Binding Sites of the Viral RNA Element TAR and of TAR Mutants for Various Peptide Ligands, Probed with LILBID: A New Laser Mass Spectrometry

Journal of the American Society for Mass Spectrometry

Volumn 19, Issue 11, 2008, Pages 1600-1611

  Morgner, Nina ^a   Barth, Hans Dieter ^a   Brutschy, Bernhard ^a   Scheffer, Ute ^a   Breitung, Sven ^a   Göbel, Michael ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; CONCENTRATION (PROCESS); DESORPTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LASERS; LIGANDS; MASS SPECTROMETERS; MASS SPECTROMETRY; NUCLEIC ACIDS; RNA; SPECTROMETERS; SPECTROMETRY; SPECTRUM ANALYSIS; STOICHIOMETRY; TAR;

AS MODELS; BINDING BEHAVIORS; BINDING EFFICIENCIES; COMPETITIVE BINDINGS; ELECTROSTATIC BINDINGS; FLUORIMETRIC METHODS; HIGHER CONCENTRATIONS; HIV TATS; LASER INDUCED LIQUID BEAD ION DESORPTIONS; LASER MASS SPECTROMETRIES; LIGAND INTERACTIONS; NUMERIC MODELS; PEPTIDE LIGANDS; POTENTIAL INHIBITORS; QUANTITATIVE EVALUATIONS; SPECIFIC BINDINGS; TERNARY COMPLEX FORMATIONS; TERNARY COMPLEXES; TRANSACTIVATION; VIRAL RNAS;

BINDING SITES;

VIRUS RNA;

ARTICLE; BINDING AFFINITY; BINDING SITE; ELECTROSPRAY MASS SPECTROMETRY; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PHOTOMETRY; STOICHIOMETRY;

ANIMALS; BASE SEQUENCE; HIV LONG TERMINAL REPEAT; HIV-1; HUMANS; MASS SPECTROMETRY; MUTATION; NUCLEIC ACID CONFORMATION; PEPTIDES; PROTEIN BINDING; RNA, VIRAL; TAT GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 55149125811     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2008.07.001     Document Type: Article

References (36)

1. Péloponèse Jr. J.-M., Collette Y., Grégoire C., Bailly C., Campèse D., Meurs E.F., Olive D., and Loret E.P. Full Peptide Synthesis, Purification, and Characterization of Six Tat Variants. J. Biol. Chem. 27417 (1999) 11473-11478
2. Bannwarth S., and Gatignol A. HIV-1 TAR RNA: The Target of Molecular Interactions Between the Virus and Its Host. Curr. HIV Res. 31 (2005) 61-71
3. Calnan B., Tidor B., Biancalana S., Hudson D., and Frankel A. Arginine-Mediated RNA Recognition: The Arginine Fork. Science 252 5009 (1991) 1167-1171
4. Frankel A.D., Biancalana S., and Hudson D. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 7397-7401
5. Karn J. Tackling Tat. J. Mol. Biol. 293 2 (1999) 235-254
6. Aboul-ela F., Karn J., and Varani G. The Structure of the Human Immunodeficiency Virus Type-1 TAR RNA Reveals Principles of RNA Recognition by Tat Protein. J. Mol. Biol. 253 2 (1995) 313-332
7. Weeks K.M., and Crothers D.M. RNA Recognition by Tat-Derived Peptides: Interaction in the Major Groove?. Cell 66 3 (1991) 577-588
8. Seewald M.J., Metzger A.U., Willbold D., Rösch P., and Sticht H. J. Biomol. Struct. Dyn. 16 (1998) 683-692
9. Farrow M.A., Aboul-ela F., Owen D., Karpeisky A., Beigelman L., and Gait M.J. Biochemistry 37 (1998) 3096-3108
10. Turner J.J., Jones S., Fabani M.M., Ivanova G., Arzumanov A.A., and Gait M.J. RNA Targeting with Peptide Conjugates of Oligonucleotides, siRNA, and PNA. Blood Cells Mol. Dis. 38 1 (2007) 1-7
11. Froeyen M., and Herdewijn P. RNA as a Target for Drug Design, the Example of Tat-TAR Interaction. Curr. Top. Med. Chem. 2 10 (2002) 1123-1145
12. Krebs A., Ludwig V., Boden O., and Göbel M.W. Targeting the HIV Trans-Activation Responsive Region-Approaches Towards RNA-Binding Drugs. Chem. BioChem. 4 10 (2003) 972-978
13. Richter S.N., and Palu G. Inhibitors of HIV-1 Tat-Mediated Transactivation. Curr. Med. Chem. 13 11 (2006) 1305-1315
14. Nandi C.K., Parui P.P., Brutschy B., Scheffer U., and Göbel M. Fluorescence Correlation Spectroscopy at Single Molecule Level on the Tat-TAR Complex and Its Inhibitors. Biopolymers 89 1 (2008) 17-25
15. Tanaka K., Waki H., Ido Y., Akita S., Yoshida Y., and Yoshida T. Protein and Polymer Analyses up to m/z 100,000 by Laser Ionization Time-of-Flight Mass Spectrometry. Rapid Commun. Mass Spectrom. 2 8 (1988) 151-153
16. Fenn J.B., Mann M., Meng C.K., Wong S.F., and Whitehouse C.M. Electrospray Ionization for Mass Spectrometry of Large Biomolecules. Science 246 (1989) 64-71
17. Hunger C. Massenspektrometrische Untersuchungen von DNA, RNA und nichtkovalenten Oligonukleotid-Komplexen (2005), Universität Frankfurt am Main, Ph.D. Thesis
18. Mei H.-Y., Mack D.P., Galan A.A., Halim N.S., Heldsinger A., Loo J.A., Moreland D.W., Sannes-Lowery K.A., Sharmeen L., Truong H.N., and Czarnik A.W. Bioorg. Med. Chem. 5 (1997) 173-1184
19. Mei H.-Y., Cui M., Heldsinger A., Lemrow S.M., Loo J.A., Sannes-Lowery K.A., Sharmeen L., and Czarnik A.W. Biochemistry 37 (1998) 14204-14212
20. Morgner N., Barth H.-D., and Brutschy B. A New Way to Detect Noncovalently Bonded Complexes of Biomolecules from Liquid Micro-Droplets by Laser Mass Spectrometry. Aust. J. Chem. 59 (2006) 109-114
21. Meier T., Morgner N., Matthies D., Pogoryelov D., Keis S., Cook G.M., Dimroth P., and Brutschy B. A Tridecameric C-Ring of the Adenosine Triphosphate (ATP) Synthase from the Thermoalkaliphilic Bacillus sp. Strain TA2.A1 Facilitates ATP Synthesis at Low Electrochemical Proton Potential. Mol. Microbiol. 65 5 (2007) 1181-1192
22. Morgner N., Kleinschroth T., Barth H.-D., Ludwig B., and Brutschy B. A Novel Approach to Analyze Membrane Proteins by Laser Mass Spectrometry: From Protein Subunits to the Integral Complex. JASMS 18 (2007) 1429-1438
23. Morgner N., Barth H.D., Schmidt T.L., Heckel A., Scheffer U., Göbel M., Fucini P., and Brutschy B. Detecting Specific Ligand Binding to Nucleic Acids: A Test for Ultrasoft Laser Mass Spectrometry. J. Phys. Chem. 221 (2007) 689-704
24. Hoffmann, J., Morgner, N., Barth, H.-D., Brutschy, B. unpublished results.
25. Sobott F., Schunk S.A., Schüth F., and Brutschy B. Examination of Condensation Products of Group 4 Alkoxides with Laser-Induced Liquid Beam Ionization/Desorption Mass Spectrometry,. Chem. Eur. J. 4 (1998) 2353-2359
26. Kleinekofort W., Avdiev J., and Brutschy B. A New Method of Laser Desorption Mass Spectrometry for the Study of Biological Macromolecules. Int. J. Mass Spectrom. Ion Processes 152 (1996) 135-142
27. Kleinekofort W., Pfenninger A., Plomer T., Griesinger C., and Brutschy B. Observation of Noncovalent Complexes Using Laser-Induced Liquid Beam Ionization/Desorption. Int. J. Mass Spectrom. Ion Processes 156 (1996) 195-202
28. Kleinekofort W., Schweitzer M., Engels J., and Brutschy B. Analysis of Double-Stranded Oligonucleotides by Laser-Induced Liquid Beam Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 163 (1997) L1-L4
29. Sannes-Lowery K.A., Hu P., Mack D.P., Mei H.-Y., and Loo J.A. HIV-1 Tat Peptide Binding to TAR RNA by Electrospray Ionization Mass Spectrometry. Anal. Chem. 69 (1997) 5130-5135
30. Scheffer U., Strick A., Ludwig V., Peter S., Kalden E., and Göbel M.W. Metal-Free Catalysts for the Hydrolysis of RNA Derived from Guanidines, 2-Aminopyridines, and 2-Aminobenzimidazoles. J. Am. Chem. Soc. 127 (2005) 2211-2217
31. Long K.S., and Crothers D.M. Characterization of the Solution Conformations of Unbound and Tat Peptide-Bound Forms of HIV-1 TAR RNA. Biochemistry 38 (1999) 10059-10069
32. Schwiegk C., Kalesse M., Kirschning A., and Carlomagno T. TAR-RNA Recognition by a Novel Cyclic Aminoglycoside Analogue. Nucleic Acids Res. 34 (2006) 3599-3608
33. Aboul-ela F., Karn J., and Varani G. The Structure of the Human Immunodeficiency Virus Type-1 TAR RNA Reveals Principles of RNA Recognition by Tat Protein. J. Mol. Biol. 253 (1995) 313-332
34. Faber C., Sticht H., Schweimer K., and Rösch P. Structural Rearrangements of HIV-1 Tat-Responsive RNA Upon Binding of Neomycin B. J. Biol. Chem. 275 (2000) 20660-20666
35. Ludwig V., Krebs A., Stoll M., Dietrich U., Ferner J., Schwalbe H., Scheffer U., Dürner G., and Göbel M.W. Tripeptides from Synthetic Amino Acids Block the Tat-TAR Association and Slow Down HIV Spread in Cell Cultures. Chem. Biochem. 8 15 (2007) 1850-1856
36. Long K.S., and Crothers D.M. Interaction of Human Immunodeficiency Virus Type 1 Tat-Derived Peptides with TAR RNA. Biochemistry 34 (1995) 8885-8895