Skip to main content

Synthetic Protein Switches: Theoretical and Experimental Considerations

  • Protocol
  • First Online:
Synthetic Protein Switches

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1596))

Abstract

Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.

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 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
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. Golynskiy MV, Koay MS, Vinkenborg JL, Merkx M (2011) Engineering protein switches: sensors, regulators, and spare parts for biology and biotechnology. Chembiochem 12:353–361. doi:10.1002/cbic.201000642

    Article  CAS  Google Scholar 

  2. Stein V, Alexandrov K (2015) Synthetic protein switches: design principles and applications. Trends Biotechnol 33:101–110. doi:10.1016/j.tibtech.2014.11.010

    Article  CAS  Google Scholar 

  3. Shekhawat SS, Ghosh I (2011) Split-protein systems: beyond binary protein-protein interactions. Curr Opin Chem Biol 15:790–797. doi:10.1016/j.cbpa.2011.10.014

    Article  CAS  Google Scholar 

  4. Michnick SW, Ear PH, Manderson EN et al (2007) Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat Rev Drug Discov 6:569–582. doi:10.1038/nrd2311

    Article  CAS  Google Scholar 

  5. Mehta S, Zhang J (2011) Reporting from the field: genetically encoded fluorescent reporters uncover signaling dynamics in living biological systems. Annu Rev Biochem 80:375–401. doi:10.1146/annurev-biochem-060409-093259

    Article  CAS  Google Scholar 

  6. Tamura T, Hamachi I (2014) Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 9:2708–2717. doi:10.1021/cb500661v

    Article  CAS  Google Scholar 

  7. Saito K, Nagai T (2015) Recent progress in luminescent proteins development. Curr Opin Chem Biol 27:46–51. doi:10.1016/j.cbpa.2015.05.029

    Article  CAS  Google Scholar 

  8. Miyawaki A, Niino Y (2015) Molecular spies for bioimaging-fluorescent protein-based probes. Mol Cell 58:632–643. doi:10.1016/j.molcel.2015.03.002

    Article  CAS  Google Scholar 

  9. Zhang K, Cui B (2015) Optogenetic control of intracellular signaling pathways. Trends Biotechnol 33:92–100. doi:10.1016/j.tibtech.2014.11.007

    Article  CAS  Google Scholar 

  10. Beyer HM, Naumann S, Weber W, Radziwill G (2015) Optogenetic control of signaling in mammalian cells. Biotechnol J 10:273–283. doi:10.1002/biot.201400077

    Article  CAS  Google Scholar 

  11. Gautier A, Gauron C, Volovitch M et al (2014) How to control proteins with light in living systems. Nat Chem Biol 10:533–541. doi:10.1038/nchembio.1534

    Article  CAS  Google Scholar 

  12. Tischer D, Weiner OD (2014) Illuminating cell signalling with optogenetic tools. Nat Rev Mol Cell Biol 15:551–558. doi:10.1038/nrm3837

    Article  CAS  Google Scholar 

  13. Ha JH, Loh SN (2012) Protein conformational switches: from nature to design. Chemistry 18:7984–7999. doi:10.1002/chem.201200348

    Article  CAS  Google Scholar 

  14. Koide S (2009) Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. Curr Opin Biotechnol 20:398–404. doi:10.1016/j.copbio.2009.07.007

    Article  CAS  Google Scholar 

  15. Way JC, Collins JJ, Keasling JD, Silver PA (2014) Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157:151–161. doi:10.1016/j.cell.2014.02.039

    Article  CAS  Google Scholar 

  16. Cameron DE, Bashor CJ, Collins JJ (2014) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390. doi:10.1038/nrmicro3239

    Article  CAS  Google Scholar 

  17. Feldmeier K, Höcker B (2013) Computational protein design of ligand binding and catalysis. Curr Opin Chem Biol 17:929–933. doi:10.1016/j.cbpa.2013.10.002

    Article  CAS  Google Scholar 

  18. Kiss G, Çelebi-Ölçüm N, Moretti R et al (2013) Computational enzyme design. Angew Chem Int Ed Engl 52:5700–5725. doi:10.1002/anie.201204077

