Chemistry in Living Systems

Nature Chemical Biology

Volumn 1, Issue 1, 2005, Pages 13-21

  Prescher, Jennifer A ^a   Bertozzi, Carolyn R ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; LIPID; POLYSACCHARIDE; PROTEIN;

ANIMAL; CELL CULTURE; CHEMISTRY; GENETIC PROCEDURES; GENETICS; MOLECULAR PROBE; REVIEW;

ANIMALS; CELLS, CULTURED; GREEN FLUORESCENT PROTEINS; LIPIDS; MOLECULAR PROBE TECHNIQUES; MOLECULAR PROBES; POLYSACCHARIDES; PROTEINS;

EID: 27944462447     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio0605-13     Document Type: Review

References (114)

1. Tsien, R.Y. The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998).
2. Lippincott-Schwartz, J. & Patterson, G.H. Development and use of fluorescent protein markers in living cells. Science 300, 87–91 (2003).
3. Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906–918 (2002).
4. Hadjantonakis, A.K., Dickinson, M.E., Fraser, S.E. & Papaioannou, V.E. Technicolour transgenics: imaging tools for functional genomics in the mouse. Nat. Rev. Genet. 4, 613–625 (2003).
5. Weissleder, R. & Ntziachristos, V. Shedding light onto live molecular targets. Nat. Med. 9, 123–128 (2003).
6. Presley, J.F. et al. ER-to-Golgi transport visualized in living cells. Nature 389, 81–85 (1997).
7. Dundr, M. et al. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298, 1623–1626 (2002).
8. Miyawaki, A., Sawano, A. & Kogure, T. Lighting up cells: labelling proteins with fluorophores. Nat. Cell Biol. 5 (Suppl.), S1–S7 (2003).
9. Shaner, N.C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567–1572 (2004).
10. Verkhusha, V.V. & Lukyanov, K.A. The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins. Nat. Biotechnol. 22, 289–296 (2004).
11. Alberts, B. Molecular Biology of the Cell (Garland Science, New York, 2002)
12. Schweppe, R.E., Haydon, C.E., Lewis, T.S., Resing, K.A. & Ahn, N.G. The characterization of protein post-translational modifications by mass spectrometry. Acc. Chem. Res. 36, 453–461 (2003).
13. Massoud, T.F. & Gambhir, S.S. Molecular imaging in living subjects: seeing fundamental biological processes in a new light. Genes Dev. 17, 545–580 (2003).
14. von Mehren, M., Adams, G.P. & Weiner, L.M. Monoclonal antibody therapy for cancer. Annu. Rev. Med. 54, 343–369 (2003).
15. Hudson, P.J. & Souriau, C. Engineered antibodies. Nat. Med. 9, 129–134 (2003).
16. Hermanson, G.T. Bioconjugate Techniques (Academic Press, San Diego, 1996).
17. Link, A.J., Vink, M.K. & Tirrell, D.A. Presentation and detection of azide functionality in bacterial cell surface proteins. J. Am. Chem. Soc. 126, 10598–10602 (2004).
18. Griffin, B.A., Adams, S.R. & Tsien, R.Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281, 269–272 (1998).
19. Chen, I., Howarth, M., Lin, W. & Ting, A.Y. Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nat. Methods 2, 99–104 (2005).
20. Zhang, Z. et al. A new strategy for the site-specific modification of proteins in vivo. Biochemistry 42, 6735–6746 (2003).
21. Saxon, E. et al. Investigating cellular metabolism of synthetic azidosugars with the Staudinger ligation. J. Am. Chem. Soc. 124, 14893–14902 (2002).
22. Mahal, L.K., Yarema, K.J. & Bertozzi, C.R. Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis. Science 276, 1125–1128 (1997).
23. Luchansky, S.J., Goon, S. & Bertozzi, C.R. Expanding the diversity of unnatural cell-surface sialic acids. ChemBioChem 5, 371–374 (2004).
24. Luchansky, S.J. et al. Constructing azide-labeled cell surfaces using polysaccharide biosynthetic pathways. Methods Enzymol. 362, 249–272 (2003).
25. Kho, Y. et al. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc. Natl. Acad. Sci. USA 101, 12479–12484 (2004).
26. Speers, A.E., Adam, G.C. & Cravatt, B.F. Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc. 125, 4686–4687 (2003).
27. Ovaa, H. et al. Chemistry in living cells: detection of active proteasomes by a twostep labeling strategy. Angew. Chem. Int. Edn. Engl. 42, 3626–3629 (2003).
28. Vocadlo, D.J. & Bertozzi, C.R. A strategy for functional proteomic analysis of glycosidase activity from cell lysates. Angew. Chem. Int. Edn. Engl. 43, 5338–5342 (2004).
29. Speers, A.E. & Cravatt, B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535–546 (2004).
30. Prescher, J.A., Dube, D.H. & Bertozzi, C.R. Chemical remodelling of cell surfaces in living animals. Nature 430, 873–877 (2004).
31. Adams, S.R. et al. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc. 124, 6063–6076 (2002).
32. Saxon, E. & Bertozzi, C.R. Cell surface engineering by a modified Staudinger reaction. Science 287, 2007–2010 (2000).
33. Kolb, H.C. & Sharpless, K.B. The growing impact of click chemistry on drug discovery. Drug Discov. Today 8, 1128–1137 (2003).
34. Agard, N.J., Prescher, J.A. & Bertozzi, C.R. A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J. Am. Chem. Soc. 126, 15046–15047 (2004).
35. Andresen, M., Schmitz-Salue, R. & Jakobs, S. Short tetracysteine tags to betatubulin demonstrate the significance of small labels for live cell imaging. Mol. Biol. Cell 15, 5616–5622 (2004).
36. Panchal, R.G. et al. In vivo oligomerization and raft localization of Ebola virus protein VP40 during vesicular budding. Proc. Natl. Acad. Sci. USA 100, 15936–15941 (2003).
37. Gaietta, G. et al. Multicolor and electron microscopic imaging of connexin trafficking. Science 296, 503–507 (2002).
38. Ju, W. et al. Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors. Nat. Neurosci. 7, 244–253 (2004).
39. Tour, O., Meijer, R.M., Zacharias, D.A., Adams, S.R. & Tsien, R.Y. Genetically targeted chromophore-assisted light inactivation. Nat. Biotechnol. 21, 1505–1508 (2003).
40. Chen, I. & Ting, A.Y. Site-specific labeling of proteins with small molecules in live cells. Curr. Opin. Biotechnol. 16, 35–40 (2005).
41. Hahn, M.E. & Muir, T.W. Manipulating proteins with chemistry: a cross-section of chemical biology. Trends Biochem. Sci. 30, 26–34 (2005).
42. Johnsson, N. & Johnsson, K. A fusion of disciplines: chemical approaches to exploit fusion proteins for functional genomics. ChemBioChem 4, 803–810 (2003).
43. van Swieten, P.F., Leeuwenburgh, M.A., Kessler, B.M. & Overkleeft, H.S. Bioorthogonal organic chemistry in living cells: novel strategies for labeling biomolecules. Org. Biomol. Chem. 3, 20–27 (2005).
44. Keppler, A., Pick, H., Arrivoli, C., Vogel, H. & Johnsson, K. Labeling of fusion proteins with synthetic fluorophores in live cells. Proc. Natl. Acad. Sci. USA 101, 9955–9959 (2004).
45. Marks, K.M., Braun, P.D. & Nolan, G.P. A general approach for chemical labeling and rapid, spatially controlled protein inactivation. Proc. Natl. Acad. Sci. USA 101, 9982–9987 (2004).
46. Miller, L.W., Sable, J., Goelet, P., Sheetz, M.P. & Cornish, V.W. Methotrexate conjugates: a molecular in vivo protein tag. Angew. Chem. Int. Edn. Engl. 43, 1672–1675 (2004).
47. Miller, L.W., Cai, Y., Sheetz, M.P. & Cornish, V.W. In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag. Nat. Methods 2, 255–257 (2005).
48. Guignet, E.G., Hovius, R. & Vogel, H. Reversible site-selective labeling of membrane proteins in live cells. Nat. Biotechnol. 22, 440–444 (2004).
