Design of Light-Controlled Protein Conformations and Functions

  • Ryan S. Ritterson
  • Daniel Hoersch
  • Kyle A. Barlow
  • Tanja Kortemme
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1414)

Abstract

In recent years, interest in controlling protein function with light has increased. Light offers a number of unique advantages over other methods, including spatial and temporal control and high selectivity. Here, we describe a general protocol for engineering a protein to be controllable with light via reaction with an exogenously introduced photoisomerizable small molecule and illustrate our protocol with two examples from the literature: the engineering of the calcium affinity of the cell–cell adhesion protein cadherin, which is an example of a protein that switches from a native to a disrupted state (Ritterson et al. J Am Chem Soc (2013) 135:12516–12519), and the engineering of the opening and closing of the chaperonin Mm-cpn, an example of a switch between two functional states (Hoersch et al.: Nat Nanotechn (2013) 8:928–932). This protocol guides the user from considering which proteins may be most amenable to this type of engineering, to considerations of how and where to make the desired changes, to the assays required to test for functionality.

Key words

Photoswitches Computational protein design Light-modulatable proteins Protein engineering 

References

  1. 1.
    Krauss U, Drepper T, Jaeger KE (2011) Enlightened enzymes: strategies to create novel photoresponsive proteins. Chemistry 17(9):2552–2560. doi:10.1002/chem.201002716 CrossRefPubMedGoogle Scholar
  2. 2.
    Banghart M, Borges K, Isacoff E, Trauner D, Kramer RH (2004) Light-activated ion channels for remote control of neuronal firing. Nat Neurosci 7(12):1381–1386. doi:10.1038/nn1356 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Ritterson RS, Kuchenbecker KM, Michalik M, Kortemme T (2013) Design of a photoswitchable cadherin. J Am Chem Soc 135(34):12516–12519. doi:10.1021/ja404992r CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Hoersch D, Roh SH, Chiu W, Kortemme T (2013) Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol 8(12):928–932. doi:10.1038/nnano.2013.242 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Woolley GA, Jaikaran ASI, Berezovski M, Calarco JP, Krylov SN, Smart OS, Kumita JR (2006) Reversible photocontrol of DNA binding by a designed GCN4-bZIP protein. Biochemistry 45(19):6075–6084. doi:10.1021/bi060142r CrossRefPubMedGoogle Scholar
  6. 6.
    Levskaya A, Weiner OD, Lim WA, Voigt CA (2009) Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461(7266):997–1001. doi:10.1038/nature08446 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Zhang F, Muller KM, Woolley GA, Arndt KM (2012) Light-controlled gene switches in mammalian cells. Methods Mol Biol 813:195–210. doi:10.1007/978-1-61779-412-4_12 CrossRefPubMedGoogle Scholar
  8. 8.
    Wyart C, del Bene F, Warp E, Scott EK, Trauner D, Baier H, Isacoff EY (2009) Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature 461(7262):407–410. doi:10.1038/nature08323 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Beharry AA, Woolley GA (2011) Azobenzene photoswitches for biomolecules. Chem Soc Rev 40(8):4422–4437. doi:10.1039/c1cs15023e CrossRefPubMedGoogle Scholar
  10. 10.
    Ali AM, Woolley GA (2013) The effect of azobenzene cross-linker position on the degree of helical peptide photo-control. Org Biomol Chem 11(32):5325–5331. doi:10.1039/c3ob40684a CrossRefPubMedGoogle Scholar
  11. 11.
    Rosetta Commons (2015) Rosette license and download. https://www.rosettacommons.org/software/license-and-download. Accessed 5/31/2015
  12. 12.
    Kortemme T, Baker D (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A 99(22):14116–14121. doi:10.1073/pnas.202485799 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Science STKE 2004(219):pl2. doi:10.1126/stke.2192004pl2 Google Scholar
  14. 14.
    Rosetta Commons (2015) Rosetta documentation. https://www.rosettacommons.org/docs. Accessed 27 June 2015
  15. 15.
    Schrodinger LLC (2010) The PyMOL molecular graphics system, Version 1.3r1Google Scholar
  16. 16.
    Samanta S, McCormick TM, Schmidt SK, Seferos DS, Woolley GA (2013) Robust visible light photoswitching with ortho-thiol substituted azobenzenes. Chem Commun (Camb) 49(87):10314–10316. doi:10.1039/c3cc46045b CrossRefGoogle Scholar
  17. 17.
    Samanta S, Babalhavaeji A, Dong MX, Woolley GA (2013) Photoswitching of ortho-substituted azonium ions by red light in whole blood. Angew Chem Int Ed Engl 52(52):14127–14130. doi:10.1002/anie.201306352 CrossRefPubMedGoogle Scholar
  18. 18.
    Beharry AA, Sadovski O, Woolley GA (2011) Azobenzene photoswitching without ultraviolet light. J Am Chem Soc 133(49):19684–19687. doi:10.1021/ja209239m CrossRefPubMedGoogle Scholar
  19. 19.
    Umeki N, Yoshizawa T, Sugimoto Y, Mitsui T, Wakabayashi K, Maruta S (2004) Incorporation of an azobenzene derivative into the energy transducing site of skeletal muscle myosin results in photo-induced conformational changes. J Biochem 136(6):839–846. doi:10.1093/jb/mvh194 CrossRefPubMedGoogle Scholar
  20. 20.
    Burns DC, Zhang F, Woolley GA (2007) Synthesis of 3,3′-bis(sulfonato)-4,4′-bis(chloroacetamido)azobenzene and cysteine cross-linking for photo-control of protein conformation and activity. Nat Protoc 2(2):251–258. doi:10.1038/nprot.2007.21 CrossRefPubMedGoogle Scholar
  21. 21.
    Schierling B, Noel AJ, Wende W, le Hien T, Volkov E, Kubareva E, Oretskaya T, Kokkinidis M, Rompp A, Spengler B, Pingoud A (2010) Controlling the enzymatic activity of a restriction enzyme by light. Proc Natl Acad Sci U S A 107(4):1361–1366. doi:10.1073/pnas.0909444107 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J (2011) Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Cell 144(2):240–252. doi:10.1016/j.cell.2010.12.017 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Abràmoff MD, Magalhães PJ, Ram SJ (2004) Image processing with ImageJ. Biophoton Int 11(7):36–42Google Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Ryan S. Ritterson
    • 1
  • Daniel Hoersch
    • 1
    • 2
  • Kyle A. Barlow
    • 3
  • Tanja Kortemme
    • 1
  1. 1.California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoUSA
  2. 2.Fachbereich PhysikFreie Universität BerlinBerlinGermany
  3. 3.Graduate Program in Bioinformatics, California Institute for Quantitative Biomedical Research, and Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoUSA

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