Elisa BOMBARDA: Publications

Elisa BOMBARDA: Publications


  1. BOMBARDA E., KEMPF O., KEMPF K., SCHOBERT R. & ULLMANN G. M. - Hydrodabcyl. International patent WO 2016/083611 A1, issued 02.06.2016; (US Patent 25.05.2017; EU Patent 24.07.2018)

  2. KEMPF O., KEMPF K., SCHOBERT R. & BOMBARDA E. - Hydrodabcyl: a superior hydrophylic alternative to the dark fluorescence quencher dabcyl. Anal. Chem. 2017, 89, 11893-11897.

  3. BOMBARDA E. & ULLMANN G. M. - Continuous electrostatic calculation of the protonation of bovin rhodopsin: protonation and the effect of the membrane potential. Photochem. Photobiol. 2017, 93, 1388-1398.

  4. ULLMANN G. M., MULLER L. & BOMBARDA E. - Theoretical analysis of electrostatics in proteins. From simple proteins to complex machineries. In Advances in Photosynthesis and Respiration, Vol. 41. Cytochrome Complexes: Evolution, Structures, Energy transduction and Signaling. (W. A. Cramer and T. Kallas Eds.), Springer Verlag, 2016, 99-127.

  5. ULLMANN G. M & BOMBARDA E. - Continuum electrostatic analysis of protein. In Protein Modelling (G. Náray-Szabó, Ed.), Springer International Publishing Switzerland, 2014, 135-163.

  6. ULLMANN G. M., DUMIT V. I. & BOMBARDA E. - Methods based on continuum electrostatics and their application to flavoproteins. In Handbook of Flavoproteins, Vol. 2. (S. Miller, B. Palfey and R. Hille, Eds), De Gruyter, Berlin, 2013, 335-360.

  7. ULLMANN G. M & BOMBARDA E. - pKa values and redox potential of proteins. What do they mean? Biol. Chem. 2013, 394, 611-619

  8. RICH A.M., BOMBARDA E., SCHENK A.D., LEE P.E., COX E.H., SPUCHES A.M., HUDSON L.D., KIEFFER B. & WILCOX D.E. - Thermodynamics of Zn2+ Binding to Cys2His2 and Cys2HisCys Zinc Fingers and a Cys4 Transcription Factor Site. J. Am. Chem. Soc. 2012, 134, 10405-10418

  9. BOMBARDA E. & ULLMANN G. M. - Continuum electrostatic investigations of charge transfer processes in biological molecules using a microstate description. Faraday Discussions, 2011, 148, 173-193.

  10. BOMBARDA E. & ULLMANN G. M. - pH-dependent pKa values in proteins - A theoretical analysis of protonation energy with practical consequences for enzymatic reactions. J. Phys. Chem. B 2010, 114, 1994-2003

  11. ULLMANN G. M.*, KLOPPMANN E., ESSIGKE T., KRAMMER E. M., KLINGEN A. R., BECKER T., BOMBARDA E.* - Investigating the mechanisms of photosynthetic proteins using continuum electrostatics. Photosynt. Res. 2008, 97(1), 33-53.

  12. BOMBARDA E.*, GRELL E., ROQUES B.P. & MELY Y. - Molecular mechanism of the Zn2+-induced folding of the distal CCHC finger motif of the HIV-1 nucleocapsid protein. Biophysical J. 2007, 93, 208-217.

  13. BOMBARDA E., BECKER T. & ULLMANN G. M. - Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatics calculations into the regulation of proton pumping. J. Am. Chem. Soc. 2006, 126, 12129-12139.

  14. KLINGEN A. R., BOMBARDA E. & ULLMANN G. M. - Theoretical investigation of the behavior of titratable groups in proteins. Photochemical and Photobiological Sciences, 2006, 5, 588-596.

  15. PION E., ULLMANN G. M., AME J. C., GERARD D., DE MURCIA G. & BOMBARDA E.* - Poly (ADP-ribose) polymerase-1 activation is triggered by dimer formation. Biochemistry 2005, 44, 14670-14681.

  16. BOMBARDA E., ROQUES B.P., MELY Y. & GRELL E.- Mechanism of zinc coordination by point-mutated structures of the distal CCHC binding motif of the HIV-1 NCp7 protein. Biochemistry 2005, 44, 7315-7325.

  17. STOTE R., KELLENBERGER E., MULLER H., BOMBARDA E., ROQUES B.P., KIEFFER B. & MELY Y.- Structure of the His44 à Ala single point mutant of the distal finger of HIV-1 nucleocapsid protein: a combined NMR molecular dynamics simulation and fluorescence study. Biochemistry 2004, 43, 7687-7697.

  18. PION E., BOMBARDA E.*, STIEGLER P., ULLMANN G. M., MELY Y., DE MURCIA G. & GERARD D. - Poly (ADP-ribose) polymerase-1 dimerizes at a 5' recessed DNA end in vitro: a fluorescence study. Biochemistry 2003, 42, 12409-12417.

  19. BOMBARDA E., CHERRADI H., MORELLET N., ROQUES B.P. & MELY Y. - Zn2+ binding properties of single point mutants of the C-terminal zinc finger of HIV-1 nucleocapsid protein: evidence of a critical role of cysteine 49 in Zn2+-dissociation. Biochemistry 2002, 41, 4312-4320.

  20. ABABOU A. & BOMBARDA E. - On the involvement of the electron transfer reaction in the fluorescence decay kinetics heterogeneity of proteins. Protein Sci. 2001, 10, 2102-2113.

  21. BOMBARDA E., MORELLET N., CHERRADI H., SPIESS B., S. BOUAZIZ, GRELL E., ROQUES B.P., & MELY Y. - Determination of the pKa values of the four Zn2+-coordinating residues of the distal finger motif of the HIV-1 nucleocapsid protein: consequences of the binding of Zn2+. J. Mol. Biol. 2001, 310, 659-672. (Correction of a printing mistake in J. Mol. Biol. 2001, 311, 1105).

  22. KINTRUP M., SCHUBERT P., KUNZ M., CHABBERT M., ALBERTI P., BOMBARDA E., SCHNEIDER S. & HILLEN W. - Trp scanning analysis of Tet repressor reveals conformational changes associated with operator and anhydrotetracycline binding. Eur. J. Biochem. 2000, 267, 821-829.

  23. VERGANI B., KINTRUP M., HILLEN W., LAMI H., PIEMONT E., BOMBARDA E., ALBERTI P., DOGLIA S.M. & CHABBERT M. - Backbone dynamics of Tet repressor a8-a9 loop. Biochemistry. 2000, 39, 2759-2768.

  24. VUILLEUMIER C., BOMBARDA E., MORELLET N., GERARD D., ROQUES B.P. & MELY Y. - Nucleic acid sequence discrimination by the HIV-1 nucleocapsid protein : a fluorescence study. Biochemistry, 1999, 38, 16816-16825.

  25. BOMBARDA E., ABABOU A., VUILLEUMIER C., GERARD D., ROQUES B.P., PIEMONT E. & MELY Y. - Time-resolved fluorescence investigation of the Human Immunodeficiency Virus Type 1 nucleocapsid protein: influence of the binding of nucleic acids. Biophys. J., 1999, 76, 1561-1570.

  26. BOMBARDA E. - Kinetic investigation of the zinc binding to the C-terminal zinc finger of the nucleocapsid protein of the virus HIV-1. Futura, 1998, 13(4), 294-296.

  27. MELY Y., BOMBARDA E., VUILLEUMIER C., DE ROCQUIGNY H., ROQUES B.P. & GERARD D. - Involvement of the aromatic aminoacid (Phe16 and Trp37) of the HIV-1 nucleocapsid protein in the binding to the homologous t-RNALys,3 and the heterologous t-RNAPhe: a fluorecence spectroscopy investigation. In Fluorescence Microscopy and Fluorescent Probes, Vol.2 (J. Slavik, Ed.), Plenum Publishing Company, New York, 1998, 181-186.

  28. ALBERTI P., BOMBARDA E., KINTRUP M., HILLEN W., LAMI H., PIEMONT E., DOGLIA S.M. & CHABBERT M. - Structural investigation of Tet Repressor Loop 154-167: a time resolved study of three single Trp mutants. Arch. Biochim. Biophys., 1997, 346: 230-240.

Elisa Bombarda