Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code

Biological Chemistry

Volumn 385, Issue 2, 2004, Pages 191-202

  Budisa, Nediljko ^a   Pal, Prajna Paramita ^a   Alefelder, Stefan ^a   Birle, Petra ^a   Krywcun, Tatjana ^a   Rubini, Marina ^a   Wenger, Waltraud ^a   Bae, Jae Hyun ^a   Steiner, Thomas ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Flourescence spectroscopy; Genetic code; Green fluorescent protein structure; Non canonical amino acids; Trytophan

Indexed keywords

AROMATIC COMPOUND; CHALCOGEN; GREEN FLUORESCENT PROTEIN; HALOGEN; INDOLE DERIVATIVE; METHYL GROUP; MUTANT PROTEIN; RECOMBINANT PROTEIN; SULFUR DERIVATIVE; TRYPTOPHAN DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; CELL MATURATION; CHEMICAL INTERACTION; CHROMATOPHORE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENETIC CODE; GENETIC VARIABILITY; GEOMETRY; MASS SPECTROMETRY; MOLECULAR PROBE; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS;

AEQUORIN; AMINO ACID SUBSTITUTION; CHALCOGENS; CRYSTALLOGRAPHY, X-RAY; GENETIC CODE; GREEN FLUORESCENT PROTEINS; HYDROCARBONS, FLUORINATED; HYDROGEN-ION CONCENTRATION; INDOLES; LUMINESCENT PROTEINS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; TRYPTOPHAN;

AEQUOREA; AEQUOREA VICTORIA; VICTORIA;

EID: 1842787741     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2004.038     Document Type: Article

References (39)