    Article  CAS  Google Scholar 

  19. Zhang J, Zheng F, Grigoryan G (2014) Design and designability of protein-based assemblies. Curr Opin Struct Biol 27:79–86. doi:10.1016/j.sbi.2014.05.009

    Article  CAS  Google Scholar 

  20. Mak WS, Siegel JB (2014) Computational enzyme design: transitioning from catalytic proteins to enzymes. Curr Opin Struct Biol 27:87–94. doi:10.1016/j.sbi.2014.05.010

    Article  CAS  Google Scholar 

  21. Schreiber G, Fleishman SJ (2013) Computational design of protein-protein interactions. Curr Opin Struct Biol 23:903–910. doi:10.1016/j.sbi.2013.08.003

    Article  CAS  Google Scholar 

  22. Miyawaki A, Llopis J, Heim R et al (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388:882–887. doi:10.1038/42264

    Article  CAS  Google Scholar 

  23. Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci U S A 96:11241–11246. doi:10.1073/pnas.96.20.11241

    Article  CAS  Google Scholar 

  24. Nagai T, Sawano A, Park ES, Miyawaki A (2001) Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proc Natl Acad Sci U S A 98:3197–3202. doi:10.1073/pnas.051636098

    Article  CAS  Google Scholar 

  25. Guntas G, Ostermeier M (2004) Creation of an allosteric enzyme by domain insertion. J Mol Biol 336:263–273. doi:10.1016/j.jmb.2003.12.016

    Article  CAS  Google Scholar 

  26. Meister GE, Joshi NS (2013) An engineered calmodulin-based allosteric switch for peptide biosensing. Chembiochem 14:1460–1467. doi:10.1002/cbic.201300168

    Article  CAS  Google Scholar 

  27. Iwai H, Kojima-Misaizu M, Dong J, Ueda H (2016) Creation of a ligand-dependent enzyme by fusing circularly permuted antibody variable region domains. Bioconjug Chem 27(4):868–873. doi:10.1021/acs.bioconjchem.6b00040

    Article  CAS  Google Scholar 

  28. Karginov AV, Ding F, Kota P et al (2010) Engineered allosteric activation of kinases in living cells. Nat Biotechnol 28:743–747. doi:10.1038/nbt.1639

    Article  CAS  Google Scholar 

  29. Dagliyan O, Shirvanyants D, Karginov AV et al (2013) Rational design of a ligand-controlled protein conformational switch. Proc Natl Acad Sci 110:6800–6804. doi:10.1073/pnas.1218319110

    Article  CAS  Google Scholar 

  30. Chu P-H, Tsygankov D, Berginski ME et al (2014) Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms. Proc Natl Acad Sci U S A 111:12420–12425. doi:10.1073/pnas.1404487111

    Article  CAS  Google Scholar 

  31. Ribeiro LF, Nicholes N, Tullman J et al (2015) Insertion of a xylanase in xylose binding protein results in a xylose-stimulated xylanase. Biotechnol Biofuels 8:1–15. doi:10.1186/s13068-015-0293-0

    Article  CAS  Google Scholar 

  32. Guo Z, Johnston WA, Stein V et al (2016) Engineering PQQ-glucose dehydrogenase into an allosteric electrochemical Ca 2+ sensor. Chem Commun 52:485–488. doi:10.1039/C5CC07824E

    Article  CAS  Google Scholar 

  33. Stratton MM, Mitrea DM, Loh SN (2008) A Ca2+−sensing molecular switch based on alternate frame protein folding. ACS Chem Biol 3:723–732. doi:10.1021/cb800177f

    Article  CAS  Google Scholar 

  34. Stratton MM, Loh SN (2011) Converting a protein into a switch for biosensing and functional regulation. Protein Sci 20:19–29. doi:10.1002/pro.541

    Article  CAS  Google Scholar 

  35. Mitrea DM, Parsons LS, Loh SN (2010) Engineering an artificial zymogen by alternate frame protein folding. Proc Natl Acad Sci U S A 107:2824–2829. doi:10.1073/pnas.0907668107

    Article  CAS  Google Scholar 

  36. Paulmurugan R, Umezawa Y, Gambhir SS (2002) Noninvasive imaging of protein-protein interactions in living subjects by using reporter protein complementation and reconstitution strategies. Proc Natl Acad Sci U S A 99:15608–15613. doi:10.1073/pnas.242594299

    Article  CAS  Google Scholar 

  37. Dixon AS, Schwinn MK, Hall MP et al (2016) NanoLuc complementation reporter optimized for accurate measurement of protein interactions in cells. ACS Chem Biol 11:400–408. doi:10.1021/acschembio.5b00753

    Article  CAS  Google Scholar 

  38. Stefan E, Aquin S, Berger N et al (2007) Quantification of dynamic protein complexes using Renilla luciferase fragment complementation applied to protein kinase A activities in vivo. Proc Natl Acad Sci U S A 104:16916–16921. doi:10.1073/pnas.0704257104

    Article  CAS  Google Scholar 

  39. Remy I, Michnick SW (2006) A highly sensitive protein-protein interaction assay based on Gaussia luciferase. Nat Methods 3:977–979. doi:10.1038/nmeth979

    Article  CAS  Google Scholar 

  40. Gray DC, Mahrus S, Wells JA (2010) Activation of specific apoptotic caspases with an engineered small-molecule-activated protease. Cell 142:637–646. doi:10.1016/j.cell.2010.07.014

    Article  CAS  Google Scholar 

  41. Wehr MC, Reinecke L, Botvinnik A, Rossner MJ (2008) Analysis of transient phosphorylation-dependent protein-protein interactions in living mammalian cells using split-TEV. BMC Biotechnol 8:55. doi:10.1186/1472-6750-8-55

    Article  CAS  Google Scholar 

  42. Wehr MC, Holder MV, Gailite I et al (2013) Salt-inducible kinases regulate growth through the Hippo signalling pathway in Drosophila. Nat Cell Biol 15:61–71. doi:10.1038/ncb2658

    Article  CAS  Google Scholar 

  43. Wehr MC, Laage R, Bolz U et al (2006) Monitoring regulated protein-protein interactions using split TEV. Nat Methods 3:985–993. doi:10.1038/nmeth967

    Article  CAS  Google Scholar 

  44. Camacho-Soto K, Castillo-Montoya J, Tye B, Ghosh I (2014) Ligand-gated split-kinases. J Am Chem Soc 136:3995–4002. doi:10.1021/ja4130803

    Article  CAS  Google Scholar 

  45. Camacho-Soto K, Castillo-Montoya J, Tye B et al (2014) Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 136:17078–17086. doi:10.1021/ja5080745

    Article  CAS  Google Scholar 

  46. Guo Z, Murphy L, Stein V, Johnston WA, Alcala-Perez S, Alexandrov K (2016) Engineered PQQ-glucose dehydrogenase as a universal biosensor platform. J Am Chem Soc 138(32):10108–10111. doi:10.1021/jacs.6b06342

    Article  CAS  Google Scholar 

  47. Möglich A, Ayers RA, Moffat K (2009) Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 385:1433–1444. doi:10.1016/j.jmb.2008.12.017

    Article  CAS  Google Scholar 

  48. Whitaker WR, Davis SA, Arkin AP, Dueber JE (2012) Engineering robust control of two-component system phosphotransfer using modular scaffolds. Proc Natl Acad Sci 109:18090–18095. doi:10.1073/pnas.1209230109

    Article  CAS  Google Scholar 

  49. Skerker JM, Perchuk BS, Siryaporn A et al (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133:1043–1054. doi:10.1016/j.cell.2008.04.040

    Article  CAS  Google Scholar 

  50. Gasser C, Taiber S, Yeh C-M et al (2014) Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. Proc Natl Acad Sci 111:8803–8808. doi:10.1073/pnas.1321600111

    Article  CAS  Google Scholar 

  51. Lai A, Sato PM, Peisajovich SG (2015) Evolution of synthetic signaling scaffolds by recombination of modular protein domains. ACS Synth Biol 4:714–722. doi:10.1021/sb5003482

    Article  CAS  Google Scholar 

  52. Peisajovich SG, Garbarino JE, Wei P, Lim WA (2010) Rapid diversification of cell signaling phenotypes by modular domain recombination. Science 328:368–372. doi:10.1126/science.1182376

    Article  CAS  Google Scholar 

  53. Wend S, Wagner HJ, Müller K et al (2014) Optogenetic control of protein kinase activity in mammalian cells. ACS Synth Biol 3:280–285. doi:10.1021/sb400090s

    Article  CAS  Google Scholar 

  54. Wu YI, Frey D, Lungu OI et al (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461:104–108. doi:10.1038/nature08241

    Article  CAS  Google Scholar 

  55. Levskaya A, Weiner OD, Lim WA, Voigt CA (2009) sup: spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461:997–1001. doi:10.1038/nature08446

    Article  CAS  Google Scholar 

  56. Nirantar SR, Yeo KS, Chee S et al (2013) A generic scaffold for conversion of peptide ligands into homogenous biosensors. Biosens Bioelectron 47:421–428. doi:10.1016/j.bios.2013.03.049

    Article  CAS  Google Scholar 

  57. Huang J, Koide A, Makabe K, Koide S (2008) Design of protein function leaps by directed domain interface evolution. Proc Natl Acad Sci U S A 105:6578–6583. doi:10.1073/pnas.0801097105

    Article  CAS  Google Scholar 

  58. Huang J, Koide S (2010) Rational conversion of affinity reagents into label-free sensors for peptide motifs by designed allostery. ACS Chem Biol 5:273–277. doi:10.1021/cb900284c

    Article  CAS  Google Scholar 

  59. Huang J, Makabe K, Biancalana M et al (2009) Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. J Mol Biol 392:1221–1231. doi:10.1016/j.jmb.2009.07.067

    Article  CAS  Google Scholar 

  60. Stein V, Alexandrov K (2014) Protease-based synthetic sensing and signal amplification. Proc Natl Acad Sci U S A 111:15934–15939. doi:10.1073/pnas.1405220111

    Article  CAS  Google Scholar 

  61. Zhang L, Lee KC, Bhojani MS et al (2007) Molecular imaging of Akt kinase activity. Nat Med 13:1114–1119. doi:10.1038/nm1608

    Article  CAS  Google Scholar 

  62. Brun MA, Tan KT, Nakata E et al (2009) Semisynthetic fluorescent sensor proteins based on self-labeling protein tags. J Am Chem Soc 131:5873–5884. doi:10.1021/ja900149e

    Article  CAS  Google Scholar 

  63. Schena A, Johnsson K (2014) Sensing acetylcholine and anticholinesterase compounds. Angew Chem Int Ed Engl 53:1302–1305. doi:10.1002/anie.201307754

    Article  CAS  Google Scholar 

  64. Brun MA, Griss R, Reymond L et al (2011) Semisynthesis of fluorescent metabolite sensors on cell surfaces. J Am Chem Soc 133:16235–16242. doi:10.1021/ja206915m

    Article  CAS  Google Scholar 

  65. Brun MA, Tan KT, Griss R et al (2012) A semisynthetic fluorescent sensor protein for glutamate. J Am Chem Soc 134:7676–7678. doi:10.1021/ja3002277

    Article  CAS  Google Scholar 

  66. Griss R, Schena A, Reymond L et al (2014) Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat Chem Biol 10:598–603. doi:10.1038/nchembio.1554

    Article  CAS  Google Scholar 

  67. Xue L, Karpenko IA, Hiblot J, Johnsson K (2015) Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 11:1–7. doi:10.1038/nchembio.1959

    Article  CAS  Google Scholar 

  68. Street AG, Mayo SL (1999) Computational protein design. Structure 7(5):R105–R109. doi:10.1016/S0969-2126(99)80062-8

    Article  CAS  Google Scholar 

  69. Samish I, MacDermaid CM, Perez-Aguilar JM, Saven JG (2011) Theoretical and computational protein design. Annu Rev Phys Chem 62:129–149. doi:10.1146/annurev-physchem-032210-103509

    Article  CAS  Google Scholar 

  70. Khoury GA, Smadbeck J, Kieslich CA, Floudas CA (2014) Protein folding and de novo protein design for biotechnological applications. Trends Biotechnol 32:99–109. doi:10.1016/j.tibtech.2013.10.008

    Article  CAS  Google Scholar 

  71. Kuhlman B, Dantas G, Ireton GC et al (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364–1368. doi:10.1126/science.1089427

    Article  CAS  Google Scholar 

  72. Koga N, Tatsumi-Koga R, Liu G et al (2012) Principles for designing ideal protein structures. Nature 491:222–227. doi:10.1038/nature11600

    Article  CAS  Google Scholar 

  73. Tinberg CE, Khare SD, Dou J et al (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501:212–216. doi:10.1038/nature12443

    Article  CAS  Google Scholar 

  74. Schreier B, Stumpp C, Wiesner S, Höcker B (2009) Computational design of ligand binding is not a solved problem. Proc Natl Acad Sci U S A 106:18491–18496. doi:10.1073/pnas.0907950106

    Article  CAS  Google Scholar 

  75. Röthlisberger D, Khersonsky O, Wollacott AM et al (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190–195. doi:10.1038/nature06879

    Article  CAS  Google Scholar 

  76. Jiang L, Althoff EA, Clemente FR et al (2008) De novo computational design of retro-aldol enzymes. Science 319:1387–1391. doi:10.1126/science.1152692

    Article  CAS  Google Scholar 

  77. Korendovych IV, Kulp DW, Wu Y et al (2011) Design of a switchable eliminase. Proc Natl Acad Sci U S A 108:6823–6827. doi:10.1073/pnas.1018191108

    Article  CAS  Google Scholar 

  78. Taylor ND, Garruss AS, Moretti R et al (2016) Engineering an allosteric transcription factor to respond to new ligands. Nat Methods 1–11. doi: 10.1038/nmeth.3696

  79. Van Dongen EMWM, Evers TH, Dekkers LM et al (2007) Variation of linker length in ratiometric fluorescent sensor proteins allows rational tuning of Zn(II) affinity in the picomolar to femtomolar range. J Am Chem Soc 129:3494–3495. doi:10.1021/ja069105d

    Article  CAS  Google Scholar 

  80. Porebski BT, Buckle AM (2016) Consensus protein design. 29:1–7. doi: 10.1093/protein/gzw015

  81. Steipe B, Schiller B, Plückthun A, Steinbacher S (1994) Sequence statistics reliably predict stabilizing mutations in a protein domain. J Mol Biol 240:188–192. doi:10.1006/jmbi.1994.1434

    Article  CAS  Google Scholar 

  82. Jacobs SA, Diem MD, Luo J et al (2012) Design of novel FN3 domains with high stability by a consensus sequence approach. Protein Eng Des Sel 25:107–117. doi:10.1093/protein/gzr064

    Article  CAS  Google Scholar 

  83. Binz HK, Stumpp MT, Forrer P et al (2003) Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332:489–503. doi:10.1016/S0022-2836(03)00896-9

    Article  CAS  Google Scholar 

  84. Lehmann M, Pasamontes L, Lassen SF, Wyss M (2000) The consensus concept for thermostability engineering of proteins. Biochim Biophys Acta 1543:408–415. doi:10.1016/S0167-4838(00)00238-7

    Article  CAS  Google Scholar 

  85. Lehmann M, Kostrewa D, Wyss M et al (2000) From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase. Protein Eng Des Sel 13:49–57. doi:10.1093/protein/13.1.49

    Article  CAS  Google Scholar 

  86. Starr T (2015) Epistasis in protein evolution. Protein Sci 00:1–8. doi:10.1002/pro

    Google Scholar 

  87. Harms MJ, Thornton JW (2010) Analyzing protein structure and function using ancestral gene reconstruction. Curr Opin Struct Biol 20:360–366. doi:10.1016/j.sbi.2010.03.005

    Article  CAS  Google Scholar 

  88. Thornton JW (2004) Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 5:366–375. doi:10.1038/nrg1324

    Article  CAS  Google Scholar 

  89. Risso VA, Gavira JA, Mejia-Carmona DF et al (2013) Hyperstability and substrate promiscuity in laboratory resurrections of precambrian β-lactamases. J Am Chem Soc 135:2899–2902. doi:10.1021/ja311630a

    Article  CAS  Google Scholar 

  90. Whitfield JH, Zhang WH, Herde MK et al (2015) Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Sci 24:1412–1422. doi:10.1002/pro.2721

    Article  CAS  Google Scholar 

  91. Gaucher EA, Thomson JM, Burgan MF, Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425:285–288. doi:10.1038/nature01977