49. Marks, K.M., Rosinov, M. & Nolan, G.P. In vivo targeting of organic calcium sensors via genetically selected peptides. Chem. Biol. 11, 347–356 (2004).
50. Franz, K.J., Nitz, M. & Imperiali, B. Lanthanide-binding tags as versatile protein coexpression probes. ChemBioChem 4, 265–271 (2003).
51. Giriat, I. & Muir, T.W. Protein semi-synthesis in living cells. J. Am. Chem. Soc. 125, 7180–7181 (2003).
52. Jencks, W.P. Studies on the mechanism of oxime and semicarbazone formation. J. Am. Chem. Soc. 81, 475–481 (1959).
53. Rideout, D. Self-assembling cytotoxins. Science 233, 561–563 (1986).
54. Rideout, D. Self-assembling drugs: a new approach to biochemical modulation in cancer chemotherapy. Cancer Invest. 12, 189–202 (1994).
55. Rideout, D., Calogeropoulou, T., Jaworski, J. & McCarthy, M. Synergism through direct covalent bonding between agents: a strategy for rational design of chemotherapeutic combinations. Biopolymers 29, 247–262 (1990).
56. Rotenberg, S.A., Calogeropoulou, T., Jaworski, J., Weinstein, I.B. & Rideout, D. A self-assembling protein kinase C inhibitor. Proc. Natl. Acad. Sci. USA 88, 2490–2494 (1991).
57. Yarema, K.J., Mahal, L.K., Bruehl, R.E., Rodriguez, E.C. & Bertozzi, C.R. Metabolic delivery of ketone groups to sialic acid residues. Application to cell surface glycoform engineering. J. Biol. Chem. 273, 31168–31179 (1998).
58. Lee, J.H. et al. Engineering novel cell surface receptors for virus-mediated gene transfer. J. Biol. Chem. 274, 21878–21884 (1999).
59. Sadamoto, R. et al. Control of bacteria adhesion by cell-wall engineering. J. Am. Chem. Soc. 126, 3755–3761 (2004).
60. Griffin, R.J. The medicinal chemistry of the azido group. Prog. Med. Chem. 31, 121–232 (1994).
61. Saegusa, T., Ito, Y. & Shimizu, T. Synthetic reactions by complex catalysts. XVII. Coppercatalyzed reaction of azide with thiol. J. Org. Chem. 35, 2979–2981 (1970).
62. Staudinger, H. & Meyer, J. Uber neue organische phosphoverbindungen III. Phosphinmethlenderivate und phosphinimine. Helv. Chim. Acta 2, 635–646 (1919).
63. Gololobov, Y.G. & Kasukhin, L.F. Recent advances in the Staudinger reaction. Tetrahedron 48, 1353–1406 (1992).
64. Hang, H.C., Yu, C., Kato, D.L. & Bertozzi, C.R. A metabolic labeling approach toward proteomic analysis of mucin-type O-linked glycosylation. Proc. Natl. Acad. Sci. USA 100, 14846–14851 (2003).
65. Vocadlo, D.J., Hang, H.C., Kim, E.J., Hanover, J.A. & Bertozzi, C.R. A chemical approach for identifying O-GlcNAc-modified proteins in cells. Proc. Natl. Acad. Sci. USA 100, 9116–9121 (2003).
66. Luchansky, S.J., Argade, S., Hayes, B.K. & Bertozzi, C.R. Metabolic functionalization of recombinant glycoproteins. Biochemistry 43, 12358–12366 (2004).
67. Nilsson, B.L., Kiessling, L.L. & Raines, R.T. Staudinger ligation: a peptide from a thioester and azide. Org. Lett. 2, 1939–1941 (2000).
68. Saxon, E., Armstrong, J.I. & Bertozzi, C.R.A. “Traceless” Staudinger ligation for the chemoselective synthesis of amide bonds. Org. Lett. 2, 2141–2143 (2000).
69. Kohn, M. et al. Staudinger ligation: a new immobilization strategy for the preparation of small-molecule arrays. Angew. Chem. Int. Edn. Engl. 42, 5830–5834 (2003).
