Skip to main content

Generation of Effective Libraries by Neutral Drift

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1179))

Abstract

Neutral drift is a recently developed experimental technique used to identify superior starting points for protein engineering. Neutral drift explores accessible sequence space by repeated rounds of mutagenesis and selection to maintain wild-type function. Mutations that are largely neutral for the native function accumulate, and those that are highly detrimental are purged, yielding a library of high diversity and quality. This technique is useful in situations where laboratory evolution is at a dead end, i.e., when the enzyme activity intended for evolution proves recalcitrant to improvements or is too low to be detected.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Hartl DL, Dykhuizen DE, Dean AM (1985) Limits of adaptation: the evolution of selective neutrality. Genetics 111(3):655–674

    CAS  PubMed Central  PubMed  Google Scholar 

  2. Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci U S A 93(1):397–401

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Dalby PA (2011) Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol 21(4):473–480

    Article  CAS  PubMed  Google Scholar 

  4. Goldsmith M, Tawfik DS (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22(4):406–412

    Article  CAS  PubMed  Google Scholar 

  5. Amitai G, Gupta RD, Tawfik DS (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1(1):67–78

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Bershtein S, Goldin K, Tawfik D (2008) Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 379(5):1029–1044

    Article  CAS  PubMed  Google Scholar 

  7. Bershtein S, Tawfik DS (2008) Ohno’s model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts. Mol Biol Evol 25(11):2311–2318

    Article  CAS  PubMed  Google Scholar 

  8. Bloom JD et al (2007) Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol 5:29

    Article  PubMed Central  PubMed  Google Scholar 

  9. Bloom JD, Romero PA, Lu Z, Arnold FH (2007) Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct 2:17

    Article  PubMed Central  PubMed  Google Scholar 

  10. Gupta RD, Tawfik DS (2008) Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5(11):939–942

    Article  CAS  PubMed  Google Scholar 

  11. Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 19(5):596–604

    Article  CAS  PubMed  Google Scholar 

  12. Tokuriki N et al (2012) Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat Commun 3:1257

    Article  PubMed  Google Scholar 

  13. Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS (2005) High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chem Biol 12(12):1281–1289

    Article  CAS  PubMed  Google Scholar 

  14. Goldsmith M, Kiss C, Bradbury AR, Tawfik DS (2007) Avoiding and controlling double transformation artifacts. Protein Eng Des Sel 20(7):315–318

    Article  CAS  PubMed  Google Scholar 

  15. Tokuriki N, Stricher F, Serrano L, Tawfik DS (2008) How protein stability and new functions trade off. PLoS Comput Biol 4(2):e1000002

    Article  PubMed Central  PubMed  Google Scholar 

  16. Aharoni A et al (2005) The ‘evolvability’ of promiscuous protein functions. Nat Genet 37(1):73–76

    CAS  PubMed  Google Scholar 

  17. Stemmer WP (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A 91(22):10747–10751

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16(3):258–261

    Article  CAS  PubMed  Google Scholar 

  19. Tokuriki N, Tawfik DS (2009) Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459(7247):668–673

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Institutes of Health Research (CIHR). N.T. is a Michael Smith Foundation for Health Research Scholar.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nobuhiko Tokuriki .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Kaltenbach, M., Tokuriki, N. (2014). Generation of Effective Libraries by Neutral Drift. In: Gillam, E., Copp, J., Ackerley, D. (eds) Directed Evolution Library Creation. Methods in Molecular Biology, vol 1179. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-1053-3_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1053-3_5

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-1052-6

  • Online ISBN: 978-1-4939-1053-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics