Functional investigations of retroviral protein-ribonucleic acid complexes by nanospray Fourier transform ion cyclotron resonance mass spectrometry

European Journal of Mass Spectrometry

Volumn 13, Issue 1, 2007, Pages 29-33

  Fabris, Daniele ^a   Chaudhari, Prajakta ^a   Hagan, Nathan ^a   Turner, Kevin ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

Chaperone; Competitive binding; ESI FT ICR; HIV 1; Non covalent complex; Protein binding; Protein nucleic acids assembly; Ribonucleoprotein; RNA conformation; RNA isomerization

Indexed keywords

NUCLEOCAPSID PROTEIN; VIRUS RNA;

ARTICLE; CHEMISTRY; DIMERIZATION; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; INFRARED SPECTROSCOPY; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; VIRUS GENOME;

DIMERIZATION; GENOME, VIRAL; HIV-1; NANOTECHNOLOGY; NUCLEOCAPSID PROTEINS; RNA, VIRAL; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 34250753915     PISSN: 14690667     EISSN: None     Source Type: Journal    
DOI: 10.1255/ejms.839     Document Type: Article

References (20)

1. J.L. Darlix, C. Gabus, M.T. Nugeyre, F. Clavel and F. Barré-Sinussi, "Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1," J. Mol. Biol. 216,689-699 (1990). doi: 10.1016/0022-2836(90)90392-Y
2. J.M. Coffin, S.H. Hughes and H. Varmus, in Retroviruses, Ed by J.M. Coffin, S.H. Hughes and H. Varmus. Cold Spring Harbor Laboratory Press, Plainview, NY, USA (1997).
3. M. Laughrea and L. Jette, "A 19-nucleotide sequence upstream of the 5′ major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA," Biochemistry 33, 13464-13474 (1994). doi: 10.1021/bi00249a035
4. E. Skripkin, J.C. Paillart, R. Marquet, B. Ehresmann and C. Ehresmann, "Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro", Proc. Natl. Acad. Sci. USA, 91, 4945-4949 (1994). doi:10.1073/pnas.91.11.4945
5. J. Clever, C. Sassetti and T.G. Parslow, "RNA secondary structure and binding sites for gag gene products in the 5′ packaging signal of human immunodeficiency virus type 1", J. Virol. 69, 2101-2109 (1995).
6. M.S. McBride and A.T. Panganiban, "The human immunodeficiency virus type-1 encapsidation site is a multipartite RNA element composed of functional hairpin structures", J. Virol. 70, 2963-2973 (1996).
7. A. Rein, L.E. Henderson and J.G. Levin, "Nucleic-acidchaperone activity of retroviral nucleocapsid proteins: significance for retroviral replication", Trends Biochem. Sci. 23, 297-301 (1998). doi: 10.1016/80968-0004(98)01256-0
8. J.G. Levin, J. Guo, I. Rouzina and K. Musier-Forsyth, "Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism", Prog. Nucleic Acid Res. Mol. Biol. 80, 217-286 (2005). doi: 10.1016/80079-6603(05)80006-6
9. M. Yamashita and J.B. Fenn, "Electrospray ion source. Another variation on the free-jet theme", J. Phys. Chem. 88, 4671-4675 (1984). doi: 10.1021/j150664a046
10. M.L. Aleksandrov, L.N. Gall, V.N. Krasnov, V.I. Nikolaev, V.A. Pavlenko and V.A. Shkurov, "Extraction of ions from solutions under atmospheric pressure: a method of mass spectrometric analysis of bioorganic compounds". Doklady Akademii Nauk. 277, 379-383 (1984).
11. B. Ganem, Y.T. Li and J.D. Henion, "Detection of noncovalent receptor-ligand complexes by mass spectrometry", J. Am. Chem. Soc. 113, 6294-6296 (1991). doi: 10.1021/ja00016a069
12. J.A. Loo, "Studying noncovalent protein complexes by electrospray ionization mass spectrometry", Mass Spectrom. Rev. 16, 1-23 (1997). doi: 10.1002/(SICI)1098-2787(1997)16:1〈1::AID-MAS1〉3.0.CO;2-L
13. M.B. Comisarow and A.G. Marshall, "Fourier transform ion cyclotron resonance", Chem. Phys. Lett. 25, 282-283 (1974). doi: 10.1016/0009-2614(74)89137-2
14. C.L. Hendrickson, M.R. Emmett and A.G. Marshall, "Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry", Ann. Rev. Phys. Chem. 50, 517-536 (1999). doi: 10.1146/annurev.physchem.50.1.517
15. N. Hagan and D. Fabris, "A direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between HIV-1 nucleocapsid protein and RNA stem-loops hairpins of the HIV-1 T-recognition element", Biochemistry 42, 10736-10745 (2003). doi: 10.1021/ bio0348922
16. K.B. Turner, N.A. Hagan and D. Fabris, "Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Ψ-RNA", Nucl. Acids Res. 34, 1305-1316 (2006). doi: 10.1093/nar/gkl004
17. J.F. Milligan and O.C. Uhlenbeck, "Synthesis of Small RNAs Using T7 RNA Polymerase", Methods Enzymol. 180, 51-62 (1989). doi: 10.1016/0076-6879(89)80091-6
18. K.I. Takahashi, S. Baba, P. Chattopadhyay, Y. Koyanagi, N. Yamamoto, H. Takaku and G. Kawai, "Structural requirement for the two-step dimerization of human immunodeficiency virus type 1 genome", RNA 6, 96-102 (2000). doi: 10.1017/S1355838200991635
19. N.A. Hagan, and D. Fabris, "Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1", J. Mol. Biol. 365, 396-410 (2007). doi: 10.1016/j.jmb.2006.09.081
20. R.J. Fisher, M.J. Fivash, A.G. Stephen, N.A. Hagan, S.R. Shenoy, M.V. Medaglia, L.R. Smith, K.M. Worthy, J.T. Simpson, R. Shoemaker, K.L. McNitt, D.J. Johnson, C.V. Hixson, R.J. Gorelick, D. Fabris, L.E. Henderson and A. Rein, "Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides", Nucl. Acids Res. 34, 472-484 (2006). doi: 10.1093/nar/gkj442