    Article  CAS  Google Scholar 

  92. Clifton BE, Jackson CJ (2016) Ancestral protein reconstruction yields insights into adaptive evolution of binding specificity in solute-binding proteins. Cell Chem Biol 23:236–245. doi:10.1016/j.chembiol.2015.12.010

    Article  CAS  Google Scholar 

  93. Süel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10:59–69. doi:10.1038/nsb881

    Article  CAS  Google Scholar 

  94. Reynolds KA, McLaughlin RN, Ranganathan R (2011) Hot spots for allosteric regulation on protein surfaces. Cell 147:1564–1575. doi:10.1016/j.cell.2011.10.049

    Article  CAS  Google Scholar 

  95. Lee J, Natarajan M, Nashine VC et al (2008) Surface sites for engineering allosteric control in proteins. Science 322:438–442. doi:10.1126/science.1159052

    Article  CAS  Google Scholar 

  96. Yu Y, Lutz S (2011) Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnol 29:18–25. doi:10.1016/j.tibtech.2010.10.004

    Article  CAS  Google Scholar 

  97. Guntas G, Mansell TJ, Kim JR, Ostermeier M (2005) Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc Natl Acad Sci U S A 102:11224–11229. doi:10.1073/pnas.0502673102

    Article  CAS  Google Scholar 

  98. Guntas G, Mitchell SF, Ostermeier M (2004) A molecular switch created by in vitro recombination of nonhomologous genes. Chem Biol 11:1483–1487. doi:10.1016/j.chembiol.2004.08.020

    Article  CAS  Google Scholar 

  99. Ribeiro LF, Tullman J, Nicholes N et al (2016) A xylose-stimulated xylanase–xylose binding protein chimera created by random nonhomologous recombination. Biotechnol Biofuels 9:119. doi:10.1186/s13068-016-0529-7

    Article  Google Scholar 

  100. Wright CM, Wright RC, Eshleman JR, Ostermeier M (2011) A protein therapeutic modality founded on molecular regulation. Proc Natl Acad Sci 108:16206–16211. doi:10.1073/pnas.1102803108

    Article  CAS  Google Scholar 

  101. Yon F, Fried M (1989) Precise gene fusion by PCR. Nucleic Acids Res 17:4145–4159

    Article  Google Scholar 

  102. Yolov AA, Shabarova ZA (1990) Constructing DNA by polymerase recombination. Nucleic Acids Res 18:3983–3986. doi:10.1093/nar/18.13.3983

    Article  CAS  Google Scholar 

  103. Ohlendorf R, Schumacher CH, Richter F, Möglich A (2016) Library-aided probing of linker determinants in hybrid photoreceptors. ACS Synth Biol 5(10):1117–1126. doi:10.1021/acssynbio.6b00028

    Article  CAS  Google Scholar 

  104. Gibson DG, Young L, Chuang R-Y et al (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345. doi:10.1038/nmeth.1318

    Article  CAS  Google Scholar 

  105. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4:251–256. doi:10.1038/nmeth1010

    Article  CAS  Google Scholar 

  106. Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4:e6441. doi:10.1371/journal.pone.0006441

    Article  CAS  Google Scholar 

  107. Zhang Y, Werling U, Edelmann W (2012) SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res 40(8):e55. doi:10.1093/nar/gkr1288

    Article  CAS  Google Scholar 

  108. Beyer HM, Gonschorek P, Samodelov SL et al (2015) AQUA cloning: a versatile and simple enzyme-free cloning approach. PLoS One 10(9):e0137652. doi:10.1371/journal.pone.0137652

    Article  CAS  Google Scholar 

  109. Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One 3(11):e3647. doi:10.1371/journal.pone.0003647

    Article  CAS  Google Scholar 

  110. Geu-Flores F, Nour-Eldin HH, Nielsen MT, Halkier BA (2007) USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res 35(7):e55. doi:10.1093/nar/gkm106

    Article  CAS  Google Scholar 

  111. Bitinaite J, Rubino M, Varma KH et al (2007) USER friendly DNA engineering and cloning method by uracil excision. Nucleic Acids Res 35:1992–2002. doi:10.1093/nar/gkm041

    Article  CAS  Google Scholar 

  112. Nour-Eldin HH, Hansen BG, Nørholm MHH et al (2006) Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments. Nucleic Acids Res 34(18):e122. doi:10.1093/nar/gkl635