70. Soellner, M.B., Dickson, K.A., Nilsson, B.L. & Raines, R.T. Site-specific protein immobilization by Staudinger ligation. J. Am. Chem. Soc. 125, 11790–11791 (2003).
71. Kohn, M. & Breinbauer, R. The Staudinger ligation—a gift to chemical biology. Angew. Chem. Int. Edn. Engl. 43, 3106–3116 (2004).
72. Huisgen, R. 1,3-Dipolar Cycloaddition Chemistry (ed. Padwa, A.) (Wiley, New York, 1984).
73. Huisgen, R. 1,3-Dipolar cycloadditions. Angew. Chem. Int. Edn. Engl. 2, 565–598 (1963).
74. Rostovtsev, V.V., Green, L.G., Fokin, V.V. & Sharpless, K.B. A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Edn. Engl. 41, 2596–2599 (2002).
75. Tornoe, C.W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057–3064 (2002).
76. Wang, Q. et al. Bioconjugation by copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc. 125, 3192–3193 (2003).
77. Seo, T.S. et al. Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry. Proc. Natl. Acad. Sci. USA 101, 5488–5493 (2004).
78. Speers, A.E. & Cravatt, B.F. Chemical strategies for activity-based proteomics. ChemBioChem 5, 41–47 (2004).
79. Link, A.J. & Tirrell, D.A. Cell surface labeling of Escherichia coli via copper(I)-catalyzed [3+2] cycloaddition. J. Am. Chem. Soc. 125, 11164–11165 (2003).
80. Turner, R., Jarrett, A.D., Goebel, P. & Mallon, B.J. Heats of hydrogenation. IX. Cyclic acetylenes and some miscellaneous olefins. J. Am. Chem. Soc. 95, 790–792 (1972).
81. Wittig, G.A.K.A. Zur Existenz niedergliedriger Cycloalkine, I. Chem. Ber. 94, 3260–3275 (1961).
82. Lin, F.L., Hoyt, H.M., van Halbeek, H., Bergman, R.G. & Bertozzi, C.R. Mechanistic investigation of the Staudinger ligation. J. Am. Chem. Soc. 127, 2686–2695 (2005).
83. Link, A.J., Mock, M.L. & Tirrell, D.A. Non-canonical amino acids in protein engineering. Curr. Opin. Biotechnol. 14, 603–609 (2003).
84. Wang, L. & Schultz, P.G. Expanding the genetic code. Angew. Chem. Int. Edn. Engl. 44, 34–66 (2004).
85. Datta, D., Wang, P., Carrico, I.S., Mayo, S.L. & Tirrell, D.A. A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins. J. Am. Chem. Soc. 124, 5652–5653 (2002).
86. Kirshenbaum, K., Carrico, I.S. & Tirrell, D.A. Biosynthesis of proteins incorporating a versatile set of phenylalanine analogues. ChemBioChem 3, 235–237 (2002).
87. van Hest, J.C.M., Kiick, K.L. & Tirrell, D.A. Efficient incorporation of unsaturated methionine analogs into proteins in vivo. J. Am. Chem. Soc. 122, 1282–1288 (2000).
88. Kiick, K.L., Saxon, E., Tirrell, D.A. & Bertozzi, C.R. Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proc. Natl. Acad. Sci. USA 99, 19–24 (2002).
89. Chin, J.W. et al. Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J. Am. Chem. Soc. 124, 9026–9027 (2002).
90. Deiters, A. & Schultz, P.G. In vivo incorporation of an alkyne into proteins in Escherichia coli. Bioorg. Med. Chem. Lett. 15, 1521–1524 (2005).
91. Wang, L., Zhang, Z., Brock, A. & Schultz, P.G. Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 100, 56–61 (2003).
92. Chin, J.W. et al. An expanded eukaryotic genetic code. Science 301, 964–967 (2003).
93. Deiters, A. et al. Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae. J. Am. Chem. Soc. 125, 11782–11783 (2003).
94. George, N., Pick, H., Vogel, H., Johnsson, N. & Johnsson, K. Specific labeling of cell surface proteins with chemically diverse compounds. J. Am. Chem. Soc. 126, 8896–8897 (2004).
95. Yin, J., Liu, F., Li, X. & Walsh, C.T. Labeling proteins with small molecules by site-specific posttranslational modification. J. Am. Chem. Soc. 126, 7754–7755 (2004).
96. Dierks, T. et al. Multiple sulfatase deficiency is caused by mutations in the gene encoding the human C(α)-formylglycine generating enzyme. Cell 113, 435–444 (2003).
97. Rudd, P.M., Elliott, T., Cresswell, P., Wilson, I.A. & Dwek, R.A. Glycosylation and the immune system. Science 291, 2370–2376 (2001).
98. Gouyer, V. et al. Inhibition of the glycosylation and alteration in the intracellular trafficking of mucins and other glycoproteins by GalNAcα-O-Bn in mucosal cell lines: an effect mediated through the intracellular synthesis of complex GalNAcα-O-Bn oligosaccharides. Front. Biosci. 6, D1235–D1244 (2001).
99. Wells, L., Vosseller, K. & Hart, G.W. Glycosylation of nucleocytoplasmic proteins: signal transduction and O-GlcNAc. Science 291, 2376–2378 (2001).
100. Slawson, C. & Hart, G.W. Dynamic interplay between O-GlcNAc and O-phosphate: the sweet side of protein regulation. Curr. Opin. Struct. Biol. 13, 631–636 (2003).
101. Orntoft, T.F. & Vestergaard, E.M. Clinical aspects of altered glycosylation of glycoproteins in cancer. Electrophoresis 20, 362–371 (1999).
102. Lowe, J.B. Glycan-dependent leukocyte adhesion and recruitment in inflammation. Curr. Opin. Cell Biol. 15, 531–538 (2003).
103. Dube, D.H. & Bertozzi, C.R. Metabolic oligosaccharide engineering as a tool for glycobiology. Curr. Opin. Chem. Biol. 7, 616–625 (2003).
104. Keppler, O.T., Horstkorte, R., Pawlita, M., Schmidt, C. & Reutter, W. Biochemical engineering of the N-acyl side chain of sialic acid: biological implications. Glycobiology 11, 11R–18R (2001).
105. Lemieux, G.A. & Bertozzi, C.R. Exploiting differences in sialoside expression for selective targeting of MRI contrast reagents. J. Am. Chem. Soc. 121, 4278–4279 (1999).
106. Hang, H.C. & Bertozzi, C.R. Ketone isosteres of 2-N-acetamidosugars as substrates for metabolic cell surface engineering. J. Am. Chem. Soc. 123, 1242–1243 (2001).
107. Zhang, F.L. & Casey, P.J. Protein prenylation: molecular mechanisms and functional consequences. Annu. Rev. Biochem. 65, 241–269 (1996).
108. Sylvers, L.A. & Wower, J. Nucleic acid-incorporated azidonucleotides: probes for studying the interaction of RNA or DNA with proteins and other nucleic acids. Bioconjug. Chem. 4, 411–418 (1993).
109. Malolanarasimhan, K. et al. Synthesis and biological study of a flavone acetic acid analogue containing an azido reporting group designed as a multifunctional binding site probe. Bioorg. Med. Chem. 13, 2717–2722 (2005).
110. Comstock, L.R. & Rajski, S.R. Efficient synthesis of azide-bearing cofactor mimics. J. Org. Chem. 69, 1425–1428 (2004).
111. Comstock, L.R. & Rajski, S.R. Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors. Nucleic Acids Res. 33, 1644–1652 (2005).
112. Poteryaev, D., Squirrell, J.M., Campbell, J.M., White, J.G. & Spang, A. Involvement of the actin cytoskeleton and homotypic membrane fusion in ER dynamics in C. elegans. Mol. Biol. Cell (2005).
113. Apweiler, R., Hermjakob, H. & Sharon, N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys. Acta 1473, 4–8 (1999).
114. Restituyo, J.A., Comstock, L.R., Petersen, S.G., Stringfellow, T. & Rajski, S.R. Conversion of aryl azides to O-alkyl imidates via modified Staudinger ligation. Org. Lett. 5, 4357–4360 (2003).