Building photonic proteins

CRC Handbook of: Organic Photochemistry and Photobiology, Second Edition

Volumn , Issue , 2003, Pages 133-1-133-21

  Rothschild, Kenneth J ^a   Gite, Sadanand ^b   Mamaev, Sergey ^b   Olejnik, Jerzy ^b  

^a BOSTON UNIVERSITY   (United States)

^b AMBERGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 53049098468     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (155)

1. Le Grand, Y., An Introduction to Photobiology, Elsevier, Amsterdam; New York, 1970.
2. Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., Sogin, M.L., and Jannasch, H.W., Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities, Appl. Environ. Microbiol., 68, 4, 1994-2007, 2002.
3. Madigan, M.T. and Marrs, B.L., Extremophiles, Sci. Am., 276, 4, 82, 1997.
4. Deisenhofer, J. and Michel, H., Nobel lecture. The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis, EMBO J., 8, 8, 2149, 1989.
5. Allen, J.P. and Williams, J.C., Photosynthetic reaction centers, FEBS Lett., 438, 1-2, 5, 1998.
6. Breton, J. and Vermeglio, A., The Photosynthetic Bacterial Reaction Center II, Plenum Press, New York, 1992.
7. Rothschild, K.J. and Sonar, S., Bacteriorhodopsin: new biophysical perspectives, in CRC Handbook of Organic Photochemistry and Photobiology, Horspool, W.M. and Song, P.-S., Eds., CRC Press LLC, Boca Raton, FL, 1995, pp. 1521-1544.
8. Beja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., Jovanovich, S.B., Gates, C.M., Feldman, R.A., Spudich, J.L., Spudich, E.N., and DeLong, E.F., Bacterial rhodopsin: evidence for a new type of phototrophy in the sea, Science, 289, 5486, 1902, 2000.
9. Dioumaev, A.K., Brown, L.S., Shih, J., Spudich, E.N., Spudich, J.L., and Lanyi, J.K., Proton transfers in the photochemical reaction cycle of proteorhodopsin, Biochemistry, 41, 17, 5348, 2002.
10. Wald, G., Molecular basis of visual excitation, Science, 162, 230, 1968.
11. Khorana, H.G., Rhodopsin, photoreceptor of the rod cell. An emerging pattern for structure and function, J. Biol. Chem., 267, 1, 1, 1992.
12. DeGrip, W.J. and Rothschild, K.J., Structure and mechanism of vertebrate visual pigments, in Molecular Mechanisms in Visual Transduction, Stravenga, D.G., de Grip, W.J., and Pugh, E.N., Elsevier, Amsterdam; New York, 2000, pp. 1-54.
13. Spudich, J.L., Variations on a molecular switch: transport and sensory signalling by archaeal rhodopsins, Mol. Microbiol., 28, 6, 1051, 1998.
14. Choi, G., Yi, H., Lee, J., Kwon, Y.K., Soh, M.S., Shin, B., Luka, Z., Hahn, T.R., and Song, P.S., Phytochrome signalling is mediated through nucleoside diphosphate kinase 2, Nature, 401, 6753, 610, 1999.
15. Smith, H., Phytochromes and light signal perception by plants -an emerging synthesis, Nature, 407, 6804, 585, 2000.
16. Briggs, W.R. and Christie, J.M., Phototropins 1 and 2: versatile plant blue-light receptors, Trends Plant Sci., 7, 5, 204, 2002.
17. Swartz, T.E., Wenzel, P.J., Corchnoy, S.B., Briggs, W.R., and Bogomolni, R.A., Vibration spectroscopy reveals light-induced chromophore and protein structural changes in the LOV2 domain of the plant blue-light receptor phototropin 1, Biochemistry, 41, 23, 7183, 2002.
18. Tsien, R.Y., The green fluorescent protein, Annu. Rev. Biochem., 67, 509, 1998.
19. Baldwin, T.O., Firefly luciferase: the structure is known, but the mystery remains, Structure, 4, 3, 223, 1996.
20. Craig, D.B., Dovichi, N.J., Multiple labeling of proteins, Anal. Chem., 70, 13, 2493, 1998.
21. Hafner, F.T., Kautz, R.A., Iverson, B.L., Tim, R.C., and Karger, B.L., Noncompetitive immunoassay of small analytes at the femtomolar level by affinity probe capillary electrophoresis: direct analysis of digoxin using a uniform-labeled scFv immunoreagent, Anal. Chem., 72, 23, 5779, 2000.
22. Tim, R.C., Kautz, R.A., and Karger, B.L., Ultratrace analysis of drugs in biological fluids using affinity probe capillary electrophoresis: analysis of dorzolamide with fluorescently labeled carbonic anhydrase, Electrophoresis, 21, 1, 220, 2000.
23. Thompson, S., Spoors, J.A., Fawcett, M.-C., and Self, C.H., Photocleavable nitrobenzyl-protein conjugates, Biochem. Biophys. Res. Commun., 201, 1213, 1994.
24. Marriott, G., Caged protein conjugates and light-directed generation of protein activity: preparation, photoactivation, and spectroscopic characterization of caged G-actin conjugates, Biochemistry, 33, 31, 9092, 1994.
25. Marriott, G., Ottl, J., Heidecker, M., and Gabriel, D., Light-directed activation of protein activity from caged protein conjugates, Methods Enzymol., 291, 95, 1998.
26. Self, C.H. and Thompson, S., Light activatable antibodies: models for remotely activatable proteins, Nat. Med., 2, 7, 817, 1996.
27. Kossel, A.H., Cambridge, S.B., Wagner, U., and Bonhoeffer, T., A caged Ab reveals an immediate/instructive effect of BDNF during hippocampal synaptic potentiation, Proc. Natl. Acad. Sci. USA, 98, 25, 14702, 2001.
28. Minden, J., Namba, R., Mergliano, J., and Cambridge, S., Photoactivated gene expression for cell fate mapping and cell manipulation, Sci. STKE 2000, 62, L1, 2000.
29. Olejnik, J., Sonar, S., Krzymanska-Olejnik, E., and Rothschild, K.J., Photocleavable biotin derivatives: versatile approach for the isolation of biomolecules, Proc. Natl. Acad. Sci. USA, 92, 7590, 1995.
30. Gite, S., Mamaev, S., Nuara, M., Chaley, S., Bayley, H., and Rothschild, K., Light-mediated activation of a-hemolysin, Biophys. J., 76, A125, 1999.
31. Moritz, M., Braunfeld, M.B., Guenebaut, V., Heuser, J., and Agard, D.A., Structure of the gammatubulin ring complex: a template for microtubule nucleation, Nat. Cell Biol., 2, 6, 365, 2000.
32. Pandori, M.W., Hobson, D.A., Olejnik, J., Krzymanska-Olejnik, E., Rothschild, K.J., Palmer, A.A., Phillips, T.J., and Sano, T., Photochemical control of the infectivity of adenoviral vectors using a novel photocleavable biotinylation reagent, Chem. Biol., 9, 5, 567, 2002.
33. Chang, C.-Y., Niblack, B., Walker, B., and Bayley, H., A photogenerated pore-forming protein, Chem. Biol., 2, 391, 1995.
34. Pan, P. and Bayley, H., Caged cysteine and triphosphoryl groups, FEBS Lett., 405, 81, 1997.
35. Bayley, H., Chang, C.Y., Miller, W.T., Niblack, B., and Pan, P., Caged peptides and proteins by targeted chemical modification, Methods Enzymol., 291, 117, 1998.
36. Zou, K., Cheley, S., Givens, R.S., and Bayley, H., Catalytic subunit of protein kinase A caged at the activating phosphothreonine, J. Am. Chem. Soc., 124, 28, 8220, 2002.
37. Sreekumar, R., Ikebe, M., Fay, F.S., and Walker, J.W., Biologically active peptides caged on tyrosine, Methods Enzymol., 291, 78, 1998.
38. Pirrung, M.C., Drabik, S.J., Ahamed, J., and Ali, H., Caged chemotactic peptides, Bioconjug. Chem., 11, 5, 679, 2000.
39. Tatsu, Y., Nishigaki, T., Darszon, A., and Yumoto, N., A caged sperm-activating peptide that has a photocleavable protecting group on the backbone amide, FEBS Lett., 525, 1-3, 20, 2002.
40. Hiraoka, T. and Hamachi, I., Caged RNase: photoactivation of the enzyme from perfect off-state by site-specific incorporation of 2-nitrobenzyl moiety, Bioorg. Med. Chem. Lett., 13, 1, 13, 2003.
41. Ottl, J., Gabriel, D., and Marriott, G., Preparation and photoactivation of caged fluorophores and caged proteins using a new class of heterobifunctional, photocleavable cross-linking reagents, Bioconjug. Chem., 9, 2, 143, 1998.
42. Politz, J.C., Use of caged fluorochromes to track macromolecular movement in living cells, Trends Cell Biol., 9, 7, 284, 1999.
43. Okabe, S. and Hirokawa, N., Differential behavior of photoactivated microtubules in growing axons of mouse and frog neurons, J. Cell Biol., 117, 1, 105, 1992.
44. Rodionov, V.I., Lim, S.S., Gelfand, V.I., and Borisy, G.G., Microtubule dynamics in fish melanophores, J. Cell Biol., 126, 6, 1455, 1994.
45. Yvon, A.M., Gross, D.J., and Wadsworth, P., Antagonistic forces generated by myosin II and cytoplasmic dynein regulate microtubule turnover, movement, and organization in interphase cells, Proc. Natl. Acad. Sci. USA, 98, 15, 8656, 2001.
46. Spudich, J.L. and Bogomolni, R.A., Sensory rhodopsin I: receptor activation and signal relay, J. Bioenerg. Biomembr., 24, 2, 193, 1992.
47. Bousché, O., Spudich, E.N., Spudich, J.L., and Rothschild, K.J., Conformational changes in sensory rhodopsin I: similarities and differences with bacteriorhodopsin, halorhodopsin, and rhodopsin, Biochemistry, 30, 22, 5395, 1991.
48. Porter, N.A., Bruhnke, J.D., and Koenigsm, P., Bioorganic photochemistry, Vol. 2, in Biological Applications of Photochemical Switches, Morrison, H., Ed., John Wiley & Sons, New York, 1993, pp. 197-241.
49. Arroyo, J.G., Jones, P.B., Porter, N.A., and Hatchell, D.L., In vivo photoactivation of caged-thrombin, Thromb. Haemost., 78, 2, 791, 1997.
50. Harvey, A.J. and Abell, A.D., Alpha-ketoester-based photobiological switches: synthesis, peptide chain extension and assay against alpha-chymotrypsin, Bioorg. Med. Chem. Lett., 11, 18, 2441, 2001.
51. James, D.A., Burns, D.C., and Woolley, G.A., Kinetic characterization of ribonuclease S mutants containing photoisomerizable phenylazophenylalanine residues, Protein Eng., 14, 12, 983, 2001.
52. Muranaka, N., Hohsaka, T., and Sisido, M., Photoswitching of peroxidase activity by positionspecific incorporation of a photoisomerizable non-natural amino acid into horseradish peroxidase, FEBS Lett., 510, 1-2, 10, 2002.
53. Weston, D.G., Kirkham, J., and Cullen, D.C., Photo-modulation of horseradish peroxidase activity via covalent attachment of carboxylated-spiropyran dyes, Biochim. Biophys. Acta, 1428, 2-3, 463, 1999.
54. Ito, Y., Sugimura, N., Kwon, O.H., and Imanishi, Y., Enzyme modification by polymers with solubilities that change in response to photoirradiation in organic media, Nat. Biotechnol., 17, 1, 73, 1999.
55. Shimoboji, T., Larenas, E., Fowler, T., Kulkarni, S., Hoffman, A.S., and Stayton, P.S., Photoresponsive polymer-enzyme switches, Proc. Natl. Acad. Sci. USA, 99, 16592, 2002.
56. Harada, M., Sisido, M., Hirose, J., and Nakanishi, M., Photoreversible antigen-antibody reactions, FEBS Lett., 286, 1-2, 6, 1991.
57. Flint, D.G., Kumita, J.R., Smart, O.S., and Woolley, G.A., Using an azobenzene cross-linker to either increase or decrease peptide helix content upon trans-to-cis photoisomerization, Chem. Biol., 9, 3, 391, 2002.
58. Renner, C., Behrendt, R., Sporlein, S., Wachtveitl, J., and Moroder, L., Photomodulation of conformational states. I. Mono-and bicyclic peptides with (4-amino)phenylazobenzoic acid as backbone constituent, Biopolymers, 54, 7, 489, 2000.
59. Renner, C., Cramer, J., Behrendt, R., and Moroder, L., Photomodulation of conformational states. II. Mono-and bicyclic peptides with (4-aminomethyl)phenylazobenzoic acid as backbone constituent, Biopolymers, 54, 7, 501, 2000.
60. Renner, C., Behrendt, R., Heim, N., and Moroder, L., Photomodulation of conformational states. III. Water-soluble bis-cysteinyl-peptides with (4-aminomethyl) phenylazobenzoic acid as backbone constituent, Biopolymers, 63, 6, 382, 2002.
61. Kumita, J.R., Flint, D.G., Smart, O.S., and Woolley, G.A., Photo-control of peptide helix content by an azobenzene cross-linker: steric interactions with underlying residues are not critical, Protein Eng., 15, 7, 561, 2002.
62. Cattani-Scholz, A., Renner, C., Oesterhelt, D., and Moroder, L., Photoresponsive dendritic azobenzene peptides, Chembiochem., 2, 7-8, 542, 2001.
63. Pieroni, O., Fissi, A., Angelini, N., and Lenci, F., Photoresponsive polypeptides, Acc. Chem. Res., 34, 1, 9, 2001.
64. Griffin, B.A., Adams, S.R., and Tsien, R.Y., Specific covalent labeling of recombinant protein molecules inside live cells, Science, 281, 5374, 269, 1998.
65. Adams, S.R., Campbell, R.E., Gross, L.A., Martin, B.R., Walkup, G.K., Yao, Y., Llopis, J., and Tsien, R.Y., New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: ynthesis and biological applications, J. Am. Chem. Soc., 124, 21, 6063, 2002.
66. Gaietta, G., Deerinck, T.J., Adams, S.R., Bouwer, J., Tour, O., Laird, D.W., Sosinsky, G.E., Tsien, R.Y., and Ellisman, M.H., Multicolor and electron microscopic imaging of connexin trafficking, Science, 296, 5567, 503, 2002.
67. Nakanishi, J., Nakajima, T., Sato, M., Ozawa, T., Tohda, K., and Umezawa, Y., Imaging of conformational changes of proteins with a new environment-sensitive fluorescent probe designed for site-specific labeling of recombinant proteins in live cells, Anal. Chem., 73, 13, 2920, 2001.
68. Marcaurelle, L.A.B. and Bertozzi, C.R., Direct incorporation of unprotected ketone groups into peptides during solid-phase synthesis: application to the one-step modification of peptides with two different biophysical probes for FRET, Tetrahedron Lett., 39, 40, 7279, 1998.
69. Gaertner, H.F. and Offord, R.E., Site-specific attachment of functionalized poly(ethylene glycol) to the amino terminus of proteins, Bioconjug. Chem., 7, 1, 38, 1996.
70. Kochendoerfer, G.G. and Kent, S.B., Chemical protein synthesis, Curr. Opin. Chem. Biol., 3, 6, 665, 1999.
71. Perler, F.B. and Adam, E., Protein splicing and its applications, Curr. Opin. Biotechnol., 11, 4, 377, 2000.
72. Hofmann, R.M. and Muir, T.W., Recent advances in the application of expressed protein ligation to protein engineering, Curr. Opin. Biotechnol., 13, 4, 297, 2002.
73. Hofmann, R.M., Cotton, G.J., Chang, E.J., Vidal, E., Veach, D., Bornmann, W., and Muir, T.W., Fluorescent monitoring of kinase activity in real time: development of a robust fluorescence-based assay for Abl tyrosine kinase activity, Bioorg. Med. Chem. Lett., 11, 24, 3091, 2001.
74. Sydor, J.R., Herrmann, C., Kent, S.B., Goody, R.S., and Engelhard, M., Design, total chemical synthesis, and binding properties of a [Leu-91-N1-methyl-7-azaTrp]Ras-binding domain of c-Raf-1, Proc. Natl. Acad. Sci. USA, 96, 14, 7865, 1999.
75. Becker, C.F., Hunter, C.L., Seidel, R.P., Kent, S.B., Goody, R.S., and Engelhard, M., A sensitive fluorescence monitor for the detection of activated Ras: total chemical synthesis of site-specifically labeled Ras binding domain of c-Raf1 immobilized on a surface, Chem. Biol., 8, 3, 243, 2001.
76. Zhang, J., Campbell, R.E., Ting, A.Y., and Tsien, R.Y., Creating new fluorescent probes for cell biology, Nat. Rev. Mol. Cell Biol., 3, 12, 906, 2002.
77. Gross, L.A., Baird, G.S., Hoffman, R.C., Baldridge, K.K., and Tsien, R.Y., The structure of the chromophore within DsRed, a red fluorescent protein from coral, Proc. Natl. Acad. Sci. US A, 97, 22, 11990, 2000.
78. Chan, F.K., Siegel, R.M., Zacharias, D., Swofford, R., Holmes, K.L., Tsien, R.Y., and Lenardo, M.J., Fluorescence resonance energy transfer analysis of cell surface receptor interactions and signaling using spectral variants of the green fluorescent protein, Cytometry, 44, 4, 361, 2001.
79. Rehm, M., Dussmann, H., Janicke, R.U., Tavare, J.M., Kogel, D., and Prehn, J.H., Single-cell fluorescence resonance energy transfer analysis demonstrates that caspase activation during apoptosis is a rapid process. Role of caspase-3, J. Biol. Chem., 277, 27, 24506, 2002.
80. Tawa, P., Tam, J., Cassady, R., Nicholson, D.W., and Xanthoudakis, S., Quantitative analysis of fluorescent caspase substrate cleavage in intact cells and identification of novel inhibitors of apoptosis, Cell Death Differ., 8, 1, 30, 2001.
81. Luo, K.Q., Yu, V.C., Pu, Y., and Chang, D.C., 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, 5, 1054, 2001.
82. Majoul, I., Straub, M., Duden, R., Hell, S.W., and Soling, H.D., Fluorescence resonance energy transfer analysis of protein-protein interactions in single living cells by multifocal multiphoton microscopy, J. Biotechnol., 82, 3, 267, 2002.
83. Truong, K. and Ikura, M., The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo, Curr. Opin. Struct. Biol., 11, 5, 573, 2001.
84. Kohl, T., Heinze, K.G., Kuhlemann, R., Koltermann, A., and Schwille, P., A protease assay for twophoton crosscorrelation and FRET analysis based solely on fluorescent proteins, Proc. Natl. Acad. Sci. USA, 99, 19, 12161, 2002.
85. Zhang, J., Ma, Y., Taylor, S.S., and Tsien, R.Y., Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering, Proc. Natl. Acad. Sci. USA, 98, 26, 14997, 2001.
86. Ting, A.Y., Kain, K.H., Klemke, R.L., and Tsien, R.Y., Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells, Proc. Natl. Acad. Sci. USA, 98, 26, 15003, 2001.
87. Sato, M., Ozawa, T., Inukai, K., Asano, T., and Umezawa, Y., Fluorescent indicators for imaging protein phosphorylation in single living cells, Nat. Biotechnol., 20, 3, 287, 2002.
88. 2+ imaging by a new calmodulin-GFP fusion molecule, Nat. Struct. Biol., 8, 12, 1069, 2001.
89. Batard, P., Szollosi, J., Luescher, I., Cerottini, J.C., MacDonald, R., and Romero, P., Use of phycoerythrin and allophycocyanin for fluorescence resonance energy transfer analyzed by flow cytometry: dvantages and limitations, Cytometry, 48, 2, 97, 2002.
90. McCartney, L.J., Pickup, J.C., Rolinski, O.J., and Birch, D.J., Near-infrared fluorescence lifetime assay for serum glucose based on allophycocyanin-labeled concanavalin A, Anal. Biochem., 292, 2, 216, 2001.
91. Rothschild, K.J. and Gite, S., tRNA-mediated protein engineering, Curr. Opin. Biotechnol., 10, 1, 64, 1999.
92. Khorana, H.G., Nucleic acid synthesis in the study of the genetic code, in Nobel Lectures in Molecular Biology, Elsevier, Amsterdam; New York, 1977, pp. 303-333.
93. Nirenberg, M.W. and Leder, P., RNA codewords and protein synthesis, Science, 145, 1399, 1964.
94. Richmond, M.H., The effect of amino acid analogs on growth and protein synthesis in microorganisms, Bacteriol. Rev., 26, 398, 1962.
95. Krieg, U.C., Walter, P., and Johnson, A.E., Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle, Proc. Natl. Acad. Sci. USA, 83, 22, 8604, 1986.
96. Krieg, U.C., Johnson, A.E., and Walter, P., Protein translocation across the endoplasmic reticulum membrane: identification by photocross-linking of a 39-kD integral membrane glycoprotein as part of a putative translocation tunnel, J. Cell Biol., 109, 5, 2033, 1989.
