 107–153

    Chapter  Google Scholar 

  27. Illanes A (2013) Enzyme kinetics in a homogeneous system. Problem solving in enzyme biocatalysis, Wiley, In, pp 11–86

    Google Scholar 

  28. Valencia PL, Astudillo-Castro C, Gajardo D, Flores S (2017) Application of the median method to estimate the kinetic constants of the substrate uncompetitive inhibition equation. J Theor Biol 418:122–128. https://doi.org/10.1016/j.jtbi.2017.01.033

    Article  CAS  PubMed  Google Scholar 

  29. Valencia PL, Astudillo-Castro C, Gajardo D, Flores S (2017) Calculation of statistic estimates of kinetic parameters from substrate uncompetitive inhibition equation using the median method. Data Brief 11:567–571. https://doi.org/10.1016/j.dib.2017.03.013

    Article  PubMed  PubMed Central  Google Scholar 

  30. Valencia PL, Sepulveda B, Gajardo D, Astudillo-Castro C (2020) Estimating the product inhibition constant from enzyme kinetic equations using the direct linear plot method in one-stage treatment. Catalysts 10(8). https://doi.org/10.3390/catal10080853

  31. Cornish-Bowden A (1979) Chapter 10—estimation of kinetic constants. In: Cornish-Bowden A (ed) Fundamentals of enzyme kinetics. Butterworth-Heinemann, pp 200–211

    Chapter  Google Scholar 

  32. Cornish-Bowden A (2001) Detection of errors of interpretation in experiments in enzyme kinetics. Methods 24(2):181–190. https://doi.org/10.1006/meth.2001.1179

    Article  CAS  PubMed  Google Scholar 

  33. Ohs R, Wendlandt J, Spiess AC (2017) How graphical analysis helps interpreting optimal experimental designs for nonlinear enzyme kinetic models. AICHE J 63(11):4870–4880. https://doi.org/10.1002/aic.15814

    Article  CAS  Google Scholar 

  34. Pinto MF, Baici A, Pereira PJB, Macedo-Ribeiro S, Pastore A, Rocha F, Martins PM (2020) interferENZY: a web-based tool for enzymatic assay validation and standardized kinetic analysis. J Mol Biol. https://doi.org/10.1016/j.jmb.2020.07.025

  35. Olp MD, Kalous KS, Smith BC (2020) ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces. BMC Bioinformatics 21(1):186. https://doi.org/10.1186/s12859-020-3513-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Lindeque R, Woodley J (2019) Reactor selection for effective continuous biocatalytic production of pharmaceuticals. Catalysts 9(3). https://doi.org/10.3390/catal9030262

  37. Illanes A, Altamirano C (2008) Enzyme reactors. Springer, pp 205–251

    Google Scholar 

  38. Sharma B, Larroche C, Dussap CG (2020) Comprehensive assessment of 2G bioethanol production. Bioresour Technol 313:123630. https://doi.org/10.1016/j.biortech.2020.123630

    Article  CAS  PubMed  Google Scholar 

  39. Su T, Zhao D, Khodadadi M, Len C (2020) Lignocellulosic biomass for bioethanol: recent advances, technology trends, and barriers to industrial development. Curr Opin Green Sustain Chem 24:56–60. https://doi.org/10.1016/j.cogsc.2020.04.005

    Article  Google Scholar 

  40. Chundawat SPS, Beckham GT, Himmel ME, Dale BE (2011) Deconstruction of lignocellulosic biomass to fuels and chemicals. In: Prausnitz JM (ed) Annual review of chemical and biomolecular engineering, vol 2. Annual Reviews, Palo Alto, pp 121–145

    Google Scholar 

  41. Sorensen A, Lubeck M, Lubeck PS, Ahring BK (2013) Fungal beta-glucosidases: a bottleneck in industrial use of lignocellulosic materials. Biomol Ther 3(3):612–631. https://doi.org/10.3390/biom3030612

    Article  CAS  Google Scholar 

  42. Saldarriaga-Hernandez S, Velasco-Ayala C, Leal-Isla Flores P, de Jesus Rostro-Alanis M, Parra-Saldivar R, Iqbal HMN, Carrillo-Nieves D (2020) Biotransformation of lignocellulosic biomass into industrially relevant products with the aid of fungi-derived lignocellulolytic enzymes. Int J Biol Macromol 161:1099–1116. https://doi.org/10.1016/j.ijbiomac.2020.06.047