1. Bae, J.H., Alefelder, S., Kaiser, J.T., Friedrich, R., Moroder, L., Huber, R., and Budisa, N. (2001). Incorporation of β-selenolo[3,2-b]pyrrolyl-alanine into proteins for phase determination in protein X-ray crystallography. J. Mol. Biol. 309, 925-936.
2. Bae, J.H., Rubini, M., Jung, G., Wiegand, G., Seifert M.H.J., Azim, M.K., Kirn, J.S., Zumbusch, A., Holak, T.A., Moroder, L. et al. (2003). Expansion of the genetic code enables design of a novel 'Gold' class of green fluorescent proteins. J. Mol. Biol. 328, 977-1202.
3. Boles, J.O., Henderson, J., Hatch, D., and Silks, L.A. (2002). Synthesis and incorporation of [6,7]-selenatryptophan into dihydrofolate reductase. Biochem. Biophys. Res. Commun. 298, 257-261.
4. Brawerman, G., and Ycas, M. (1957). Incorporation of the amino acid analog tryptazan into the protein of Escherichia coli. Arch. Biochem. Biophys. 68, 112-117.
5. Bronskill, P. M., and Wong, J.T. (1988). Suppression of fluorescence of tryptophan residues in proteins by replacement with 4-fluorotryptophan. Biochem. J. 249, 305-308.
6. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., and Grosse-Kunstleve, R.W. (1998). Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Cryst. D54, 905-921.
7. Budisa, N. (2003). Expression of 'tailor-made' proteins via incorporation of synthetic amino acids by using cell-free protein synthesis. In: Cell Free Protein Expression, J. R. Swartz, ed. (Springer Verlag, Berlin, Heidelberg, New York), pp 89-98.
8. Budisa, N., Alefelder, S., Bae, J.H., Golbik, R., Minks, C., Huber, R., and Moroder, L. (2001). Proteins with β-(thienopyrrolyl)alanines as alternative chromophores and pharmaceutically active amino acids. Protein Sci. 10, 1281-1292.
9. Budisa, N., Minks, C., Medrano, F.J., Lutz, J., Huber, R., and Moroder, L. (1998). Residue-specific bioincorporation of non-natural biologically active amino acids into proteins as possible drug carriers. Structure and stability of per-thiaproline mutant of annexin V. Proc. Natl. Acad. Sci. USA 95, 455-459.
10. Budisa, N., Minks, C., Alefelder, S., Wenger, W., Dong, F., Moroder, L., and Huber, R. (1999a). Toward the experimental codon reassignment in vivo: Protein building with an expanded amino acid repertoire. FASEB J. 13, 41-51.
11. Budisa, N., Moroder, L., and Huber, R. (1999b). Structure and evolution of the genetic code viewed from the perspective of the experimentally expanded amino acid repertoire in vivo. Cell. Mol. Life Sci. 55, 1626-1635.
12. Budisa, N., Rubini, M., Bae, J.H., Weyher, E., Wenger, W., Golbik, R., Huber, R., and Moroder, L. (2002). Global replacement of tryptophan with amino-tryptophans generates non-invasive protein-based optical pH sensors. Angew. Chem. Int. Ed. 41, 4066-4069.
13. Budisa, N., Steipe, B., Demange, P., Eckerskorn, C., Kellermann, J., and Huber, R. (1995). High level biosynthetic substitution of methionine in proteins by its analogues 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli. Eur. J. Biochem. 230, 788-796.
14. Burley, S.K., and Petsko, G.A. (1988). Weakly polar interactions in proteins. Adv. Prot. Chem. 39, 125-186.
15. 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, 802-895.
16. Cody, C.W., Prasher, D.C., Westler, W.M, Prendergast, E.G., and Ward, W.W. (1993). Chemical-structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. Biochemistry 32, 1212-1218.
17. Cubbit, A.B., Heim, R., Adams, S.R., Boyd, A.E., Gross, L.A., and Tsien, R.Y. (1995). Understanding and improving using green fluorescent proteins. Trends Biochem. Sci. 20, 448-455.
18. Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133-7155.
19. Groesbeck, O., Baird, G.S., Campbell, R.E., Zacharias, D.A., and Tsien, R.Y. (2001). Reducing the environmental sensitivity of Yellow Fluorescent Protein. J. Biol. Chem. 276, 29 188-29 194.
20. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M.T. (1991). Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Cryst. A47, 110-119.
21. Lakowitz, J.R. (1999). Protein fluorescence. In: Principles of fluorescence spectroscopy. 2nd Ed. (Kluwer Academic/Plenum Publisher, New York) pp. 446-485.
22. Lossau, H., Kummer, A., Heinecke, R., Pollinger-Dammer, F., Kompa, C., Bieser, G., Jonsson, T., Silva, C.M., Yang, M.M., Youvan, D.C., and Michel-Beyerle, M.E. (1996). Time-resolved spectroscopy of wild-type and mutant Green Fluorescent Proteins reveals excited state deprotonation consistent with fluorophore-protein interactions. Chem. Phys. 213, 1-16.
23. Minks, C., Alefelder, S., Moroder, L., Huber, R. and Budisa, N. (2000). Towards new protein engineering: In vivo building and folding of protein shuttles for drug delivery and targeting by the selective pressure incorporation (SPI) method. Tetrahedron 56, 9431-9442.
24. Minks, C., Huber, R., Moroder, L., and Budisa, N. (1999). Atomic mutations at the single tryptophan residue of human recombinant annexin V: Effects on structure, stability and activity. Biochemistry 38, 10 649-10 659.
25. Ormö, 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 96, 1392-1395.
26. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
27. Palm, G.J., and Wlodawer, A. (1999). Spectral variants of green fluorescent protein. Methods Enzymol. 33, 378-394.
28. Pardee, A.B, Shore, V.G., and Prestidge, L.S. (1956). Incorporation of azatryptophan into proteins of bacteria and bacteriophage. Biochim. Biophys. Acta 21, 406-407.
29. Phillips, G.N. (1997). Structure and dynamics of green fluorescent protein. Curr. Opin. Struct. Biol. 7, 821-827.
30. Prat, E.A., and Ho, C. (1975). Incorporation of fluorotryptophans into proteins of Escherichia coli. Biochemistry 14, 3035-3040.
31. Prendergast, F. (1999). Biophysics of the green fluorescent protein. Methods Cell Biol. 58, 1-18.
32. Ross, J.B., Szabo, A.G., and Hogue, C.W. (1997) Enhancement of protein spectra with tryptophan analogues: Fluorescence spectroscopy of protein-protein and protein-nucleic acid interactions. Methods Enzymol. 278, 151-190.
33. Schlesinger, S. (1968). Effect of amino acid analogues on alkaline phosphatase formation in Escherichia coli K-12: Replacement of tryptophan by azatryptophan and by tryptazan. J. Biol. Chem. 243, 3877-3883.
34. Seifert, M.H.J., Ksiazek, D., Smialowski, P., Azim, M.K. Budisa, N. and Holak, T.A. (2002). Slow Conformational Exchange Processes in Green Fluorescent Protein Variants evidenced by NMR Spectroscopy. J. Am. Chem. Soc. 124, 7932-7942.
35. Shimimura, O. (11979). Structure of the chromophore of Aequorea Green Fluorescent Protein. FEBS Lett. 104, 220-222.
36. Tsien, R. (1999). Green Fluorescent Protein. Annu. Rev. Biochem. 67, 509-544.
37. Yang, F., Moss L.G., and Phillips, G.N. (1996). The molecular structure of green fluorescent protein. Nat. Biotechnol. 14, 1246-1251.
38. Wang, L., and Schultz, P.G, (2002). Expanding the genetic code. Chem. Commun. 1, 1-11.
39. Woody, R.W., and Dunker, K. (1996). Aromatic and Cystine side-chain circular dichroism in proteins. In: Circular Dichroism and the Conformational Analysis of Biomolecules, G. D. Fasman ed. (Plenum Press, New York), pp. 109-159.