    Article  Google Scholar 

  113. Stein V, Hollfelder F (2009) An efficient method to assemble linear DNA templates for in vitro screening and selection systems. Nucleic Acids Res 37(18):e122. doi:10.1093/nar/gkp589

    Article  CAS  Google Scholar 

  114. Villiers BRM, Stein V, Hollfelder F (2010) USER friendly DNA recombination (USERec): a simple and flexible near homology-independent method for gene library construction. Protein Eng Des Sel 23:1–8. doi:10.1093/protein/gzp063

    Article  CAS  Google Scholar 

  115. Vinkenborg JL, Evers TH, Reulen SWA et al (2007) Enhanced sensitivity of FRET-based protease sensors by redesign of the GFP dimerization interface. Chembiochem 8:1119–1121. doi:10.1002/cbic.200700109

    Article  CAS  Google Scholar 

  116. Ohashi T, Galiacy SD, Briscoe G, Erickson HP (2007) An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins. Protein Sci 16:1429–1438. doi:10.1110/ps.072845607

    Article  CAS  Google Scholar 

  117. Janssen BMG, Engelen W, Merkx M (2015) DNA-directed control of enzyme-inhibitor complex formation: a modular approach to reversibly switch enzyme activity. ACS Synth Biol 4:547–553. doi:10.1021/sb500278z

    Article  CAS  Google Scholar 

  118. Banala S, Aper SJA, Schalk W, Merkx M (2013) Switchable reporter enzymes based on mutually exclusive domain interactions allow antibody detection directly in solution. ACS Chem Biol 8:2127–2132. doi:10.1021/cb400406x

    Article  CAS  Google Scholar 

  119. Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–1317. doi:10.1126/science.4001944

    Article  CAS  Google Scholar 

  120. Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557. doi:10.1038/nbt0697-553

    Article  CAS  Google Scholar 

  121. Gai SA, Wittrup KD (2007) Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 17:467–473. doi:10.1016/j.sbi.2007.08.012

    Article  CAS  Google Scholar 

  122. Wilson DS, Keefe AD, Szostak JW (2001) The use of mRNA display to select high-affinity protein-binding peptides. Proc Natl Acad Sci U S A 98:3750–3755. doi:10.1073/pnas.061028198

    Article  CAS  Google Scholar 

  123. Hanes J, Pluckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci 94:4937–4942. doi:10.1073/pnas.94.10.4937

    Article  CAS  Google Scholar 

  124. Zahnd C, Amstutz P, Plückthun A (2007) Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 4:269–279. doi:10.1038/nmeth1003

    Article  CAS  Google Scholar 

  125. Odegrip R, Coomber D, Eldridge B et al (2004) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Proc Natl Acad Sci U S A 101:2806–2810. doi:10.1073/pnas.0400219101

    Article  CAS  Google Scholar 

  126. Bertschinger J, Neri D (2004) Covalent DNA display as a novel tool for directed evolution of proteins in vitro. Protein Eng Des Sel 17:699–707. doi:10.1093/protein/gzh082

    Article  CAS  Google Scholar 

  127. Stein V, Sielaff I, Johnsson K, Hollfelder F (2007) A covalent chemical genotype-phenotype linkage for in vitro protein evolution. Chembiochem 8:2191–2194. doi:10.1002/cbic.200700459

    Article  CAS  Google Scholar 

  128. Kaltenbach M, Stein V, Hollfelder F (2011) SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution. Chembiochem 12:2208–2216. doi:10.1002/cbic.201100240

    Article  CAS  Google Scholar 

  129. Diamante L, Gatti-Lafranconi P, Schaerli Y, Hollfelder F (2013) In vitro affinity screening of protein and peptide binders by megavalent bead surface display. Protein Eng Des Sel 26:713–724. doi:10.1093/protein/gzt039

    Article  CAS  Google Scholar 

  130. Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol 13:245–255. doi:10.1016/j.cbpa.2009.04.627

    Article  CAS  Google Scholar 

  131. Binz HK, Amstutz P, Plückthun A (2005) Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23:1257–1268. doi:10.1038/nbt1127