    Article  CAS  PubMed  Google Scholar 

  43. Wojtusik M, Yepes CM, Villar JC, Cordes A, Arroyo M, Garcia-Ochoa F, Ladero M (2018) Kinetic modeling of cellobiose by a β-glucosidase from Aspergillus fumigatus. Chem Eng Res Des 136:502–512. https://doi.org/10.1016/j.cherd.2018.06.020

    Article  CAS  Google Scholar 

  44. Josephson K (1925) Enzymatic fission of glucosides. On the mode of action of beta-glucosidase of emulsin. Hoppe Seylers Z Physiol Chem 147:1–154. https://doi.org/10.1515/bchm2.1925.147.1-6.1

    Article  CAS  Google Scholar 

  45. Ionescu CN, Kizyk A (1936) Kinetics of the beta-glucosidase-effect. Ber Dtsch Chem Ges 69:592–597. https://doi.org/10.1002/cber.19360690324

    Article  Google Scholar 

  46. Cornish-Bowden A (2013) Fundamentals of enzyme kinetics. Wiley

    Google Scholar 

  47. Hong J, Ladisch MR, Gong CS, Wankat PC, Tsao GT (1981) Combined product and substrate-inhibition equation for cellobiase. Biotechnol Bioeng 23(12):2779–2788. https://doi.org/10.1002/bit.260231212

    Article  CAS  Google Scholar 

  48. Bravo V, Paez MP, Aoulad M, Reyes A, Garcia AI (2001) The influence of pH upon the kinetic parameters of the enzymatic hydrolysis of cellobiose with Novozym 188. Biotechnol Prog 17(1):104–109. https://doi.org/10.1021/bp000142x

    Article  CAS  PubMed  Google Scholar 

  49. Corazza FC, Calsavara LPV, Moraes FF, Zanin GM, Neitzel I (2005) Determination of inhibition in the enzymatic hydrolysis of cellobiose using hybrid neural modeling. Braz J Chem Eng 22(1):19–29. https://doi.org/10.1590/s0104-66322005000100003

    Article  CAS  Google Scholar 

  50. Wang GS, Post WM, Mayes MA, Frerichs JT, Sindhu J (2012) Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics. Soil Biol Biochem 48:28–38. https://doi.org/10.1016/j.soilbio.2012.01.011

    Article  CAS  Google Scholar 

  51. Resa P, Buckin V (2011) Ultrasonic analysis of kinetic mechanism of hydrolysis of cellobiose by beta-glucosidase. Anal Biochem 415(1):1–11. https://doi.org/10.1016/j.ab.2011.03.003

    Article  CAS  PubMed  Google Scholar 

  52. Wojtusik M, Vergara P, Villar JC, Garcia-Ochoa F, Ladero M (2019) Thermal and operational deactivation of Aspergillus fumigatus beta-glucosidase in ethanol/water pretreated wheat straw enzymatic hydrolysis. J Biotechnol 292:32–38. https://doi.org/10.1016/j.jbiotec.2019.01.009

    Article  CAS  PubMed  Google Scholar 

  53. Dunn IJ, Heinzle E, Prenosil JE, Snape J (2007) Chemical engineering dynamics: an introduction to modelling and computer simulation. Wiley VCH

    Google Scholar 

  54. Berkeley Madonna (2009) https://berkeley-madonna.myshopify.com/

Download references

Acknowledgments

Alvaro Lorente-Arevalo and Alberto Garcia-Martin contributed equally to this work.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Miguel Ladero or Juan M. Bolivar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Lorente-Arevalo, A., Garcia-Martin, A., Ladero, M., Bolivar, J.M. (2022). Chemical Reaction Engineering to Understand Applied Kinetics in Free Enzyme Homogeneous Reactors. In: Magnani, F., Marabelli, C., Paradisi, F. (eds) Enzyme Engineering. Methods in Molecular Biology, vol 2397. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1826-4_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1826-4_15

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1825-7

  • Online ISBN: 978-1-0716-1826-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics