Skip to main content

Engineering Tools for Enzymes

  • Chapter
  • First Online:
Fundamentals of Enzyme Engineering
  • 2075 Accesses

Abstract

Since new millennia, application of industrial enzymes in manufacturing process including pharmaceuticals, fine chemicals, bio-based chemicals remarkably gained much attention. There is a fundamental limitation to apply industrial enzymes since enzymes have not been evolved to meet the requirements as biocatalysts.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 139.99
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

References

  • Bornscheuer UT and Pohl M. Improved biocatalysts by directed evolution and rational protein design. Current Opinion in Chemical Biology, 2001, 5:137-143.

    Google Scholar 

  • Crameri A, Raillard SA, Bermudez E and Stemmer WP. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature, 1998, 391:288-291.

    Google Scholar 

  • Eijsink VGH, Bjork A, Gaseidnes S, Sirevag R, Synstad B, Burg B,and Vriend G. Rational engineering of enzyme stability. J. Biotechnology, 2004, 113:105-120.

    Google Scholar 

  • Fox RJ, Davis SC, Mundorff EC, Newman LM, Gavrilovic V, Ma SK, Chung LM, Ching C, Tam S, Muley S, Grate J, Gruber J, Whitman JC, Sheldon RA and Huisman GW. Improving catalytic function by ProSAR-driven enzyme evolution. Nature Biotechnology, 2007, 25:338-344.

    Google Scholar 

  • Greener A, Callahan M and Jerpseth B. An efficient random mutagenesis technique using an E. coli mutator strain. Methods in Molecular Biology, 1996, 57:375-385.

    Google Scholar 

  • Heinis C and Johnsson K. Using peptide loop insertion mutagenesis for the evolution of proteins. Methods in Molecular Biology, 2010, 634:217-232.

    Google Scholar 

  • Heinzelman P, Snow CD, Wu I, Nguyen C, Villalobos A, Govindarajan S, Minshull J and Arnold FH. A family of thermostable fungal cellulases created by structure-guided recombination. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106:5610-5615.

    Google Scholar 

  • Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL and Baker D. De novo computational design of retro-aldol enzymes. Science, 2008, 319:1387-1391.

    Google Scholar 

  • Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas RJ and Bornscheuer UT. Converting an esterase into an epoxide hydrolase. Angewandte Chemie International Edition, 2009, 48:3532-3535.

    Google Scholar 

  • Kazlauskas RJ and Bornscheuer UT. Finding better protein engineering strategies. Nature Chemical Biology, 2009, 5:526-529.

    Google Scholar 

  • Labrou NE. Random Mutagenesis Methods for in vitro directed enzyme evolution. Current Protein and Peptide Science, 2010, 11:91-100.

    Google Scholar 

  • Li B, Yang G, Wu L and Feng Y. Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum. PLoS One, 2012, 7:e46881.

    Google Scholar 

  • Lutz S, Ostermeier M, Moore GL, Maranas CD and Benkovic SJ. Creating multiple-crossover DNA libraries independent of sequence identity. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98:11248-11253.

    Google Scholar 

  • Matsuura T, Miyai K, Trakulnaleamsai S, Yomo T, Shima Y, Miki S, Yamamoto K and Urabe I. Evolutionary molecular engineering by random elongation mutagenesis. Nature Biotechnology, 1999, 17:58-61.

    Google Scholar 

  • Morley KL and Kazlauskas RJ. Improving enzyme properties: when are closer mutations better? Trends in Biotechnology, 2005, 23:231-237.

    Google Scholar 

  • Murakami H, Hohsaka T and Sisido M. Random insertion and deletion mutagenesis for construction of protein library containing nonnatural amino acids. Nucleic Acids Symposium Series, 2000, 44:69-70.

    Google Scholar 

  • O’Maille PE, Bakhtina M and Tsai MD. Structure-based combinatorial protein engineering (SCOPE). Journal of Molecular Biology, 2002, 321:677-691.

    Google Scholar 

  • Ostermeier M, Shim JH and Benkovic SJ. A combinatorial approach to hybrid enzymes independent of DNA homology. Nature Biotechnology, 1999, 17:1205-1209.

    Google Scholar 

  • Park HS, Nam SH, Lee JK, Yoon CN, Mannervik B, Benkovic SJ and Kim HS. Design and evolution of new catalytic activity with an existing protein scaffold. Science, 2006, 311:535-538.

    Google Scholar 

  • Reetz MT, Bocola M, Carballeira JD, Zha D and Vogel A. Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test. Angewandte Chemie International Edition, 2005, 44:4192-4196.

    Google Scholar 

  • Reetz MT, Carballeira JD and Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angewandte Chemie International Edition, 2006, 45:7745-7751.

    Google Scholar 

  • Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS and Baker D. Kemp elimination catalysts by computational enzyme design. Nature, 2008, 453:190-195.

    Google Scholar 

  • Shao Z, Zhao H, Giver L and Arnold FH. Random-priming in vitro recombination: an effective tool for directed evolution. Nucleic Acids Research, 1998, 26:681-683.

    Google Scholar 

  • Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE and Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science, 2010, 329:309-313.

    Google Scholar 

  • Stemmer WP. Rapid evolution of a protein in vitro by DNA shuffling. Nature, 1994a, 370:389-391.

    Google Scholar 

  • Stemmer WP. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proceedings of the National Academy of Sciences of the United States of America, 1994b, 91:10747-10751.

    Google Scholar 

  • Wong TS, Tee KL, Hauer B and Schwaneberg U. Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. Nucleic Acids Research, 2004, 32:e26.

    Google Scholar 

  • Yu Y and Lutz S. Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnology, 2011, 29:18-25.

    Google Scholar 

  • Zhao H, Giver L, Shao Z, Affholter JA and Arnold FH. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nature Biotechnology, 1998, 16:258-261.

    Google Scholar 

  • Zheng S and Kwon I. Manipulation of enzyme properties by noncanonical amino acid incorporation. Biotechnology Journal, 2012, 7:47-60.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Young Je Yoo .

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Yoo, Y.J., Feng, Y., Kim, Y.H., Yagonia, C.F.J. (2017). Engineering Tools for Enzymes. In: Fundamentals of Enzyme Engineering. Springer, Dordrecht. https://doi.org/10.1007/978-94-024-1026-6_8

Download citation

Publish with us

Policies and ethics