Novel chromophores and buried charges control color in mFruits

Biochemistry

Volumn 45, Issue 32, 2006, Pages 9639-9647

  Shu, Xiaokun ^a   Shaner, Nathan C ^b   Yarbrough, Corinne A ^a   Tsien, Roger Y ^b   Remington, S James ^a  

^a UNIVERSITY OF OREGON   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTALLOGRAPHY; PIGMENTS; PROTEINS; SPECTROSCOPIC ANALYSIS;

2 HYDROXY DIHYDROOXAZOLE; ELECTRON DENSITY DISTRIBUTIONS; MONOMERIC RED FLUORESCENT PROTEINS (MRFP);

FRUITS;

2 HYDROXYDIHYDROOXAZOLE; CARBONYL DERIVATIVE; DSRED PROTEIN; GLUTAMIC ACID; HETEROCYCLIC COMPOUND; IMINE; LYSINE; MCHERRY PROTEIN; MFRUIT PROTEIN; MONOMER; MONOMERIC RED FLUORESCENT PROTEIN 1; MORANGE PROTEIN; MSTRAWBERRY PROTEIN; MUTANT PROTEIN; OXAZOLE DERIVATIVE; POLYPEPTIDE; PROTEIN; PROTEIN PRECURSOR; RED FLUORESCENT PROTEIN; THREONINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BRIGHTNESS; CHROMATOPHORE; COLOR; CONTROLLED STUDY; COVALENT BOND; CRYSTALLOGRAPHY; CYCLIZATION; ELECTRON; ELECTRON DENSITY MAP; ELECTRON DIFFRACTION; ENERGY ABSORPTION; EXCITATION; MOLECULAR INTERACTION; MUTAGENESIS; OXIDATION; PH; PHOTOACTIVATION; PHOTOREACTIVITY; PHOTOSTABILITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; PROTEIN VARIANT; PROTON TRANSPORT; SPECTROFLUOROMETRY;

ANIMALS; COLOR; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; HYDROGEN-ION CONCENTRATION; LUMINESCENT PROTEINS; MODELS, MOLECULAR; TIME FACTORS;

CRYSTALLOGRAPHY; FRUITS; PIGMENT; SPECTROCHEMICAL ANALYSIS;

EID: 33747479549     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060773l     Document Type: Article

References (28)

1. Matz, M. V., Arkady, F. F., Labas, Y. A., Savitsky, A. P., Zaraisky, A. G., Markelov, M. L., and Lukyanov, S. A. (1999) Fluorescent proteins from nonbioluminescent Anthozoa species, Nat. Biotechnol. 17, 969-973.
2. Verkhusha, V. V., and Lukyanov, K. A. (2004) The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins, Nat. Biotechnol. 22, 289-196.
3. Henderson, J. N., and Remington, S. J. (2005) Crystal structures and mutational analysis of amFP486, a cyan fluorescent protein from Anemonia majano, Proc. Natl. Acad. Sci. U.S.A. 102, 12712-12717.
4. Remington, S. J., Wachter, R. M., Yarbrough, D. K., Branchaud, B., Anderson, D. C., Kallio, K., and Lukyanov, K. A. (2005) zFP538, a yellow fluorescent protein from Zoanthus, contains a novel three-ring chromophore, Biochemistry 44, 202-212.
5. 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. U.S.A. 97, 11984-11989.
6. 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. U.S.A. 87, 11990-11995.
7. Yarbrough, D., Wachter, R. M., Kallio, K., Matz, M. V., and Remington, S. J. (2001) Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0 Å resolution, Proc. Natl. Acad. Sci. U.S.A. 98, 462-467.
8. Wall, M. A., Socolich, M., and Ranganathan, R. (2000) The structural basis for red fluorescence in the tetrameric GFP homolog DsRed, Nat. Struct. Biol. 7, 1133-1138.
9. Petersen, J., Wilmann, P. G., Beddoe, T., Oakley, A. J., Devenish, R. J., Prescott, M., and Rossjohn, J. (2003) The 2.0 Å crystal structure of eqFP611, a far-red fluorescent protein from the sea anemone Entacmaea quadricolor, J. Biol. Chem. 278, 44626-44631.
10. Prescott, M., Ling, M., Beddoe, T., Oakley, A. J., Hoegh-Guldberg, O., Devenish, R. J., and Rossjohn, J. (2003) The 2.2 Å crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation, Structure 11, 275-284.
11. Wilmann, P. G., Petersen, J., Dvenish, R. J., Prescott, M., and Rossjohn, J. (2005) A polypeptide fragmentation within the chromophore revealed in the 2.1 Å crystal structure of a non fluorescent chromoprotein from Anemonia sulcata, J. Biol. Chem. 280, 2401-2404.
12. Quillin, M. L., Anstrom, D. M., Shu, X., O'Leary, S., Kallio, K., Lukyanov, K. A., and Remington, S. J. (2005) The kindling fluorescent protein from Anemonia sulcata: Dark state structure at 1.38 Å resolution, Biochemistry 44, 5774-5787.
13. Zagranichny, V. E., Rudenko, N. V., Gorokhovatsky, A. Y., Zakharov, M. V., Balashova, T. A., and Arseniev, A. S. (2004) Traditional GFP-type cyclization and unexpected fragmentation site in a purple chromoprotein from Anemonia sulcata, asFP595, Biochemistry 43, 13598-13603.
14. Yampolsky, I. V., Remington, S. J., Martynov, V. I., Potapov, V. K., Lukyanov, S., and Lukyanov, K. A. (2005) Synthesis and properties of the chromophore of asFP595 chromoprotein from Anemonia sulcata. Biochemistry 44, 5788-5793.
15. He, X., Bell, A. F., and Tonge, P. J. (2002) Synthesis and spectroscopic studies of model red fluorescent protein chromophores, Org. Lett. 9, 1523-1526.
16. 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.
17. 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. U.S.A. 99, 7877-7882.
18. 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.
19. Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55, 484-491.
20. Tronrud, D. E., Ten Eyck, L. F., and Matthews, B. W. (1987) An efficient general-purpose least-squares refinement program for macromolecular structures, Acta Crystallogr., Sect. A: Found. Crystallogr. 43, 489-503.
21. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr., Sect. A: Found. Crystallogr. 47, 110-119.
22. Sheldrick, G. M., and Schneider, T. R. (1997) SHELXL: High-resolution refinement, Methods Enzymol. 277, 319-343.
23. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
24. Burgi, H. B., Dunitz, J. D., Lehn, J. M., and Wipff, G. (1974) Stereochemistry of reaction paths at carbonyl centres, Tetrahedron 30, 1563-1572.
25. Dunitz, J. D. (1979) X-ray Analysis and the Structure of Organic Molecules, Cornell University Press, Ithaca, NY.
26. Cieplak, A. S. (1994) Organic addition and elimination reactions; transformation paths of carbonyl derivatives, in Structure Correlation (Burgi, H. B., and Dunitz, J. D., Eds.) pp 205-302, VCH, Weinheim, Germany.
27. Allen, F. H. (2002) The Cambridge Structural Database: A quarter of a million crystal structures and rising, Acta Crystallogr., Sect. B: Struct. Sci. 58, 380-388.
28. Tubbs, J. L., Tainer, J. A., and Getzoff, E. D. (2005) Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: Linking peptide bond transcis isomerization and acylimine formation in chromophore maturation, Biochemistry 44, 9833-9840.