Relationship between structure and optical properties in green fluorescent proteins: A quantum mechanical study of the chromophore environment

Chemical Physics

Volumn 298, Issue 1-3, 2004, Pages 17-28

  Laino, Teodoro ^a   Nifosì, Riccardo ^a   Tozzini, Valentina ^a  

^a SCUOLA NORMALE SUPERIORE   (Italy)

Author keywords

Density functional theory; Green fluorescent proteins; Semiempirical calculations

Indexed keywords

AMINO ACID; GREEN FLUORESCENT PROTEIN; MUTANT PROTEIN;

ARTICLE; CALCULATION; CHROMATOPHORE; DENSITY FUNCTIONAL THEORY; MOLECULAR MODEL; PHOTODYNAMICS; PREDICTION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; QUANTUM MECHANICS; SPECTROSCOPY; SURFACE PROPERTY; VIBRATION; WILD TYPE;

EID: 1242293051     PISSN: 03010104     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphys.2003.10.040     Document Type: Article

References (53)

1. Recent review articles on GFPs: Tsien R.J. Annu. Rev. Biochem. 67:1998;509.
2. Zimmer Z. Chem. Rev. 102:2002;759.
3. Tozzini V., Pellegrini V., Beltram F. Horsphool W.M., Lenci F. Handbook of Organic Photochemistry and Photobiology. 2003;CRC, Washington, DC. chapter 139.
4. Palm G.J., Zdanov A., Gaitanaris G.A., Stauber R., Pavlakis G.N., Wlodawer A. Nat. Strut. Biol. 4:1997;361.
5. Brejc K., Sixma T.K., Kitts P.A., Steven R.K., Tsien R.Y., Ormö M., Remington S.J. Proc. Natl. Acad. Sci. 94:1997;2306.
6. Chattoraj M., King B.A., Bublitz G.U., Boxer S.G. Proc. Natl. Acad. Sci. USA. 93:1996;8362.
7. Lossau H., Kummer A., Heinecke R., Pöllinger-dammer F., Kompa C., Bieser G., Jonsson T., Silva C.M., Yang M.M., Youvan D.C., Michel-Beyerle M.E. Chem. Phys. 213:1996;1.
8. Cotlet M., Hofkens J., Michael M., Gensch T., Van der Auweraer M., Michiels J., Dirix G., VanGuyse M., Van der leyden J., Visser A.J.W.G., DeSchryver F.C. J. Phys. Chem. B. 105:2001;4999.
9. Winkler K., Lindner J., Subramaniam V., Jovin T.M., Wöhringer P. Phys. Chem. Chem. Phys. 4:2002;1072.
10. Nielsen S.B., Lapierre A., Andersen J.U., Pedersen U.V., Tomita S., Andersen L.H. Phys. Rev. Lett. 87:2001;228102.
11. Andersen L.H., Lapierre A., Nielsen S.B., Pedersen S.U., Pedersen U.V., Tomita S. Eur. Phys. J. D. 20:2002;597.
12. Kummer A.D., Wiehler J., Renhaber H., Kompa C., Steipe B., Michel-Beyerle M.-E. J. Phys. Chem. B. 104:2000;4791.
13. Heim R., Tsien R. Curr. Biol. 6:1996;178.
14. Wachter R.M., Elsliger M.-A., Kallio K., Hanson G.T., Remington S.J. Structure. 6:1998;2790.
15. Voityuk A.A., Michel-Beyerle M.-E., Rösch N. Chem. Phys. Lett. 272:1997;162.
16. Voityuk A.A., Michel-Beyerle M.-E., Rösch N. Chem. Phys. 231:1998;13.
17. Weber W., Helms V., McCammon J.A., Langhoff P.W. Proc. Natl. Acad. Sci. USA. 96:1999;6177.
18. Scharnagl C., Raupp-Kossmann R., Fisher R.S. Biophys. J. 77:1999;1839.
19. Stübner M., Schellenberg P. J. Phys. Chem. A. 107:2003;1246.
20. Nifosì R., Tozzini V. Proteins. 51:2003;378.
21. Cubitt A.B., Woolenweber L.A., Heim R. Methods Cell Biol. 58:1999;19.
22. Creemers T.M.H., Lock A.J., Subramaniam B., Jovin T.M., Wölker S. Chem. Phys. 275:2002;109.
23. Becke D.A. Phys. Rev. A. 38:1988;3098.
24. Lee C., Yang W., Parr R.G. Phys. Rev. B. 37:1988;785.
25. Troullier N., Martins J.L. Phys. Rev. B. 43:1991;1993.
26. The core radii used for pseudopotential were 1.23 a.u. (C and N) and 1. 25 a.u. (O) and the pseudopotential for H was obtained as in Pavesi L., Giannozzi P., Reinhart F.K. Phys. Rev. B. 42:1990;1864.
27. This set of pseudopotential with a 60 Ryd cutoff was already verified to reproduce the experimental geometries within 0.5% and the vibrational frequencies within 3% (see for instance) Tozzini V., Bizzarri A.R., Pellegrini V., Nifosì R., Giannozzi P., Iuliano A., Cannistraro S., Beltram F. Chem. Phys. 287:2003;33.
28. Car R., Parrinello M. Phys. Rev. Lett. 55:1985;2471.
29. Tassone F., Mauri F., Car R. Phys. Rev. B. 50:1994;10561.
30. CPMD3.4: Hutter J., Alavi A., Deutsch T., Ballone P., Bernasconi M., Focher P., Fois E., Goedecker S., Marx D., Parrinello M., Tuckerman M., MPI für Festkörperforschung, Stuttgart and IBM Zurich Research Laboratory.
31. Thiel W. J. Am. Chem. Soc. 103:1981;1413.
32. Schweig A., Thiel W. J. Am. Chem. Soc. 103:1981;1425.
33. Granucci G., Toniolo A. Chem. Phys. Lett. 325:2000;79.
34. Stewart J.J.P. MOPAC 2000. 1999;Fujitsu Limited, Tokio, Japan.
35. In our calculation the percentage of HOMO-LUMO transition is 63-67% depending on the model, a value slightly lower than those reported in the literature (up to 80-90%).
36. See for instance Dreizler R.M., Gross E.K. Density Functional Theory. 1990;Springer, Berlin. (Chapters 6 and 7).
37. Choi C.H., Kertesz M. J. Chem. Phys. 107:1997;6712.
38. Perpète E.A., Champagne B. Theor. Chem. 487:1999;39.
39. Protein Data Bank. Available from: http://www.rcsb.org/pdb/.
40. Marques M.A.L., López X., Varsano D., Castro A., Rubio A. Phys. Rev. Lett. 90:2003;258101.
41. Tozzini V., Nifosì R. J. Phys. Chem. B. 105:2001;5797.
42. Bell A.F., He X., Wachter R.M., Tonge P.J. Biochemistry. 39:2000;4423.
43. He X., Bell A.F., Tonge P.J. J. Phys. Chem. B. 106:2002;6056.
44. Esposito A.P., Schellenberg P., Parson W.W., Reid P.J. J. Mol. Struct. 569:2001;25.
45. We heated the system for 1 ps up to 300 K, then we performed microcanonical dynamics for about 2 ps and reduced again the temperature to zero during about 1 ps.
46. Kummer A.D., Kompa C., Lossau H., Pöllinger-Dammer F., Michel-Beyerle M.-E., Silva C.M., Bylina E.J.B., Coleman W.J., Yang M.M., Youvan D.C. Chem. Phys. 237:1998;183.
47. Heikal A.A., Hess S.T., Webb W.W. Chem. Phys. 274:2001;37.
48. Nifosì R., Ferrari A., Arcangeli C., Tozzini V., Pellegrini V., Beltram F. J. Phys. Chem. B. 107:2003;1679.
49. Creemers T.M.H., Lock A.J., Subramaniam V., Jovin T.M., Völker S. Proc. Natl. Acad. Sci. USA. 97:2000;2974.
50. Yang F., Moss L.G., Phillips G.N. Jr. Nat. Biotechnol. 14:1996;1246.
51. Lill M.A., Helms V. Proc. Natl. Acad. Sci. USA. 99:2002;2778.
52. Kohanoff J. Comput. Mater. Sci. 2:1994;221.
53. Kurimoto M., Subramony P., Gurney R.W., Lovell S., Chmielewski J., Kahr B. J. Am. Chem. Soc. 121:1999;6952.