Molecular biology and mutation of green fluorescent protein

Methods of Biochemical Analysis

Volumn 47, Issue , 2005, Pages 83-120

  Zacharias, David A ^a   Tsien, Roger Y ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; AMINO ACID; GREEN FLUORESCENT PROTEIN; RECOMBINANT PROTEIN;

AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HYDROZOA; METABOLISM; METHODOLOGY; MUTAGENESIS; MUTATION; POLYMERASE CHAIN REACTION; PROTEIN CONFORMATION; PROTEIN FOLDING; SINGLE NUCLEOTIDE POLYMORPHISM;

ADENOSINE TRIPHOSPHATE; AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; GREEN FLUORESCENT PROTEINS; HYDROZOA; MODELS, MOLECULAR; MUTAGENESIS; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION; PROTEIN FOLDING; RECOMBINANT PROTEINS;

CRYSTALLOGRAPHY;

GREEN FLUORESCENT PROTEIN; THREE-DIMENSIONAL STRUCTURE;

MOLECULAR BIOLOGY;

EID: 33644623648     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: 10.1002/0471739499.ch5     Document Type: Article

References (158)

1. Akemann, W., Raj, C. D., and Knopfel, T. (2001). Functional characterization of permuted enhanced green fluorescent proteins comprising varying linker peptides. Photochem. Photobiol. 74:356-363.
2. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H., and Miyawaki, A. (2002). An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl. Acad. Sci. USA 99:12651-12656.
3. Arnaudeau, S., Frieden, M., Nakamura, K., Castelbou, C., Michalak, M., and Demaurex, N. (2002). Calreticulin differentially modulates calcium uptake and release in the endoplasmic reticulum and mitochondria. J. Biol. Chem. 277:46696-46705.
4. Ataka, K., and Pieribone, V. A. (2002). A genetically targetable fluorescent probe of channel gating with rapid kinetics. Biophys. J. 82:509-516.
5. Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (1999). Circular permutation and receptor insertion within green fluorescent proteins. Proc. Natl. Acad. Sci. USA 96:11241-11246.
6. Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2000). Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. USA 97:11984-11989.
7. Barondeau, D. P., Putnam, C. D., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2003). Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Proc. Natl. Acad. Sci. USA. 100:12111-12116.
8. Battistutta, R., Negro, A., and Zanotti, G. (2000). Crystal structure and refolding properties of the mutant F99S/M153T/V163A of the green fluorescent protein. Proteins 41:429-437.
9. Bell, A. F., He, X., Wachter, R. M., and Tonge, P. J. (2000). Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy. Biochemistry 39:4423-4431.
10. Bokman, S. H., and Ward, W. W. (1981). Renaturation of Aequorea green-fluorescent protein. Biochem. Biophys. Res. Commun. 101:1372-1380.
11. Brejc, K., Sixma, T. K., Kitts, P. A., Kain, S. R., Tsien, R. Y., Ormo, M., and Remington, S. J. (1997). Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein. Proc. Natl. Acad. Sci. USA 94:2306-2311.
12. Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2002). A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. USA 99:7877-7882.
13. Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2002). A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. USA 99:7877-7882.
14. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., and Prasher, D. C. (1994). Green fluorescent protein as a marker for gene expression. Science 263:802-805.
15. Chattoraj, M., King, B. A., Bublitz, G. U., and Boxer, S. G. (1996). Ultra-fast excited state dynamics in green fluorescent protein: Multiple states and proton transfer. Proc. Natl. Acad. Sci. USA 93:8362-8367.
16. Cheng, L., Fu, J., Tsukamoto, A., and Hawley, R. G. (1996). Use of green fluorescent protein variants to monitor gene transfer and expression in mammalian cells. Nat. Biotechnol. 14:606-609.
17. Cody, C. W., Prasher, D. C., Westler, W. M., Prendergast, F. G., and Ward, W. W. (1993). Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. Biochemistry 32:1212-1218.
18. Cormack, B. P., Valdivia, R. H., and Falkow, S. (1996). FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173:33-38.
19. Cotlet, M., Hofkens, J., Habuchi, S., Dirix, G., Van Guyse, M., Michiels, J., Vanderleyden, J., and De Schryver, F. C. (2001). Identification of different emitting species in the red fluorescent protein DsRed by means of ensemble and single-molecule spectroscopy. Proc. Natl. Acad. Sci. USA 27:27.
20. Crameri, A., Whitehorn, E. A., Tate, E., and Stemmer, W. P. (1996). Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14:315-319.
21. Creemers, T. M., Lock, A. J., Subramaniam, V., Jovin, T. M., and Volker, S. (1999). Three photoconvertible forms of green fluorescent protein identified by spectral hole-burning. Nat. Struct. Biol. 6:557-560.
22. Cubitt, A. B., Heim, R., Adams, S. R., Boyd, A. E., Gross, L. A., and Tsien, R. Y. (1995). Understanding, improving and using green fluorescent proteins. Trends Biochem. Sci. 20:448-455.
23. Cubitt, A. B., Woollenweber, L. A., and Heim, R. (1999). Understanding structure-function relationships in the Aequorea victoria green fluorescent protein. Methods Cell Biol. 58:19-30.
24. Davenport, D., and Nichol, J. A. C. (1955). Proc. R. Soc. London, Ser. B 144:399-411.
25. De Angelis, D. A., Miesenbock, G., Zemelman, B. V., and Rothman, J. E. (1998). PRIM: proximity imaging of green fluorescent protein-tagged polypeptides. Proc. Natl. Acad. Sci. USA 95:12312-12316.
26. Delagrave, S., Hawtin, R. E., Silva, C. M., Yang, M. M., and Youvan, D. C. (1995). Red-shifted excitation mutants of the green fluorescent protein. Biotechnology (NY) 13:151-154.
27. 2+) concentration with targeted "cameleon" fluorescent proteins. Cell Calcium 34:109-119.
28. Dewey, T. G., and Hammes, G. G. (1980). Calculation on fluorescence resonance energy transfer on surfaces. Biophys. J. 32:1023-1035.
29. Dewey, T. G., and Datta, M. M. (1989). Determination of the fractal dimension of membrane protein aggregates using fluorescence energy transfer. Biophys. J. 56:415-420.
30. Doi, N., and Yanagawa, H. (1999). Design of generic biosensors based on green fluorescent proteins with allosteric sites by directed evolution. FEBS Lett. 453:305-307.
31. Dopf, J., and Horiagon, T. M. (1996). Deletion mapping of the Aequorea victoria green fluorescent protein. Gene 173:39-44.
32. Dove, S. G., Hoegh-Guldberg, O., and Ranganathan, S. (2001). Major colour patterns of reef-building corals are due to a family of GFP-like proteins. Coral Reefs 19:197-204.
33. Ehrig, T., O'Kane, D. J., and Prendergast, F. G. (1995). Green-fluorescent protein mutants with altered fluorescence excitation spectra. FEBS Lett. 367:163-166.
34. Fukuda, H., Arai, M., and Kuwajima, K. (2000). Folding of green fluorescent protein and the cycle3 mutant. Biochemistry 39:12025-12032.
35. Fung, B. K., and Stryer, L. (1978). Surface density determination in membranes by fluorescence energy transfer. Biochemistry 17:5241-5248.
36. Garcia-Parajo, M. F., Koopman, M., van Dijk, E. M., Subramaniam, V., and van Hulst, N. F. (2001). The nature of fluorescence emission in the red fluorescent protein DsRed, revealed by single-molecule detection. Proc. Natl. Acad. Sci. USA 27:27.
37. Gerami-Nejad, M., Berman, J., and Gale, C. A. (2001). Cassettes for PCR-mediated construction of green, yellow, and cyan fluorescent protein fusions in Candida albicans. Yeast 18:859-864.
38. Gibbs, M. D., Nevalainen, K. M., and Bergquist, P. L. (2001). Degenerate oligonucleotide gene shuffling (DOGS): A method for enhancing the frequency of recombination with family shuffling. Gene 271:13-20.
39. Giver, L., and Arnold, F. H. (1998). Combinatorial protein design by in vitro recombination. Curr. Opin. Chem. Biol. 2:335-338.
40. Graf, R., and Schachman, H. K. (1996). Random circular permutation of genes and expressed polypeptide chains: Application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 93:11591-11596.
41. Griesbeck, O., Baird, G. S., Campbell, R. E., Zacharias, D. A., and Tsien, R. Y. (2001). Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications. J. Biol. Chem. 276:29188-29194.
42. Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K., and Tsien, R. Y. (2000). The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. USA 97:11990-11995.
43. Guerrero, G., Siegel, M. S., Roska, B., Loots, E., and Isacoff, E. Y. (2002). Tuning Flash: Redesign of the dynamics, voltage range, and color of the genetically encoded optical sensor of membrane potential. Biophys. J. 83:3607-3618.
44. Gurskaya, N. G., Fradkov, A. F., Pounkova, N. I., Staroverov, D. B., Bulina, M. E., Yanushevich, Y. G., Labas, Y. A., Lukyanov, S., and Lukyanov, K. A. (2003). A colourless green fluorescent protein homologue from the non-fluorescent hydromedusa Aequorea coerulescens and its fluorescent mutants. Biochem. J. 373:403-408.
45. Hanson, G. T., McAnaney, T. B., Park, E. S., Rendell, M. E., Yarbrough, D. K., Chu, S., Xi, L., Boxer, S. G., Montrose, M. H., and Remington, S. J. (2002). Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application. Biochemistry 41:15477-15488.
46. Harpur, A. G., Wouters, F. S., and Bastiaens, P. I. (2001). Imaging FRET between spectrally similar GFP molecules in single cells. Nat. Biotechnol. 19:167-169.
47. Haseloff, J., and Amos, B. (1995). GFP in plants. Trends Genet. 11:328-329.
48. Hauser, K., Haynes, W. J., Kung, C., Plattner, H., and Kissmehl, R. (2000). Expression of the green fluorescent protein in Paramecium tetraurelia. Eur. J. Cell. Biol. 79:144-149.
49. Heikal, A. A., Hess, S. T., Baird, G. S., Tsien, R. Y., and Webb, W. W. (2000). Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: Coral red (dsRed) and yellow (Citrine). Proc. Natl. Acad. Sci. USA 97:11996-12001.
50. Heim, R. (1999). Green fluorescent protein forms for energy transfer. Methods Enzymol. 302:408-423.
51. Heim, R., and Tsien, R. Y. (1996). Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr. Biol. 6:178-182.
52. Heim, R., Prasher, D. C., and Tsien, R. Y. (1994). Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA 91:12501-12504.
53. Heim, R., Cubitt, A. B., and Tsien, R. Y. (1995). Improved green fluorescence. Nature 373:663-664.
54. Hofmann, A., Iwai, H., Hess, S., Pluckthun, A., and Wlodawer, A. (2002). Structure of cyclized green fluorescent protein. Acta Crystallogr. D Biol. Crystallogr. 58:1400-1406.
55. Hopf, M., Gohring, W., Ries, A., Timpl, R., and Hohenester, E. (2001). Crystal structure and mutational analysis of a perlecan-binding fragment of nidogen-1. Nat. Struct. Biol. 8:634-640.
56. Hyun Bae, J., Rubini, M., Jung, G., Wiegand, G., Seifert, M. H., Azim, M. K., Kim, J. S., Zumbusch, A., Holak, T. A., Moroder, L., Huber, R., and Budisa, N. (2003). Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins. J. Mol. Biol. 328:1071-1081.
57. Isshiki, M., Ying, Y. S., Fujita, T., and Anderson, R. G. (2002). A molecular sensor detects signal transduction from caveolae in living cells. J. Biol. Chem. 277:43389-43398.
58. Jayaraman, S., Haggie, P., Wachter, R. M., Remington, S. J., and Verkman, A. S. (2000). Mechanism and cellular applications of a green fluorescent protein-based halide sensor. J. Biol. Chem. 275:6047-6050.
59. Jones, J., Heim, R., Hare, E., Stack, J., and Pollok, B. A. (2000). Development and application of a GFP-FRET intracellular caspase assay for drug screening. J. Biomol. Screen 5:307-318.
60. Kaether, C., and Gerdes, H. H. (1995). Visualization of protein transport along the secretory pathway using green fluorescent protein. FEBS Lett. 369:267-271.
61. Kahana, J. A., and Silver, P. A. (1996). Use of the A. Victoria green fluorescent protein to study protein dynamics in vivo. In Current Protocols in Molecular Biology, Aosobel, F. M., Brent, R., Kingston, R. E., Moore, D. E., Seidman, J. G., Smith, J. A., and Struhl, K., Eds., (New York, NY, John Wiley & Sons, Inc.), pp. 9.7.22-29.27.27.
62. Kelmanson, I. V., and Matz, M. V. (2003). Molecular basis and evolutionary origins of color diversity in great star coral Montastraea cavernosa (Scleractinia: Faviida). Mol. Biol. Evol. 20:1125-1133.
63. Kerr, R., Lev-Ram, V., Baird, G., Vincent, P., Tsien, R. Y., and Schafer, W. R. (2000). Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans. Neuron 26:583-594.
64. Kim, H. K., and Kaang, B. K. (1998). Truncated green fluorescent protein mutants and their expression in Aplysia neurons. Brain. Res. Bull. 47:35-41.
65. Kimata, Y., Iwaki, M., Lim, C. R., and Kohno, K. (1997). A novel mutation which enhances the fluorescence of green fluorescent protein at high temperatures. Biochem. Biophys. Res. Commun. 232:69-73.
66. Kozak, M. (1989). The scanning model for translation: An update. J. Cell Biol. 108:229-241.
67. Kummer, A. D., Wiehler, J., Schuttrigkeit, T. A., Berger, B. W., Steipe, B., and Michel-Beyerle, M. E. (2002). Picosecond time-resolved fluorescence from blue-emitting chromophore variants Y66F and Y66H of the green fluorescent protein. Chembiochem 3:659-663.
68. Kuner, T.. and Augustine G. J. (2000). A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons. Neuron 27:447-459.
69. Lakowicz, J. (1999). Principles of Fluorescence Spectroscopy, 2nd ed., Plenum, New York.
70. Levy, J. P., Muldoon, R. R., Zolotukhin, S., and Link, C. J., Jr. (1996). Retroviral transfer and expression of a humanized, red-shifted green fluorescent protein gene into human tumor cells. Nat. Biotechnol. 14:610-614.
71. Lim, C. R., Kimata, Y., Oka, M., Nomaguchi, K., and Kohno, K. (1995). Thermosensitivity of green fluorescent protein fluorescence utilized to reveal novel nuclear-like compartments in a mutant nucleoporin NSP1. J. Biochem. (Tokyo) 118:13-17.
72. Liu, L., Yermolaieva, O., Johnson, W. A., Abboud, F. M., and Welsh, M. J. (2003). Identification and function of thermosensory neurons in Drosophila larvae. Nat. Neurosci. 6:267-273.
73. Llopis, J., McCaffery, J. M., Miyawaki, A., Farquhar, M. G., and Tsien, R. Y. (1998). Measurement of cytosolic, mitochondrial, and Golgi pH in single living cells with green fluorescent proteins. Proc. Natl. Acad. Sci. USA 95:6803-6808.
74. Luo, K. Q., Yu, V. C., Pu, Y., and Chang, D. C. (2001). Application of the fluorescence resonance energy transfer method for studying the dynamics of caspase-3 activation during UV-induced apoptosis in living HeLa cells. Biochem. Biophys. Res. Commun. 283:1054-1060.
75. 2+ elevation during agonist stimulation. J. Biol. Chem. 278:10807-10815.
76. Martynov, V. I., Savitsky, A. P., Martynova, N. Y., Savitsky, P. A., Lukyanov, K. A., and Lukyanov, S. A. (2001). Alternative cyclization in GFP-like proteins family. The formation and structure of the chromophore of a purple chromoprotein from Anemonia sulcata. J. Biol. Chem. 276:21012-21016.
77. Matz, M. V., Lukyanov, K. A., and Lukyanov, S. A. (2002). Family of the green fluorescent protein: Journey to the end of the rainbow. Bioessays 24:953-959.
78. McAnaney, T. B., Park, E. S., Hanson, G. T., Remington, S. J., and Boxer, S. G. (2002). Green fluorescent protein variants as ratiometric dual emission pH sensors. 2. Excited-state dynamics. Biochemistry 41:15489-15494.
79. McElroy, W. D. (1947). The energy source for biolominescence in an isolated system, Proc. Natl. Acad. Sci. USA 33:342-345.
80. McRorie, D., and Voelker, P. (1993). Self-Associating Systems in the Analytical Ultracentrifuge, Beckman Instruments, Fullerton, CA.
81. Miesenbock, G., De Angelis, D. A., and Rothman, J. E. (1998). Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature 394:192-195.
82. Minshull, J., and Stemmer, W. P. (1999). Protein evolution by molecular breeding. Curr. Opin. Chem. Biol. 3:284-290.
83. Mitra, R. D., Silva, C. M., and Youvan, D. C. (1996). Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein. Gene 173:13-17.
84. 2+ based on green fluorescent proteins and calmodulin. Nature 388:882-887.
85. Miyawaki, A. (2003). Visualization of the spatial and temporal dynamics of intracellular signaling. Dev. Cell. 4:295-305.
86. Mizuno, H., Sawano, A., Eli, P., Hama, H., and Miyawaki, A. (2001). Red fluorescent protein from Discosoma as a fusion tag and a partner for fluorescence resonance energy transfer. Biochemistry 40:2502-2510.
87. Morise, H., Shimomura, O., Johnson, F. H., and Winant, J. (1974). Intermolecular energy transfer in the bioluminescent system of Aequorea. Biochemistry 13:2656-2662.
88. Muhlrad, D., Hunter, R., and Parker, R. (1992). A rapid method for localized mutagenesis of yeast genes. Yeast 8:79-82.
89. 2+. Proc. Natl. Acad. Sci. USA 98:3197-3202.
90. Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., and Miyawaki, A. (2002). A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20:87-90.
91. 2+) probe composed of a single green fluorescent protein. Nat. Biotechnol. 19:137-141.
92. Niwa, H., Inouye, S., Hirano, T., Matsuno, T., Kojima, S., Kubota, M., Ohashi, M., and Tsuji, F. I. (1996). Chemical nature of the light emitter of the Aequorea green fluorescent protein. Proc. Natl. Acad. Sci. USA 93:13617-13622.
93. Ormo, M., Cubitt, A. B., Kallio, K., Gross, L. A., Tsien, R. Y., and Remington, S. J. (1996). Crystal structure of the Aequorea victoria green fluorescent protein. Science 273:1392-1395.
94. Palm, G., and Wlodawer, A. (1999). Spectral variants of green fluorescent protein. Methods Enzymol. 302:378-394.
95. Palm, G. J., Zdanov, A., Gaitanaris, G. A., Stauber, R., Pavlakis, G. N., and Wlodawer, A. (1997). The structural basis for spectral variations in green fluorescent protein. Nat. Struct. Biol. 4:361-365.
96. 2+ analyzed with an improved genetically encoded fluorescent sensor. Proc. Natl. Acad. Sci. USA 101:17404-17409.
97. Patterson, G. H., and Lippincott-Schwartz, J. (2002). A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297:1873-1877.
98. Patterson, G. H., Knobel, S. M., Sharif, W. D., Kain, S. R., and Piston, D. W. (1997). Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys. J. 73:2782-2790.
99. Patterson, G. H., Piston, D. W., and Barisas, B. G. (2000). Forster distances between green fluorescent protein pairs. Anal. Biochem. 284:438-440.
100. Prasher, D. (1995). Using GFP to see the light. Trends Genet. 11:320-232.
101. Prasher, D. C., Eckenrode, V. K., Ward, W. W., Prendergast, F. G., and Cormier, M. J. (1992). Primary structure of the Aequorea victoria green-fluorescent protein. Gene 111:229-233.
102. Reiff, D. F., Thiel, P. R., and Schuster, C. M. (2002). Differential regulation of active zone density during long-term strengthening of Drosophila neuromuscular junctions. J. Neurosci. 22:9399-9409.
103. Rekas, A., Alattia, J. R., Nagai, T., Miyawaki, A., and Ikura, M. (2002). Crystal structure of Venus, a yellow fluorescent protein with improved maturation and reduced environmental sensitivity. J. Biol. Chem. 4:4.
104. Richmond, T. A., Takahashi, T. T., Shimkhada, R., and Bernsdorf, J. (2000). Engineered metal binding sites on green fluorescence protein. Biochem. Biophys. Res. Commun. 268:462-465.
105. Rizzo, M. A., Springer, G. H., Granada, B., and Piston, D. W. (2004). An improved cyan fluorescent protein variant useful for FRET. Nat. Biotechnol. 22:445-449.
106. Rizzuto, R., Brini, M., De Giorgi, F., Rossi, R., Heim, R., Tsien, R. Y., and Pozzan, T. (1996). Double labelling of subcellular structures with organelle-targeted GFP mutants in vivo. Curr. Biol. 6:183-188.
107. Salih, A., Larkum, A., Cox, G., Kuhl, M., and Hoegh-Guldberg, O. (2000). Fluorescent pigments in corals are photoprotective. Nature 408:850-853.
108. Sankaranarayanan, S., De Angelis, D., Rothman, J. E., and Ryan, T. A. (2000). The use of pHluorins for optical measurements of presynaptic activity. Biophys. J. 79:2199-2208.
109. Sawano, A., and Miyawaki, A. (2000). Directed evolution of green fluorescent protein by a new versatile PCR strategy for site-directed and semi-random mutagenesis. Nucleic Acids Res. 28:E78.
110. Scharnagl, C., Raupp-Kossmann, R., and Fischer, S. F. (1999). Molecular basis for pH sensitivity and proton transfer in green fluorescent protein: Protonation and conformational substates from electrostatic calculations. Biophys. J. 77:1839-1857.
111. Shaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N., Palmer, A. E., and Tsien, R. Y. (2004). Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22:1567-1572.
112. Shimomura, O. (1979). Structure of the chromophore of Aequorea green fluorescent protein. FEBS Lett. 104:220-222.
113. Siegel, M. S., and Isacoff, E. Y. (1997). A genetically encoded optical probe of membrane voltage. Neuron 19:735-741.
114. Siemering, K. R., Golbik, R., Sever, R., and Haseloff, J. (1996). Mutations that suppress the thermosensitivity of green fluorescent protein. Curr. Biol. 6:1653-1663.
115. Sikorski, R. S., and Boeke, J. D. (1991). In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods Enzymol. 194:302-318.
116. Simon, S. M. (1996). Cellular probes on the move. Nat. Biotechnol. 14:1221.
117. Snyder, B., and Freire, E. (1982). Fluorescence energy transfer in two dimensions. A numeric solution for random and nonrandom distributions. Biophys. J. 40:137-148.
118. Tawa, P., Tam, J., Cassady, R., Nicholson, D. W., and Xanthoudakis, S. (2001). Quantitative analysis of fluorescent caspase substrate cleavage in intact cells and identification of novel inhibitors of apoptosis. Cell Death Differ. 8:30-37.
119. Ting, A. Y., Kain, K. H., Klemke, R. L., and Tsien, R. Y. (2001). Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells. Proc. Natl. Acad. Sci. USA 98:15003-15008.
120. Topell, S., Hennecke, J., and Glockshuber, R. (1999). Circularly permuted variants of the green fluorescent protein. FEBS Lett. 457:283-289.
121. Tsien, R. Y. (1998). The green fluorescent protein. Annu. Rev. Biochem. 67:509-544.
122. Tsien, R. Y., Bacskai, B., and Adams, S. R. (1993). FRET for studying intracellular signalling. Trends Cell Biol. 3:242-245.
123. van Thor, J. J., Gensch, T., Hellingwerf, K. J., and Johnson, L. N. (2002). Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222. Nat. Struct. Biol. 9:37-41.
124. Violin, J. D., Zhang, J., Tsien, R. Y., and Newton, A. C. (2003). A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J. Cell Biol. 161:899-909.
125. Volkov, A. A., Shao, Z., and Arnold, F. H. (1999). Recombination and chimeragenesis by an in vitro heteroduplex formation and in vivo repair. Nucleic Acids Res. 27:e18 i-vi.
126. Wachter, R. M., King, B. A., Heim, R., Kallio, K., Tsien, R. Y., Boxer, S. G., and Remington, S. J. (1997). Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein. Biochemistry 36:9759-9765.
127. Wachter, R. M., Elsliger, M. A., Kallio, K., Hanson, G. T., and Remington, S. J. (1998). Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. Structure 6:1267-1277.
128. Wachter, R. M., and Remington, S. J. (1999). Sensitivity of the yellow variant of green fluorescent protein to halides and nitrate. Curr. Biol. 9:R628-R629.
129. Wachter, R. M., Yarbrough, D., Kallio, K., and Remington, S. J. (2000). Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein. J. Mol. Biol. 301:157-171.
130. Waldo, G. S., Standish, B. M., Berendzen, J., and Terwilliger, T. C. (1999). Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol. 17:691-695.
131. Wang, L., Jackson, W. C., Steinbach, P. A., and Tsien, R. Y. (2004) Evolution of new nonantibody proteins via iterative somatic hypermutation. Proc. Natl. Acad. Sci. USA 101:16745-16749.
132. Wang, L., Xie, J., Deniz, A. A., and Schultz, P. G. (2003). Unnatural amino acid mutagenesis of green fluorescent protein. J. Org. Chem. 68:174-176.
133. Ward, W. W. (1998). In GFP Green Fluorescent Protein Properties, Applications and Protocols, Chalfie, M., and Kain, S, Ed. Wiley-Liss, New York, pp. 45-75.
134. Ward, W. W., and Bokman, S. H. (1982). Reversible denaturation of Aequorea green-fluorescent protein: Physical separation and characterization of the renatured protein. Biochemistry 21:4535-4540.
135. Ward, W. W., and Cormier, M. J. (1979). An energy transfer protein in coelenterate bioluminescence. Characterization of the Renilla green-fluorescent protein. J. Biol. Chem. 254:781-788.
136. Ward, W., Prentice, H., Roth, A., Cody, C., and Reeves, S. (1982). Spectral perturbations of the Aequorea green fluorescent protein. Photochem. Photobiol. 35:803-808.
137. Wiedenmann, J., Elke, C., Spindler, K. D., and Funke, W. (2000). Cracks in the beta-can: Fluorescent proteins from Anemonia sulcata (Anthozoa, Actinaria). Proc. Natl. Acad. Sci. USA 97:14091-14096.
138. Wiedenmann, J., Schenk, A., Rocker, C., Girod, A., Spindler, K. D., and Nienhaus, G. U. (2002). A far-red fluorescent protein with fast maturation and reduced oligomerization tendency from Entacmaea quadricolor (Anthozoa, Actinaria). Proc. Natl. Acad. Sci. USA 99:11646-11651.
139. Wolber, P. K., and Hudson, B. S. (1979). An analytic solution to the Forster energy transfer problem in two dimensions. Biophys. J. 28:197-210.
140. Wu, P., and Brand, L. (1994). Resonance energy transfer: Methods and applications. Anal. Biochem. 218:1-13.
141. Xu, X., Gerard, A. L., Huang, B. C., Anderson, D. C., Payan, D. G., and Luo, Y. (1998). Detection of programmed cell death using fluorescence energy transfer. Nucleic Acids Res. 26:2034-2035.
142. Yang, F., Moss, L. G., and Phillips, G. N., Jr. (1996a). The molecular structure of green fluorescent protein. Nat. Biotechnol. 14:1246-1251.
143. Yang, T. T., Kain, S. R., Kitts, P., Kondepudi, A., Yang, M. M., and Youvan, D. C. (1996b). Dual color microscopic imagery of cells expressing the green fluorescent protein and a red-shifted variant. Gene. 173:19-23.
144. Yang, T. T., Sinai, P., Green, G., Kitts, P. A., Chen, Y. T., Lybarger, L., Chervenak, R., Patterson, G. H., Piston, D. W., and Kain, S. R. (1998). Improved fluorescence and dual color detection with enhanced blue and green variants of the green fluorescent protein. J. Biol. Chem. 273:8212-8216.
145. Yguerabide, J. (1994). Theory for establishing proximity relations in biological membranes by excitation energy transfer measurements. Biophys. J. 66:683-693.
146. Yokoe, H., and Meyer, T. (1996). Spatial dynamics of GFP-tagged proteins investigated by local fluorescence enhancement. Nat. Biotechnol. 14:1252-1256.
147. Youvan, D. C., Goldman, E., Delagrave, S., and Yang, M. M. (1995). Digital imaging spectroscopy for massively parallel screening of mutants. Methods Enzymol. 246:732-748.
148. Yu, D., Baird, G. S., Tsien, R. Y., and Davis, R. L. (2003). Detection of calcium transients in Drosophila mushroom body neurons with camgaroo reporters. J. Neurosci. 23:64-72.
149. Zacharias, D. A., Baird, G. S., and Tsien, R. Y. (2000). Recent advances in technology for measuring and manipulating cell signals. Curr. Opin. Neurobiol. 10:416-421.
150. Zacharias, D. A., Violin, J. D., Newton, A. C., and Tsien, R. Y. (2001). Partitioning of monomeric lipid modified GFPs inot lipid rafts of living cells. Science 296:913-916.
151. Zacharias, D. A. (2002). Sticky caveats in an otherwise glowing report: Oligomerizing fluorescent proteins and their use in cell biology. Sci. STKE 2002:PE23.
152. Zapata-Hommer, O., and Griesbeck, O. (2003). Efficiently folding and circularly permuted variants of the Sapphire mutant of GFP. BMC Biotechnol. 3:5.
153. Zhang, C. L., Chen, D. F., McCormac, A. C., Scott, N. W., Elliott, M. C., and Slater, A. (2001a). Use of the GFP reporter as a vital marker for Agrobacterium-mediated transformation of sugar beet (Beta vulgaris L.). Mol. Biotechnol. 17:109-117.
154. Zhang, J., Ma, Y., Taylor, S. S., and Tsien, R. Y. (2001b). Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc. Natl. Acad. Sci. USA 98:14997-15002.
155. Zhang, J., Campbell, R. E., Ting, A. Y., and Tsien, R. Y. (2002). Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3:906-918.
156. Zimet, D. B., Thevenin, B. J., Verkman, A. S., Shohet, S. B., and Abney, J. R. (1995). Calculation of resonance energy transfer in crowded biological membranes. Biophys. J. 68:1592-1603.
157. Zimmer, M. (2002). Green fluorescent protein (GFP): Applications, structure, and related photophysical behavior. Chem. Rev. 102:759-781.
158. Zolotukhin, S., Potter, M., Hauswirth, W. W., Guy, J., and Muzyczka, N. (1996). A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J. Virol. 70:4646-4654.