86
1. Wang H, Nakata E, Hamachi I (2009) Recent
progress in strategies for the creation of
protein- based
fluorescent
biosensors.
Chembiochem 10:2560–2577
2. Okada S, Ota K, Ito T (2009) Circular permutation of ligand-binding module improves
dynamic range of genetically encoded FRETbased nanosensor. Protein Sci 18:2518–2527
3. Hires SA, Zhu Y, Tsien RY (2008) Optical
measurement of synaptic glutamate spillover
and reuptake by linker optimized glutamatesensitive fluorescent reporters. Proc Natl Acad
Sci 105:4411–4416
4. Okumoto S, Looger LL, Micheva KD et al
(2005) Detection of glutamate release from
neurons by genetically encoded surfacedisplayed FRET nanosensors. Proc Natl Acad
Sci 102:8740–8745
5. Dwyer MA, Hellinga HW (2004) Periplasmic
binding proteins: a versatile superfamily for
protein engineering. Curr Opin Struct Biol
14:495–504
6. Whitfield JH, Zhang W, Herde MK et al
(2015) Construction of a robust and sensitive
arginine biosensor through ancestral protein
reconstruction. Protein Sci 24:1412–1422
7. Gaucher EA, Govindarajan S, Ganesh OK
(2008)
Palaeotemperature
trend
for
Precambrian life inferred from resurrected
proteins. Nature 451:704–707
8. Akanuma S, Nakajima Y, Yokobori S et al
(2013) Experimental evidence for the thermophilicity of ancestral life. Proc Natl Acad Sci
USA 110:11067–11072
9. 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
10. Perez-Jimenez R, Inglés-Prieto A, Zhao Z-M
et al (2011) Single-molecule paleoenzymology
probes the chemistry of resurrected enzymes.
Nat Struct Mol Biol 18:592–596
11. Risso VA, Gavira JA, Sanchez-Ruiz JM (2013)
Thermostable and promiscuous Precambrian
proteins. Environ Microbiol 16:1485–1489
12. Gaucher EA, Thomson JM, Burgan MF et al
(2003) Inferring the palaeoenvironment of
ancient bacteria on the basis of resurrected
proteins. Nature 425:285–288
13. Cole MF, Gaucher EA (2011) Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin
Chem Biol 15:399–406
14. Williams PD, Pollock DD, Blackburne BP et al
(2006) Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput
Biol 2:e69
15. Bershtein S, Goldin K, Tawfik DS (2008)
Intense neutral drifts yield robust and evolvable
consensus proteins. J Mol Biol 379:1029–1044
22. The FRET sensors are expressed with N-terminal hexahistidine tags, allowing purification by nickel affinity chromatography. In our experience, further purification by size-exclusion
chromatography can also improve the dynamic range of the
sensor. Finally, extensive dialysis may be required to remove
any endogenously bound ligands, as sensor molecules that are
already ligand-bound do not exhibit a ligand-dependent
change in FRET, reducing the observed FRET efficiency.
Acknowledgments
Research was funded by Human Frontiers Science Program Young
Investigator Award (HFSP to H.J., C.H., and C.J.J., grant number: RGY0084/2012), German Academic Exchange Service
(DAAD-Go8) Travel Fellowship (to C.H. and C.J.J.), NRWRückkehrerprogramm (to C.H.), and German Research
Foundation (DFG, SFB1089 B03, SPP1757 HE6949/1-1 and
HE6949/3-1, all to C.H.).
References
Ben E. Clifton et al.
1. Wang H, Nakata E, Hamachi I (2009) Recent
progress in strategies for the creation of
protein- based
fluorescent
biosensors.
Chembiochem 10:2560–2577
2. Okada S, Ota K, Ito T (2009) Circular permutation of ligand-binding module improves
dynamic range of genetically encoded FRETbased nanosensor. Protein Sci 18:2518–2527
3. Hires SA, Zhu Y, Tsien RY (2008) Optical
measurement of synaptic glutamate spillover
and reuptake by linker optimized glutamatesensitive fluorescent reporters. Proc Natl Acad
Sci 105:4411–4416
4. Okumoto S, Looger LL, Micheva KD et al
(2005) Detection of glutamate release from
neurons by genetically encoded surfacedisplayed FRET nanosensors. Proc Natl Acad
Sci 102:8740–8745
5. Dwyer MA, Hellinga HW (2004) Periplasmic
binding proteins: a versatile superfamily for
protein engineering. Curr Opin Struct Biol
14:495–504
6. Whitfield JH, Zhang W, Herde MK et al
(2015) Construction of a robust and sensitive
arginine biosensor through ancestral protein
reconstruction. Protein Sci 24:1412–1422
7. Gaucher EA, Govindarajan S, Ganesh OK
(2008)
Palaeotemperature
trend
for
Precambrian life inferred from resurrected
proteins. Nature 451:704–707
8. Akanuma S, Nakajima Y, Yokobori S et al
(2013) Experimental evidence for the thermophilicity of ancestral life. Proc Natl Acad Sci
USA 110:11067–11072
9. 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
10. Perez-Jimenez R, Inglés-Prieto A, Zhao Z-M
et al (2011) Single-molecule paleoenzymology
probes the chemistry of resurrected enzymes.
Nat Struct Mol Biol 18:592–596
11. Risso VA, Gavira JA, Sanchez-Ruiz JM (2013)
Thermostable and promiscuous Precambrian
proteins. Environ Microbiol 16:1485–1489
12. Gaucher EA, Thomson JM, Burgan MF et al
(2003) Inferring the palaeoenvironment of
ancient bacteria on the basis of resurrected
proteins. Nature 425:285–288
13. Cole MF, Gaucher EA (2011) Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin
Chem Biol 15:399–406
14. Williams PD, Pollock DD, Blackburne BP et al
(2006) Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput
Biol 2:e69
15. Bershtein S, Goldin K, Tawfik DS (2008)
Intense neutral drifts yield robust and evolvable
consensus proteins. J Mol Biol 379:1029–1044
22. The FRET sensors are expressed with N-terminal hexahistidine tags, allowing purification by nickel affinity chromatography. In our experience, further purification by size-exclusion
chromatography can also improve the dynamic range of the
sensor. Finally, extensive dialysis may be required to remove
any endogenously bound ligands, as sensor molecules that are
already ligand-bound do not exhibit a ligand-dependent
change in FRET, reducing the observed FRET efficiency.
Acknowledgments
Research was funded by Human Frontiers Science Program Young
Investigator Award (HFSP to H.J., C.H., and C.J.J., grant number: RGY0084/2012), German Academic Exchange Service
(DAAD-Go8) Travel Fellowship (to C.H. and C.J.J.), NRWRückkehrerprogramm (to C.H.), and German Research
Foundation (DFG, SFB1089 B03, SPP1757 HE6949/1-1 and
HE6949/3-1, all to C.H.).
References
Ben E. Clifton et al.