97. Thrift, R.N., Andrews, D.W., Walter, P., and Johnson, A.E., A nascent membrane protein is located adjacent to ER membrane proteins throughout its integration and translation, J. Cell Biol., 112, 5, 809, 1991.
98. Noren, C.J., Anthony-Cahill, S.J., Griffith, M.C., and Schultz, P.G., A general method for sitespecific incorporation of unnatural amino acids into proteins, Science, 244, 182, 1989.
99. Anthony-Cahill, S.J., Griffith, M.C., Noren, C.J., Suich, D.J., and Schultz, P.G., Site-specific mutagenesis with unnatural amino acids, TIBS, 14, 10, 400, 1990.
100. Thorson, J.S., Cornish, V.W., Barrett, J.E., Cload, S.T., Yano, T., and Schultz, P.G., A biosynthetic approach for the incorporation of unnatural amino acids into proteins, Methods Mol. Biol., 77, 43, 1998.
101. Furter, R., Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli, Protein Sci., 7, 2, 419, 1998.
102. Budisa, N., Minks, C., Medrano, F.J., Lutz, J., Huber, R., and Moroder, L., Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: tructure and stability of the per-thiaproline mutant of annexin V, Proc. Natl. Acad. Sci. USA, 95, 2, 455, 1998.
103. Bessho, Y., Hodgson, D.R., and Suga, H., A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme, Nat. Biotechnol., 20, 7, 723, 2002.
104. Ma, C., Kudlicki, W., Odom, O.W., Kramer, G., and Hardesty, B., In vitro protein engineering using synthetic tRNA(Ala) with different anticodons, Biochemistry, 32, 31, 7939, 1993.
105. Kramer, G., Kudlicki, W., and Hardesty, B., In vitro engineering using synthetic tRNAs with altered anticodons including four-nucleotide anticodons, Methods Mol. Biol., 77, 105, 1998.
106. Hohsaka, T.A., Murakami, H., and Sisido, M., Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression, J. Am. Chem. Soc., 118, 40, 9778, 1996.
107. Hohsaka, T., Ashizuka, Y., Taira, H., Murakami, H., and Sisido, M., Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system, Biochemistry, 40, 37, 11060., 2001.
108. Hohsaka, T., Ashizuka, Y., Murakami, H., and Sisido, M., Five-base codons for incorporation of nonnatural amino acids into proteins, Nucleic Acids Res., 29, 17, 3646, 2001.
109. Magliery, T.J., Anderson, J.C., and Schultz, P.G., Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of “shifty” four-base codons with a library approach in Escherichia coli, J. Mol. Biol., 307, 3, 755, 2001.
110. Anderson, J.C., Magliery, T.J., and Schultz, P.G., Exploring the limits of codon and anticodon size, Chem. Biol., 9, 2, 237, 2002.
111. Johnson, A.E., Protein translocation across the ER membrane: a fluorescent light at the end of the tunnel, Trends Biochem. Sci., 18, 12, 456, 1993.
112. Cornish, V.W., Benson, D.R., Altenbach, C.A., Hideg, K., Hubbell, W.L., and Schultz, P.G., Sitespecific incorporation of biophysical probes into proteins, Proc. Natl. Acad. Sci. USA, 91, 8, 2910, 1994.
113. Steward, L.E., Collins, C.S., Gilmore, M.A., Carlson, J.E., Ross, J.B.A., and Chamberlin, A.R., In vitro site-specific incorporation of fluorescent probes into beta-galactosidase, J. Am. Chem. Soc., 119, 6, 1997.
114. Turcatti, G., Nemeth, K., Edgerton, M.D., Meseth, U., Talabot, F., Peitsch, M., Knowles, J., Vogel, H., and Chollet, A., Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites, J. Biol. Chem., 271, 33, 19991, 1996.
115. Turcatti, G., Nemeth, K., Edgerton, M.D., Knowles, J., Vogel, H., and Chollet, A., Fluorescent labeling of NK2 receptor at specific sites in vivo and fluorescence energy transfer analysis of NK2 ligand-receptor complexes, Receptors Channels, 5, 3-4, 201, 1997.
116. Cohen, B.E., McAnaney, T.B., Park, E.S., Jan, Y.N., Boxer, S.G., and Jan, L.Y., Probing protein electrostatics with a synthetic fluorescent amino acid, Science, 296, 5573, 1700, 2002.
117. Gite, S., Mamaev, S., Olejnik, J., and Rothschild, K., Ultrasensitive fluorescence-based detection of nascent proteins in gels, Anal. Biochem., 279, 2, 218, 2000.
118. Nemoto, N., Miyamoto-Sato, E., and Yanagawa, H., Fluorescence labeling of the C-terminus of proteins with a puromycin analogue in cell-free translation systems, FEBS Lett., 462, 1-2, 43, 1999.
119. Doi, N., Takashima, H., Kinjo, M., Sakata, K., Kawahashi, Y., Oishi, Y., Oyama, R., Miyamoto-Sato, E., Sawasaki, T., Endo, Y., and Yanagawa, H., Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions, Genome Res., 12, 3, 487, 2002.
120. Murakami, H., Hohsaka, T., Ashizuka, Y., Hashimoto, K., and Sisido, M., Site-directed incorporation of fluorescent nonnatural amino acids into streptavidin for highly sensitive detection of biotin, Biomacromolecules, 1, 1, 118, 2000.
121. Taki, M., Hohsaka, T., Murakami, H., Taira, K., and Sisido, M., Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/anticodon pairs, J. Am. Chem. Soc., 124, 49, 14586, 2002.
122. Hohsaka, T., Daisuke, K., Ashizuka, Y., Murakami, H., and Sisido, M., Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems, J. Am. Chem. Soc., 121, 34, 1999.
123. Taki, M., Hohsaka, T., Murakami, H., Taira, K., and Sisido, M., A non-natural amino acid for efficient incorporation into proteins as a sensitive fluorescent probe, FEBS Lett., 507, 1, 35, 2001.
124. Anderson, R.D., III, Zhou, J., and Hecht, S.M., Fluorescence resonance energy transfer between unnatural amino acids in a structurally modified dihydrofolate reductase, J. Am. Chem. Soc., 124, 33, 9674, 2002.
125. Mendel, D., Ellman, J.A., and Schultz, P.G., Construction of a light-activated protein by unnatural amino acid mutagenesis, J. Am. Chem. Soc., 113, 2758, 1991.
126. England, P.M., Lester, H.A., Davidson, N., and Dougherty, D.A., Site-specific, photochemical proteolysis applied to ion channels in vivo, Proc. Natl. Acad. Sci. USA, 94, 20, 11025, 1997.
127. Philipson, K.D., Gallivan, J.P., Brandt, G.S., Dougherty, D.A., and Lester, H.A., Incorporation of caged cysteine and caged tyrosine into a transmembrane segment of the nicotinic ACh receptor, Am. J. Physiol. Cell Physiol., 281, 1, C195, 2001.
128. Tong, Y., Brandt, G.S., Li, M., Shapovalov, G., Slimko, E., Karschin, A., Dougherty, D.A., and Lester, H.A., Tyrosine decaging leads to substantial membrane trafficking during modulation of an inward rectifier potassium channel, J. Gen. Physiol., 117, 2, 103, 2001.
129. Mamaev, S., Olejnik, J., Krzymanska-Olejnik, E., and Rothschild, K.J., Efficient N-terminal labeling of proteins using amber suppresor initator tRNA in an in vitro system, Protein Sci., 11, suppl. 1, 171, 2002.
130. Rothschild, K.J., Gite, S., and Olejnik, J., U.S. Patent 6,303,337, 2001, N-terminal and C-terminal markers in nascent proteins, October 16, 2001.
131. Gite, S., Lim, M., Carlson, R., Olejnik, J., Zehnbauer, B., and Rothschild, K., A high throughput non-isotopic protein truncation test, Nat. Biotechnol., 21, 194, 2003.
132. Kobs, G., Hurst, R., Betz, N., and Godat, B., FluoroTect GreenLys in vitro translation labeling system, Promega Notes, 77, 23, 2001.
133. Beernink, P.T., Segelke, B.W., and Coleman, M.A., High-throughput, cell-free protein expression screening using the RTS 100 E. coli HY kit, Biochemica (Roche), 1, 4, 2003.
134. Iborra, F.J., Jackson, D.A., and Cook, P.R., Coupled transcription and translation within nuclei of mammalian cells, Science, 293, 5532, 1139, 2001.
135. Lien, L., Ananda, P., Seneviratne, K., Jaikaran, A.S., and Andrew Woolley, G., Site-specific biosynthetic incorporation of a fluorescent tag into proteins via Cysteine-tRNA(Cys), Anal. Biochem., 307, 2, 252, 2002.
136. Den Dunnen, J.T. and Van Ommen, G.J., The protein truncation test: a review, Hum. Mutat., 14, 2, 95, 1999.
137. Roest, P., Roberts, R., Sugino, S., van Ommen, G., and den Dunnen, J., Protein truncation test (PTT) for rapid detection of translation-terminating mutations, Hum. Mol. Genet., 2, 10 (Oct.), 1719-1721, 1993.
138. Powell, S.M., Petersen, G.M., Krush, A.J., Booker, S., Jen, J., Giardiello, F.M., Hamilton, S.R., Vogelstein, B., and Kinzler, K.W., Molecular diagnosis of familial adenomatous polyposis [see comments], N. Engl. J. Med., 329, 27, 1982, 1993.
139. DeGrado, W.F., Summa, C.M., Pavone, V., Nastri, F., and Lombardi, A., De novo design and structural characterization of proteins and metalloproteins, Annu. Rev. Biochem., 68, 779, 1999.
140. Neidigh, J.W., Fesinmeyer, R.M., and Andersen, N.H., Designing a 20-residue protein, Nat. Struct. Biol., 9, 6, 425, 2002.
141. Luque, I., Leavitt, S.A., and Freire, E., The linkage between protein folding and functional cooperativity: wo sides of the same coin?, Annu. Rev. Biophys. Biomol. Struct., 31, 235, 2002.
142. Luecke, H., Schobert, B., Cartailler, J.P., Richter, H.T., Rosengarth, A., Needleman, R., and Lanyi, J.K., Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin, J. Mol. Biol., 300, 5, 1237, 2000.
143. Subramaniam, S. and Henderson, R., Molecular mechanism of vectorial proton translocation by bacteriorhodopsin, Nature, 406, 6796, 653, 2000.
144. Luecke, H., Schobert, B., Lanyi, J.K., Spudich, E.N., and Spudich, J.L., Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction, Science, 293, 5534, 1499, 2001.
145. Royant, A., Nollert, P., Edman, K., Neutze, R., Landau, E.M., Pebay-Peyroula, E., and Navarro, J., X-ray structure of sensory rhodopsin II at 2.1-A resolution, Proc. Natl. Acad. Sci. USA, 98, 18, 10131, 2001.
146. Gordeliy, V.I., Labahn, J., Moukhametzianov, R., Efremov, R., Granzin, J., Schlesinger, R., Bueldt, G., Savopol, T., Scheidig, A.J., Klare, J.P., and Engelhard, M., Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex, in Nature (London, United Kingdom), 2002, pp. 484-487.
147. Spudich, J.L., Spot light on receptor/transducer interations, Nature Struct. Biol., 9, 11, 707, 2002.
148. Hunt, J.F., Rath, P., Rothschild, K.J., and Engelman, D.M., Spontaneous, pH-dependent membrane insertion of a transbilayer alpha-helix, Biochemistry, 36, 49, 15177, 1997.
149. Hunt, J.F., Earnest, T.N., Bousche, O., Kalghatgi, K., Reilly, K., Horvath, C., Rothschild, K.J., and Engelman, D.M., A biophysical study of integral membrane protein folding, Biochemistry, 36, 49, 15156, 1997.
150. Shen, Y., Safinya, C.R., Liang, K.S., Ruppert, A.F., and Rothschild, K.J., Stabilization of the membrane protein bacteriorhodopsin to 140 C in two dimensional films, Nature, 366, 48, 1993.
151. Bayley, H., Building a door into cells, Sci. Am., 277 (September), 62, 1997.
152. Wang, H. and Branton, D., Nanopores with a spark for single-molecule detection, Nat. Biotechnol., 19, 7, 622-623, 2001.
153. Vercoutere, W., Winters-Hilt, S., Olsen, H., Deamer, D., Haussler, D., and Akeson, M., Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel, Nat. Biotechnol., 19, 3, 248, 2001.
154. Howorka, S., Cheley, S., and Bayley, H., Sequence-specific detection of individual DNA strands using engineered nanopores, Nat. Biotechnol., 19, 7, 636, 2001.
155. Yang, H. and Xie, X.S., Probing single molecule dynamics photon by photon, J. Chem. Phys., 117, 10965, 2002.