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66. Hanson GT et al (2004) Investigating mitochondrial redox potential with redox-sensitive green
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cells with green fluorescent proteins. Proc Natl Acad Sci U S A 95(12):6803–6808
69. Sankaranarayanan S et al (2000) The use of pHluorins for optical measurements of presynaptic
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J Am Chem Soc 131(37):13212–13213
71. Violot S et al (2009) Reverse pH-dependence of chromophore protonation explains the large
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72. Fang EF et al (2017) In vitro and in vivo detection of mitophagy in human cells, C. Elegans,
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73. Shinoda H, Shannon M, Nagai T (2018) Fluorescent proteins for investigating biological
events in acidic environments. Int J Mol Sci 19(6):1543
74. Tantama M, Hung YP, Yellen G (2011) Imaging intracellular pH in live cells with a
genetically encoded red fluorescent protein sensor. J Am Chem Soc 133(26):10034–10037
75. Shcherbakova DM, Subach OM, Verkhusha VV (2012) Red fluorescent proteins: advanced
imaging applications and future design. Angew Chem Int Ed Engl 51(43):10724–10738
178
U. K. Sukumar et al.
(4):042006
52. Miesenbock G, De Angelis DA, Rothman JE (1998) Visualizing secretion and synaptic
transmission with pH-sensitive green fluorescent proteins. Nature 394(6689):192–195
53. Johnson DE et al (2009) Red fluorescent protein pH biosensor to detect concentrative
nucleoside transport. J Biol Chem 284(31):20499–20511
54. Tallini YN et al (2006) Imaging cellular signals in the heart in vivo: cardiac expression of the
high-signal Ca2+ indicator GCaMP2. Proc Natl Acad Sci U S A 103(12):4753–4758
55. Souslova EA et al (2007) Single fluorescent protein-based Ca2+ sensors with increased
dynamic range. BMC Biotechnol 7:37
56. Griesbeck O et al (2001) Reducing the environmental sensitivity of yellow fluorescent protein.
Mechanism and applications. J Biol Chem 276(31):29188–29194
57. Belousov VV et al (2006) Genetically encoded fluorescent indicator for intracellular hydrogen
peroxide. Nat Methods 3(4):281–286
58. Gallegos LL, Kunkel MT, Newton AC (2006) Targeting protein kinase C activity reporter to
discrete intracellular regions reveals spatiotemporal differences in agonist-dependent signaling. J Biol Chem 281(41):30947–30956
59. Goedhart J et al (2007) Sensitive detection of p65 homodimers using red-shifted and fluorescent protein-based FRET couples. PLoS One 2(10):e1011
60. Miyawaki A et al (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins
and calmodulin. Nature 388(6645):882–887
61. Berney C, Danuser G (2003) FRET or no FRET: a quantitative comparison. Biophys J 84
(6):3992–4010
62. Hanson GT et al (2002) Green fluorescent protein variants as ratiometric dual emission
pH sensors. 1. Structural characterization and preliminary application. Biochemistry 41
(52):15477–15488
63. Kneen M et al (1998) Green fluorescent protein as a noninvasive intracellular pH indicator.
Biophys J 74(3):1591–1599
64. Jayaraman S et al (2000) Mechanism and cellular applications of a green fluorescent proteinbased halide sensor. J Biol Chem 275(9):6047–6050
65. DiPilato LM, Cheng X, Zhang J (2004) Fluorescent indicators of cAMP and Epac activation
reveal differential dynamics of cAMP signaling within discrete subcellular compartments.
Proc Natl Acad Sci U S A 101(47):16513–16518
66. Hanson GT et al (2004) Investigating mitochondrial redox potential with redox-sensitive green
fluorescent protein indicators. J Biol Chem 279(13):13044–13053
67. Ashby MC, Ibaraki K, Henley JM (2004) It’s green outside: tracking cell surface proteins with
pH-sensitive GFP. Trends Neurosci 27(5):257–261
68. Llopis J et al (1998) Measurement of cytosolic, mitochondrial, and Golgi pH in single living
cells with green fluorescent proteins. Proc Natl Acad Sci U S A 95(12):6803–6808
69. Sankaranarayanan S et al (2000) The use of pHluorins for optical measurements of presynaptic
activity. Biophys J 79(4):2199–2208
70. Henderson JN et al (2009) Excited state proton transfer in the red fluorescent protein mKeima.
J Am Chem Soc 131(37):13212–13213
71. Violot S et al (2009) Reverse pH-dependence of chromophore protonation explains the large
Stokes shift of the red fluorescent protein mKeima. J Am Chem Soc 131(30):10356–10357
72. Fang EF et al (2017) In vitro and in vivo detection of mitophagy in human cells, C. Elegans,
and mice. J Vis Exp 129:e56301
73. Shinoda H, Shannon M, Nagai T (2018) Fluorescent proteins for investigating biological
events in acidic environments. Int J Mol Sci 19(6):1543
74. Tantama M, Hung YP, Yellen G (2011) Imaging intracellular pH in live cells with a
genetically encoded red fluorescent protein sensor. J Am Chem Soc 133(26):10034–10037
75. Shcherbakova DM, Subach OM, Verkhusha VV (2012) Red fluorescent proteins: advanced
imaging applications and future design. Angew Chem Int Ed Engl 51(43):10724–10738
178
U. K. Sukumar et al.