Atomic force microscopy studies of APOBEC3G oligomerization and dynamics

Journal of Structural Biology

Volumn 184, Issue 2, 2013, Pages 217-225

  Shlyakhtenko, Luda S ^a   Lushnikov, Alexander Y ^a   Miyagi, Atsushi ^a   Li, Ming ^b   Harris, Reuben S ^b   Lyubchenko, Yuri L ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

Author keywords

AFM; APOBEC3G; Atomic force microscopy; High speed AFM; Single stranded DNA binding proteins; Site search mechanisms

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3G; MONOMER; OLIGOMER; SINGLE STRANDED DNA;

ARTICLE; ATOMIC FORCE MICROSCOPY; CONCENTRATION (PARAMETERS); DEAMINATION; DISSOCIATION; DNA BINDING; DNA PROTEIN COMPLEX; HUMAN; MOLECULAR DYNAMICS; OLIGOMERIZATION; PRIORITY JOURNAL; RETROPOSON; STOICHIOMETRY;

A3G; AFM; AMINOPROPYL SILATRANE TREATED MICA; APOBEC; APOBEC3G; APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC POLYPEPTIDE-LIKE; APS-MICA; ATOMIC FORCE MICROSCOPY; HIGH-SPEED AFM; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA BINDING PROTEINS; SITE SEARCH MECHANISMS; SSDNA;

CYTIDINE DEAMINASE; DNA, SINGLE-STRANDED; HEK293 CELLS; HUMANS; MICROSCOPY, ATOMIC FORCE; PARTICLE SIZE; PROTEIN BINDING; PROTEIN MULTIMERIZATION; TIME-LAPSE IMAGING;

EID: 84887232734     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.09.008     Document Type: Article

References (21)

1. Ando T., Uchihashi T., Kodera N. High-speed AFM and applications to biomolecular systems. Annu. Rev. Biophys. 2013, 42:393-414.
2. Bennett R.P., Salter J.D., Liu X., Wedekind J.E., Smith H.C. APOBEC3G subunits self-associate via the C-terminal deaminase domain. J. Biol. Chem. 2008, 283:33329-33336.
3. Chelico L., Pham P., Calabrese P., Goodman M.F. APOBEC3G DNA deaminase acts processively 3'→5' on single-stranded DNA. Nat. Struct. Mol. Biol. 2006, 13:392-399.
4. Chelico L., Sacho E.J., Erie D.A., Goodman M.F. A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIV. J. Biol. Chem. 2008, 283:13780-13791.
5. Chelico L., Prochnow C., Erie D.A., Chen X.S., Goodman M.F. Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G. J. Biol. Chem. 2010, 285:16195-16205.
6. Friew Y.N., Boyko V., Hu W.S., Pathak V.K. Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA. Retrovirology 2009, 6:56.
7. Harris R.S., Hultquist J.F., Evans D.T. The restriction factors of human immunodeficiency virus. J. Biol. Chem. 2012, 287:40875-40883.
8. Huthoff H., Autore F., Gallois-Montbrun S., Fraternali F., Malim M.H. RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1. PLoS Pathog. 2009, 5:e1000330.
9. Imahashi M., Nakashima M., Iwatani Y. Antiviral mechanism and biochemical basis of the human APOBEC3 family. Front. Microbiol. 2012, 3:250.
10. Li M., Shandilya S.M., Carpenter M.A., Rathore A., Brown W.L., Perkins A.L., Harki D.A., Solberg J., et al. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem. Biol. 2012, 7:506-517.
11. Lyubchenko Y.L., Shlyakhtenko L.S. AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods 2009, 47:206-213.
12. Lyubchenko Y.L., Shlyakhtenko L.S., Ando T. Imaging of nucleic acids with atomic force microscopy. Methods 2011, 54:274-283.
13. Malim M.H., Bieniasz P.D. HIV restriction factors and mechanisms of evasion. Cold Spring Harb. Perspect Med. 2012, 2:a006940.
14. McDougall W.M., Okany C., Smith H.C. Deaminase activity on ssDNA occurred in vitro when APOBEC3G forms homotetramers and higher-order complexes. J Biol Chem 2011, 286:30655-30661.
15. Nowarski R., Britan-Rosich E., Shiloach T., Kotler M. Hypermutation by intersegmental transfer of APOBEC3G cytidine deaminase. Nat. Struct. Mol. Biol. 2008, 15:1059-1066.
16. Opi S., Takeuchi H., Kao S., Khan M.A., Miyagi E., Goila-Gaur R., Iwatani Y., Levin J.G., et al. Monomeric APOBEC3G is catalytically active and has antiviral activity. J. Virol. 2006, 80:4673-4682.
17. Salter J.D., Krucinska J., Raina J., Smith H.C., Wedekind J.E. A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function. Biochemistry 2009, 48:10685-10687.
18. Shlyakhtenko L.S., Lushnikov A.Y., Li M., Lackey L., Harris R.S., Lyubchenko Y.L. Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G. J. Biol. Chem. 2011, 286:3387-3395.
19. Shlyakhtenko L.S., Lushnikov A.Y., Miyagi A., Li M., Harris R.S., Lyubchenko Y.L. Nanoscale Structure and dynamics of ABOBEC3G complexes with single-stranded DNA. Biochemistry 2012, 32:6432-6440.
20. Shlyakhtenko L.S., Lushnikov A.Y., Miyagi A., Lyubchenko Y.L. Specificity of binding of single-stranded DNA-binding protein to its target. Biochemistry 2012, 51:1500-1509.
21. Wedekind J.E., Gillilan R., Janda A., Krucinska J., Salter J.D., Bennett R.P., Raina J., Smith H.C. Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits. J. Biol. Chem. 2006, 281:38122-38126.