Levels of HIV1 gp120 3D B-cell Epitopes Mutability and Variability: Searching for Possible Vaccine Epitopes

REFERENCES

• Alsmadi, O., Tilley, S. A. Antibody-Dependent cellular cytotoxicity directed against cells expressing human immunodeficiency virus type 1 envelope of primary or laboratory-adapted strains by human and chimpanzee monoclonal antibodies of different epitope specificities. J. Virol. 72(1):286–293.
   PubMed Web of Science ®Google Scholar
• Andersen, P. H., Nielsen, M., Lund, O. Prediction of residues in discontinuous B cell epitopes using protein 3D structures. Protein Science 15:2558–2567.
   PubMed Web of Science ®Google Scholar
• Bailey, J. R., Lassen, K. G., Yang, H. C. Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy. J Virol. 80:4758–4770.
   PubMed Web of Science ®Google Scholar
• Bishop, K. N., Holmes, R. K., Sheehy, A. M., Malim, M. H. APOBEC-mediated editing of viral RNA. Science 305:645.
   PubMed Web of Science ®Google Scholar
• Berkhout, B., Paxton, W. A. HIV vaccine: it may take two to tango, but no party time yet. Retrovirology 6(1):88.
   PubMed Web of Science ®Google Scholar
• Bunnik, E. M., Pisas, L. van Nuenen, A. C., Schuitemaker, H. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. J Virol. 82:7932–7941.
   PubMed Web of Science ®Google Scholar
• Fransen, S., Bridger, G., Whitcomb, J. M., Toma, J., Stawiski, E., Parkin, N., Petropoulos, C. J., Huang, W. Suppression of dualtropic human immunodeficiency virus type 1 by the CXCR4 antagonist AMD3100 is associated with efficiency of CXCR4 use and baseline virus composition. Antimicrob Agents Chemother 52:2608–2615.
   PubMed Web of Science ®Google Scholar
• Haynes, B. F., Montefiori, D. C. Aiming to induce broadly reactive neutralizing antibody responses with HIV-1 vaccine candidates. Expert Rev. Vaccines 5(3):347–363.
   PubMed Web of Science ®Google Scholar
• Hopp, T. P. Protein antigen conformation: folding patterns and predictive algorithms; selection of antigenic and immunogenic peptides. Ann. Sclavo. 2:47–60.
   Google Scholar
• Hopp, T. P., Woods, K. R. A computer program for predicting protein antigenic determinants. Mol. Immunol. 20(4):483–489.
   PubMed Web of Science ®Google Scholar
• Hoxie, J. A. Toward an antibody-based HIV vaccine. Annu. Rev. Med. 61: Epub ahead of print.
   PubMed Web of Science ®Google Scholar
• Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., Dimitrov, D. S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P. D. Structure of a V3-containing HIV-1 gp120 core. Science 310(5750):1025–1028.
   PubMed Web of Science ®Google Scholar
• Izumi, T., Shirakawa, K. Takaori-Kondo, A. Cytidine deaminases as a weapon against retroviruses and a new target for antiviral therapy. Mini Rev. Med. Chem. 8:231–238.
   PubMed Web of Science ®Google Scholar
• Kamath-Loeb, A. S., Hizi, A., Kasai, H. and Loeb, L. A. Incorporation of the guanosine triphosphate analogs 8-oxo-dGTP and 8-NH2-dGTP by reverse transcriptases and mammalian DNA polymerases. JBC 272(9): 5892–5898.
   PubMed Web of Science ®Google Scholar
• Khrustalev, V. V., Barkovsky, E. V. An in-silico study of alphaherpesviruses ICP0 genes: Positive selection or strong mutational GC-pressure? IUBMB Life 60(7):456–460.
   PubMed Web of Science ®Google Scholar
• Khrustalev, V. V. HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it. In Silico Biology 9:0022.
   Google Scholar
• Khrustalev, V. V. Can mutational GC-pressure create new linear B-cell epitopes in herpes simplex virus type 1 glycoprotein B? Immunol. Investig. 38(7):613–623.
   PubMed Web of Science ®Google Scholar
• Kim, Y. B., Han, D. P., Cao, C., Cho, M. W. Immunogenicity and ability of variable loop-deleted human immunodeficiency virus type 1 envelope glycoproteins to elicit neutralizing antibodies. Virology 305(1):124–137.
   PubMed Web of Science ®Google Scholar
• Larsen, J. E. P., Lund, O., Nielsen, M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2:2.
   PubMedGoogle Scholar
• Liang, S., Zheng, D., Zhang, C., Zacharias, M. Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics 10:302.
   PubMed Web of Science ®Google Scholar
• Petit, V. Guétard, D., Renard, M., Keriel, A., Sitbon, M., Wain-Hobson, S., Vartanian, J. P. Murine APOBEC1 is a powerful mutator of retroviral and cellular RNA in vitro and in vivo. J. Mol. Biol. 385:65–78.
   PubMed Web of Science ®Google Scholar
• Rubinstein, N. D., Mayrose, I., Martz, E., Pupko, T. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics 10:287.
   PubMed Web of Science ®Google Scholar
• Singer, G. A. C., Hickey, D. A. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17:1581–1588.
   PubMed Web of Science ®Google Scholar
• Sueoka, N. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85:2653–2657.
   PubMed Web of Science ®Google Scholar
• Tamura, K., Dudley, J., Nei, M., Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596–1599.
   PubMed Web of Science ®Google Scholar
• Yang, O. O. Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation. PLoS One 4(10): e7388.
   Google Scholar
• Zhou, T., Xu, L., Dey, B., Hessell, A. J., Ryk, D.V., Xiang, S. H., Yang, X., Zhang, M. Y., Zwick, M. B., Arthos, J., Burton, D. R., Dimitrov, D. S. Sodroski, J., Wyatt, R., Nabel, G. J., Kwong, P. D. Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature 445(7129):732–737.
   PubMed Web of Science ®Google Scholar