    Article  CAS  Google Scholar 

  132. Gilbreth RN, Koide S (2012) Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol 22:413–420. doi:10.1016/j.sbi.2012.06.001

    Article  CAS  Google Scholar 

  133. Kalko EKV, Dukas R, Ratcliffe JM et al (2011) An expanded palette of genetically encoded Ca2+ indicators. Science 333:1888–1891. doi:10.1126/science.1208592

    Article  CAS  Google Scholar 

  134. Litzlbauer J, Schifferer M, Ng D et al (2015) Large Scale Bacterial Colony Screening of Diversified FRET Biosensors. PLoS One 10:e0119860. doi:10.1371/journal.pone.0119860

    Article  CAS  Google Scholar 

  135. Tian L, Hires SA, Mao T et al (2009) Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6:875–881. doi:10.1038/nmeth.1398

    Article  CAS  Google Scholar 

  136. Wright RC, Khakhar A, Eshleman JR, Ostermeier M (2014) Advancements in the development of hif-1a-activated protein switches for use in enzyme prodrug therapy e114032. PLoS One 9:1–19. doi:10.1371/journal.pone.0114032

    Google Scholar 

  137. Nadler DC, Morgan S-A, Flamholz A et al (2016) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Nat Commun 7:12266. doi:10.1038/ncomms12266

    Article  CAS  Google Scholar 

  138. Feng J, Jester BW, Tinberg CE et al (2015) A general strategy to construct small molecule biosensors in eukaryotes. Elife. doi:10.7554/eLife.10606

    Google Scholar 

  139. Yi L, Gebhard MC, Li Q et al (2013) Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci U S A 110:7229–7234. doi:10.1073/pnas.1215994110

    Article  CAS  Google Scholar 

  140. Kaminski TS, Scheler O, Garstecki P (2016) Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip 16:2168–2187. doi:10.1039/C6LC00367B

    Article  CAS  Google Scholar 

  141. Colin P-Y, Zinchenko A, Hollfelder F (2015) Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 33:42–51. doi:10.1016/j.sbi.2015.06.001

    Article  CAS  Google Scholar 

  142. Vyawahare S, Griffiths AD, Merten CA (2010) Miniaturization and parallelization of biological and chemical assays in microfluidic devices. Chem Biol 17:1052–1065. doi:10.1016/j.chembiol.2010.09.007

    Article  CAS  Google Scholar 

  143. Kintses B, Hein C, Mohamed MF et al (2012) Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. Chem Biol 19:1001–1009. doi:10.1016/j.chembiol.2012.06.009

    Article  CAS  Google Scholar 

  144. Colin P-Y, Kintses B, Gielen F et al (2015) Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun 6:10008. doi:10.1038/ncomms10008

    Article  CAS  Google Scholar 

  145. Agresti JJ, Antipov E, Abate AR et al (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci 107:4004–4009. doi:10.1073/pnas.0910781107

    Article  CAS  Google Scholar 

  146. Wang BL, Ghaderi A, Zhou H et al (2014) Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 32:473–478. doi:10.1038/nbt.2857\rhttp://www.nature.com/nbt/journal/v32/n5/abs/nbt.2857.html#supplementary-information

    Google Scholar 

  147. Debs BE, Utharala R, Balyasnikova IV et al (2012) Functional single-cell hybridoma screening using droplet-based microfluidics. Proc Natl Acad Sci 109:11570–11575. doi:10.1073/pnas.1204514109

    Article  Google Scholar 

  148. Nicholes N, Date A, Beaujean P et al (2015) Modular protein switches derived from antibody mimetic proteins. Protein Eng Des Sel 29:77–85. doi:10.1093/protein/gzv062

    Article  CAS  Google Scholar 

  149. Cosentino C, Alberio L, Gazzarrini S et al (2015) Engineering of a light-gated potassium channel. Science 348:707–710. doi:10.1126/science.aaa2787

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded by the Hessen’s LOEWE Federal State iNAPO research network.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Viktor Stein .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Stein, V. (2017). Synthetic Protein Switches: Theoretical and Experimental Considerations. In: Stein, V. (eds) Synthetic Protein Switches. Methods in Molecular Biology, vol 1596. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6940-1_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6940-1_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6938-8

  • Online ISBN: 978-1-4939-6940-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics