Skip to main content
SpringerLink
Log in

Combined and Iterative Use of Computational Design and Directed Evolution for Protein–Ligand Binding Design

  • Protocol
  • First Online:
Computational Design of Ligand Binding Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1414))

Abstract

The advantages of computational design and directed evolution are complementary, and only through combined and iterative use of both approaches, a daunting task such as protein–ligand interaction design, can be achieved efficiently. Here, we describe a systematic strategy to combine structure-guided computational design, iterative site saturation mutagenesis, and yeast two-hybrid system (Y2H)-based phenotypic screening to engineer novel and orthogonal interactions between synthetic ligands and human estrogen receptor α (hERα) for the development of novel gene switches.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

  1. Weatherman RV, Fletterick RJ, Scanlan TS (1999) Nuclear-receptor ligands and ligand-binding domains. Annu Rev Biochem 68:559–581

    Article  CAS  PubMed  Google Scholar 

  2. Anand P, Nagarajan D, Mukherjee S, Chandra N (2014) PLIC: protein-ligand interaction clusters. Database (Oxford) 2014:bau029

    Google Scholar 

  3. Damborsky J, Brezovsky J (2014) Computational tools for designing and engineering enzymes. Curr Opin Chem Biol 19:8–16

    Article  CAS  PubMed  Google Scholar 

  4. Feldmeier K, Höcker B (2013) Computational protein design of ligand binding and catalysis. Curr Opin Chem Biol 17:929–933

    Article  CAS  PubMed  Google Scholar 

  5. Brustad EM, Lelyveld VS, Snow CD, Crook N, Jung ST, Martinez FM, Scholl TJ, Jasanoff A, Arnold FH (2012) Structure-guided directed evolution of highly selective p450-based magnetic resonance imaging sensors for dopamine and serotonin. J Mol Biol 422:245–262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Shapiro MG, Westmeyer GG, Romero PA, Szablowski JO, Kuster B, Shah A, Otey CR, Langer R, Arnold FH, Jasanoff A (2010) Directed evolution of a magnetic resonance imaging contrast agent for noninvasive imaging of dopamine. Nat Biotechnol 28:264–270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. de Las HA, Carreno CA, Martinez-Garcia E, de Lorenzo V (2010) Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev 34:842–865

    Article  Google Scholar 

  8. Collins CH, Arnold FH, Leadbetter JR (2005) Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Mol Microbiol 55:712–723

    Article  CAS  PubMed  Google Scholar 

  9. Scholz O, Kostner M, Reich M, Gastiger S, Hillen W (2003) Teaching TetR to recognize a new inducer. J Mol Biol 329:217–227

    Article  CAS  PubMed  Google Scholar 

  10. Tang SY, Fazelinia H, Cirino PC (2008) AraC regulatory protein mutants with altered effector specificity. J Am Chem Soc 130:5267–5271

    Article  CAS  PubMed  Google Scholar 

  11. Vee Aune TE, Bakke I, Drablos F, Lale R, Brautaset T, Valla S (2010) Directed evolution of the transcription factor XylS for development of improved expression systems. Microb Biotechnol 3:38–47

    Article  PubMed  PubMed Central  Google Scholar 

  12. Amiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB (2007) Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Sci 16:2350–2359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. East AK, Mauchline TH, Poole PS (2008) Biosensors for ligand detection. Adv Appl Microbiol 64:137–166

    Article  CAS  PubMed  Google Scholar 

  14. Reetz MT, Bocola M, Carballeira JD, Zha D, Vogel A (2005) Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test. Angew Chem Int Ed Engl 44:4192–4196

    Article  CAS  PubMed  Google Scholar 

  15. Reetz MT, Carballeira JD, Vogel A (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 45:7745–7751

    Article  CAS  PubMed  Google Scholar 

  16. Chockalingam K, Chen Z, Katzenellenbogen JA, Zhao H (2005) Directed evolution of specific receptor-ligand pairs for use in the creation of gene switches. Proc Natl Acad Sci U S A 102:5691–5696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501:212–216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Khare SD, Kipnis Y, Greisen P Jr, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D (2012) Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol 8:294–300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D (2013) Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat Chem Biol 9:494–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. McLachlan MJ, Chockalingam K, Lai KC, Zhao H (2009) Directed evolution of orthogonal ligand specificity in a single scaffold. Angew Chem Int Ed Engl 48:7783–7786

    Article  CAS  PubMed  Google Scholar 

  21. Ding XF, Anderson CM, Ma H, Hong H, Uht RM, Kushner PJ, Stallcup MR (1998) Nuclear receptor-binding sites of coactivators glucocorticoid receptor interacting protein 1 (GRIP1) and steroid receptor coactivator 1 (SRC-1): multiple motifs with different binding specificities. Mol Endocrinol 12:302–313

    Article  CAS  PubMed  Google Scholar 

  22. Katzenellenbogen JA, Johnson HJ, Carlson KE, Myers HN (1974) Photoreactivity of some light-sensitive estrogen derivatives. Use of an exchange assay to determine their photointeraction with the rat uterine estrogen binding protein. Biochemistry 13:2986–2994

    Article  CAS  PubMed  Google Scholar 

  23. Chen Z, Katzenellenbogen BS, Katzenellenbogen JA, Zhao H (2004) Directed evolution of human estrogen receptor variants with significantly enhanced androgen specificity and affinity. J Biol Chem 279:33855–33864

    Article  CAS  PubMed  Google Scholar 

  24. Halgren TA (1999) MMFF VI. MMFF94s option for energy minimization studies. J Comput Chem 20:720–729

    Article  CAS  Google Scholar 

  25. Hart TN, Read RJ (1992) A multiple-start Monte Carlo docking method. Proteins 13:206–222

    Article  CAS  PubMed  Google Scholar 

  26. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51–59

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Meng Wang & Huimin Zhao

  2. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Huimin Zhao

  3. Department of Chemistry, and Bioengineering, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Huimin Zhao

  4. 215 Rogers Adams Lab, Box C-3 600 S. Matthews Ave., Urbana, IL, 61801, USA

    Huimin Zhao

Authors
  1. Meng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huimin Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Huimin Zhao .

Editor information

Editors and Affiliations

  1. Division of Basic Sciences, Fred Hutchinson Cancer Research Cen, Seattle, Washington, USA

    Barry L. Stoddard

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Wang, M., Zhao, H. (2016). Combined and Iterative Use of Computational Design and Directed Evolution for Protein–Ligand Binding Design. In: Stoddard, B. (eds) Computational Design of Ligand Binding Proteins. Methods in Molecular Biology, vol 1414. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3569-7_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-3569-7_8

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3567-3

  • Online ISBN: 978-1-4939-3569-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation