1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
2Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan,Iran.
HIV-1 envelope (env) glycoprotein mediates an important role in entry of the virus into the susceptible target cells. As env glycoprotein of HIV-1 is highly variable in the different geographical regions, in the present study, different properties of this protein in Iran are compared with five nearby countries. The sequences of HIV-1 env glycoproteins of Iran, Afghanistan, Russia, Turkey, Pakistan and Saudi Arabia databases were collected from databases. Amino acid composition and physical and chemical properties of the proteins from these countries were studied using Protparam and COPid tools. Receiver-operating characteristic (ROC) curve analysis and Support Vector Machine (SVM) were used to evaluate association between the properties of HIV-1 env glycoprotein of Iran with five nearby countries. The results verify that amino acid composition and four physical and chemical properties (molecular weight, isoelectric point, Aliphatic Index, and grand average of hydropathicity) of HIV-1 env protein in Iran and Russia were not significantly different. In conclusion, the results indicate that in silico techniques provide valuable information for comparing HIV-1 envelop glycoprotein in different geographical locations.
1. Kandathil A, Ramalingam S, Kannangai R, David S, Sridharan G. Molecular epidemiology of HIV. Indian J Med Res 2005;121:333-344.
2. Potter SJ, Chew CB, Steain M, Dwyer DE, Saksena NK. Obstacles to successful antiretroviral treatment of HIV-1 infection: problems & perspectives. Indian J Med Res 2004;119:217-237.
3. Sakoda T, Kasahara N, Hamamori Y, Kedes L. A high-titer lentiviral production system mediates efficient transduction of differentiated cells including beating cardiac myocytes. J Mol Cell Cardiol 1999;31:2037-2047.
4. Spira S, Wainberg MA, Loemba H, Turner D, Brenner BG. Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J Antimicrob Chemother 2003;51:229-240.
5. Roy CN, Khandaker I, Oshitani H. Intersubtype genetic variation of HIV-1 Tat exon 1. AIDS Res Hum Retroviruses 2015;31:641-648.
6. Khan S, Rai MA, Khanani MR, Khan MN, Ali SH. HIV-1 subtype A infection in a community of intravenous drug users in Pakistan. BMC Infect Dis 2006;6:164.
7. Berg RK, Melchjorsen J, Rintahaka J, Diget E, Søby S, Horan KA. Genomic HIV RNA induces innate immune responses through RIG-I-dependent sensing of secondary-structured RNA. PloS one 2012;7:e29291.
8. Korkut A, Hendrickson WA. Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120. PloS one 2012;7:e52170.
9. Hoffer LJ. How much protein do parenteral amino acid mixtures provide? Am J Clin Nutr 2011;94:1396-1398.
10. Ahn I, Son HS. Epidemiological comparisons of codon usage patterns among HIV-1 isolates from Asia, Europe, Africa and the Americas. Exp Mol Med 2006;38: 643-651.
11. Singh S, Gupta SK, Gupta MK, Seth PP. Phylogenetic analysis of HIV-1 envelope glycoprotein in Asian countries. Proceeding of International Conference on Applied Bioenginering 2007;200-204.
12. Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol 2013;19:337-348.
13. Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook: Springer; 2005; pp:571-607.
14. Kumar M, Thakur V, Raghava GP. COPid: composition based protein identification. In Silico Biol 2008;8:121-128.
15. Fawcett T. An introduction to ROC analysis. Pattern Recognit Lett 2006;27:861-874.
16. Mikut R, Reischl M. Data mining tools. Data Min Knowl Discov 2011;1:431-443.
17. Avupati VR, Kurre PN, Bagadi SR, Muthyala MK, Yejella RP. De novo based ligand generation and docking studies of PPARδ agonists: Correlations between predicted biological activity vs. biopharmaceutical descriptors. Chem-Bio Informatics J 2010;10:74-86.
18. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D. Diversity considerations in HIV-1 vaccine selection. Science 2002;296:2354-2360.
19. Yuan T, Li J, Zhang MY. HIV-1 envelope glycoprotein variable loops are indispensable for envelope structural integrity and virus entry. PLoS One 2013 1;8:e69789.
20. Robertson D, Anderson J, Bradac J, Carr J, Foley B, Funkhouser R. HIV-1 nomenclature proposal. Science 2000;288:55-56.
21. Suslov KV. AID-mediated somatic hypermutation for generation of viral envelope protein diversity in patient-specific therapeutic HIV vaccines based on induction of neutralizing antibodies. Immunol Lett 2010;128:86-87.
22. Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sönnerborg A, Neogi U. Phylogenetic analysis of Ethiopian HIV-1 subtype C near full-length genomes reveals high intrasubtype diversity and a strong geographical cluster. AIDS Res Hum Retroviruses 2016;32:471-474.
23. Becker ML, DE Jager G, Becker WB. Analysis of partial gag and env gene sequences of HIV type 1 strains from southern Africa. AIDS Res Hum Retroviruses 1995;11:1265-1267.
24. Zhu W, Zeng N, Wang N. Sensitivity, specificity, accuracy, associated confidence interval and ROC analysis with practical SAS implementations. NESUG proceedings: health care and life sciences, Baltimore, Maryland. 2010.
25. Bobkov A, Kazennova E, Selimoval L, Bobkova M, Khanina T, Ladnaya N, Karvchenko A, Pokrovsky V, Cheingsong-Popov R, Weber J. A sudden epidemic of HIV type 1 among injecting drug users in the former Soviet Union: Identification of subtype A, subtype B, and novel gag A/env B recombinants. AIDS Res Hum Retroviruses 1998;14:669-676.
26. Nabatov AA, Kravchenko ON, Lyulchuk MG, Shcherbinskaya AM, Lukashov VV. Simultaneous introduction of HIV type 1 subtype A and B viruses into injecting drug users in southern Ukraine at the beginning of the epidemic in the former Soviet Union. AIDS Res Hum Retroviruses 2002;18:891-889.
27. Sarrami-Forooshani R, Das SR, Sabahi F, Adeli A, Esmaeili R, Wahren B, Molecular analysis and phylogenetic characterization of HIV in Iran. J Med Virol 2006;78:853-863.