• UNDETY BENJAMIN JASON Sathyabama University
  • Daniel Alex Anand



 Objective: The variations of p6 in the host in horizontal transmission were studied. The conserved regions are found in viral factor when analyzed with host factors. Sequence and structural analysis were carried out to understand the interaction between viral and host factors. Sequences of host factors were extracted. Study the variation and conserved regions of P6 protein of GAG gene accross horinzontal transmission.

Methods: Pairwise alignment, multiple sequence alignment, secondary structure analysis, and three-dimensional structure analysis of p6 sequence with host sequences were performed. Databases National Center for Biotechnology Information and protein data bank (PDB) were used to download sequences. Tools Swiss-PDB viewer, Needleman–Wunsch Clustal W and Dicovery Studio version 2.0, were used for the analysis. Through literature host factors TSG101, NEDD4, AIP1, and ALIX were found for p6.

Results: The percentages of conserved regions of p6 with respect to four host factors were calculated. Fragments frs†and gvetttppq†have 66.66% and 23.33% with respect to TSG101, frsgâ€and ppeesfrsg†are 85.15% and 46.66% with respect to NEDD4, eptappeesf†and idk†are 73.91% and 78.26% with respect to AIP1 and lqsrpe†and pqkqe†are 61.53% and 84.61% with respect to ALIX.

Conclusion: Modeled structures of the host and viral factors contain 89% of amino acids in favorable region. Whole study was concerned on finding out variation in horizontal transmission of p6 gag gene protein. Among all the conserved fragments frsg†of NEDD4, pqkqe†of ALIX, idk†of AIP1 and eptappeesf†of AIP1 are consensus fragments with the presence of hydrophobic amino acids and hence these regions are treated as active sites for viral target. Conformational analysis of host factors reached active potential at 10 μ seconds with viral factor

Keywords: Conserved, Pairwise alignment, Variation, Horizontal transmission.


Berger EA, Murphy PM, Farber JM. Chemokine receptors as HIV 1 coreceptors: Roles in viral entry, tropism, and disease. Annu Rev Immunol 1999;17:657-700.

Doms RW. Beyond receptor expression: The influence of receptor conformation, density, and affinity in HIV-1 infection. Virology 2000;276(2):229-37.

Freed EO, Martin MA. HIVs and their replication. In: Knipe DM, Howley PM, editors. Fields Virology. Philadelphia: Lippincott, Williams & Wilkins; 2007. p. 2107-85.

Melikyan GB. Common principles and intermediates of viral protein-mediated fusion: The HIV-1 paradigm. Retrovirology 2008;5:111.

Miyauchi K, Kim Y, Latinovic O, Morozov V, Melikyan GB. HIV enters cells via endocytosis and dynamin-dependent fusion with endosomes. Cell 2009;137(3):433-44.

Telesnitsky A, Goff SP. Reverse transcriptase and the generation of retroviral DNA. In: Coffin J, Varmus H, Hughes S, editors. Retroviruses. Cold Spring Harbor New York: Cold Spring Harbor Laboratory; 1997. p. 121-60.

Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: Critical role in reverse transcription and molecular mechanism. Prog Nucleic Acid Res Mol Biol 2005;80:217-86.

Hulme AE, Perez O, Hope TJ. Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription. Proc Natl Acad Sci U S A 2011;108(24):9975-80.

Song B. TRIM5alpha. Curr Top Microbiol Immunol 2009;339:47-66.

Towers GJ. The control of viral infection by tripartite motif proteins and cyclophilin A. Retrovirology 2007;4:40.

Dismuke DJ, Aiken C. Evidence for a functional link between uncoating of the human immunodeficiency virus type 1 core and nuclear import of the viral preintegration complex. J Virol 2006;80(8):3712-20.

Yamashita M, Emerman M. Capsid is a dominant determinant of retrovirus infectivity in nondividing cells. J Virol 2004;78(11):5670-8



How to Cite

JASON, U. B. ., and D. A. Anand. “STUDY OF VARIATION IN P6 REGION OF GAG ACROSS MULTIPLE STRAINS OF HIV-1”. Asian Journal of Pharmaceutical and Clinical Research, vol. 7, no. 5, Nov. 2014, pp. 28-31,



Original Article(s)