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The genome and proteins of Human Immunodeficiency Virus ( HIV ) have been the topic of big sum of research since the find of the virus in 1983, two old ages after the first major instances of Acquired immune lack syndrome ( AIDS ) associated unwellnesss were reported.


Figure Structure of HIV

HIV is a retrovirus, but a small different in construction from others. It is about 120 nanometers in diameter and approximately spherical. HIV-1 is composed of two transcripts of single-stranded RNA enclosed by a conelike mirid bug consisting the viral protein p24, typical of lentiviruses. The RNA constituent is more than 9000 bases long. This is in bend surrounded by a plasma membrane of host-cell beginning.

Human immunodeficiency virus type I ( HIV-1 ) is an enveloped RNA virus, belongs to the Lentivirinae of Retroviridae. Analysis of HIV-1 env cistrons of virus strains from different geographic parts reveals that HIV-1 can be divided into three chief groups: M ( major ) , O ( outlier ) , and N ( new ) . HIV-1 group M has been farther subdivided into genetically equidistant bunchs of HIV-1 env cistrons, consisting subtypes A to J.

Figure Structure of HIV genome

HIV has several major cistrons coding for structural proteins that are found in all retroviruses, and several nonstructural cistrons that are alone to HIV. The gag cistron provides the basic physical substructure of the virus, and pol provides the basic mechanism by which retroviruses reproduce, while the others help HIV to come in the host cell and heighten its reproduction. Though they may be altered by mutant, all of these cistrons except tev exist in all known discrepancies of HIV

joke ( group-specific antigen ) : codifications for the Gag polyprotein, which is processed during ripening to MA ( matrix protein, p17 ) ; CA ( mirid bug protein, p24 ) ; SP1 ( spacer peptide 1, p2 ) ; NC ( nucleocapsid protein, p7 ) ; SP2 ( spacer peptide 2, p1 ) and p6.

pol: codifications for viral enzymes rearward RNA polymerase, integrase, and HIV peptidase.

env ( envelope ) : codifications for gp160, the precursor to gp120 and gp41, proteins embedded in the viral envelope which enable the virus to attach to and blend with mark cells.

Transactivators: cheapness, rpm, vpr

Other regulators: vif, nef, vpu

tev: This cistron is merely present in a few HIV-1 isolates. It is a merger of parts of the cheapness, env, and rpm cistrons, and codifications for a protein with some of the belongingss of cheapness, but small or none of the belongingss of rpm.

Figure Envelope glycoprotein gp120

The envelop protein gp120 and its variable parts

Envelope glycoprotein gp120 is a glycoprotein exposed on the surface of the HIV envelope. The 120 in its name comes from its molecular weight of 120 kilodaltons. The envelope protein gp120 initiates the procedure of cell entry by interacting with the chief receptor CD4 and one of the chemokine receptors CCR5 or CXCR4. It is derived from the polyprotein gp160, which besides contains the transmembrane protein gp41. This polyprotein is encoded by the env cistron, present in all retroviruses. Inconsistent and inaccurate enumeration, caused by frequent interpolations and omissions, has been a serious job in the literature on gp120.

The Human Immunodeficiency Virus ( HIV ) can mutate often to remain in front of the immune system. There is nevertheless a extremely conserved part in the virus genome closed to its receptor binding site. The glycoprotein gp120 is anchored to the viral membrane, or envelope, via non-covalent bonds with the transmembrane glycoprotein, gp41. It is involved in entry into cells by adhering to CD4 receptors, peculiarly helper T-cells. Binding to CD4 is chiefly electrostatic although there are van der Waals interactions and H bonds. Several surveies have shown the utility of phyletic methods to corroborate known or to find unknown relationships among HIV isolates. The V3 and V4 part are two variable parts of pg120 that most researches focused on.In about all published surveies a part in the env cistron incorporating the V3 cringle was used for comparing entirely or in combination with the p17 part located in the gag cistron or the RT part located in the pol cistron. In one survey merely the p17 part was analysed, in another p17 and RT, and in yet another all three parts.

Phylogenetic Analysis


HIV Type 1



























HIV Type 2















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AGM / ringer GRI-1







In this survey, phyletic treed of HIV env cistron and the protein gp120 coded by this cistron were reconstructed. Besides, the phyletic analysis of them was implemented. 24 samples were collected from the Pfam database of gp120 ( hypertext transfer protocol: // ) , including 13 strains of HIV type 1. For comparing, 6 strains of HIV type 2 and 5 strains of SIV ( Simian immunodeficiency virus ) were besides included. Alliances of V3 cringle and V4 cringle was obtained. Then the phyletic tree of env cistron and gp120 were reconstructed based on the alliance. The 24 isolates were shown in the left tabular array.


Aligned the nucleotide sequence of 24 samples with ClustalX package, consequences were acquired and used for phyletic tree analysis after unreal accommodation. The phyletic tree was reconstructed with Neighbor-Joining method.

To obtain an estimation of familial fluctuation in each sphere ( V3, V4 ) of the env cistron, an analysis was performed on the complete protein sequence alliance. This analysis shows the figure of polymorphous sites in an overlapping window of nine amino acids, applied to each of the protein sequence alliance.

Figure 5 Multiple alliance of V3 loop derived from the 24 samples.

Figure The figure shows an alliance of 24 samples. In the alliance, we can see some conserved parts and variable parts, and the V3 and V4 cringle were boxed.

The V3 cringle of the outer membrane gp120 of HIV-1 is the sphere with the highest fluctuation rate ; nevertheless, it is besides conservative comparatively, particularly at the beginning and the terminal of it. In all of the HIV-1, HIV-2, and SIV, there is invariant cysteine at both the beginning and the terminal, which can organize a disulfide span. Besides, a difference between HIV-1 and HIV-2, SIV can be observed.

The cysteine and the disulfide span play an of import function in the procedure of cell entry. The V3 cringle binds to the cell surface in a conformation dependent mode and its N-terminal sphere is responsible for the interaction. It has been observed that V3 cringle can heighten the entry of its ain HIV strains. Pre-treatment of the mark cells with V3 peptides followed by remotion of the peptides besides enhanced infectivity, bespeaking that the binding of the peptides to the mark cells besides plays a function in this sweetening. The V3 root is responsible for gp120 binding to the CCR5 N-terminus. Both the V3 Crown and root are required for soluble gp120 adhering to cell surface CCR5. The V3 Crown interacts with residues in the EC of CCR5, most likely ECL2. The V3 Crown entirely is necessary and sufficient to direct sole use of CCR5 or CXCR4. The V3 root, despite being able to intercede specific adhering to CCR5 Nt sulfopeptides, is non the chief determiner of coreceptor Figure Multiple alliance of V4 loop derived from the 24 samples.


The V4 cringle, similar with V3, besides has cysteine at both there is invariant cysteine at both the beginning and the terminal, which form a disulfide span. A consistent characteristic of this analysis is that for most MIPs, higher degrees of fluctuation were observed in the C3 and V4 parts than in the V3 cringle, and length fluctuation besides was more often encountered in V4.

Phylogenetic tree of phyletic tree of env cistron

The phyletic trees of env cistron and gp120 were reconstructed by utilizing clustalW ( hypertext transfer protocol: // ) and phylodraw with Neighbor-Joining method.

Figure 7 Phylogenetic tree of env gene.F: UsersLeonDocumentsMy DropboxBIOL 550Dataenv gene.bmp

Figure 8 Phylogenetic tree of gp120.F: UsersLeonDocumentsMy DropboxBIOL 550Datagp120.bmp

Discussion and decision

The V3 cringle of the outer membrane gp120 of HIV-1 is the sphere with the highest fluctuation rate ; nevertheless, it is besides conservative comparatively. Furthermore, the V3 cringle is one of the HIV-1major antigenic antigenic determinants and is the chief neutralizing determiner ( PND ) . The fluctuation of the same virus strain in different persons is limited. To some extent, the fluctuation of V3 part could non menace the being of HIV, while fluctuation out of choice force per unit area makes virus hard to populate. Tetramer on the tip of V3 cringle is the functional and immunogenical sphere, any small alteration of which could decrease the antibody combination significantly.

Since CD4 receptor binding is the most obvious measure in HIV infection, gp120 was among the first marks of HIV vaccinum research. Attempts to develop HIV vaccinums aiming gp120, nevertheless, have been hampered by the chemical and structural belongingss of gp120, which make it hard for antibodies to adhere to it. gp120 can besides easy be shed from the surface of the virus and captured by T cells due to its loose binding with gp41. A conserved part in the gp120 glycoprotein that is involved in the metastable fond regard of gp120 to CD4 has now been identified and aiming of invariant part has been achieved with a loosely neutralising antibody, b12.

Research presented at the 17th International AIDS Conference in Mexico City provided the possibility of a new vaccinum based on antibodies that hydrolyze or cleave apart the gp120 protein, rendering it incapable of adhering to lymph cells. This binding is the first measure in the procedure of HIV infection. The antibody, IgA, is present in all human existences, but its possible for battling HIV was first recognized in patients with lupus, who exhibited both an unnatural opposition to HIV infection and an abnormally high concentration of IgA. Scientists confirmed that IgA purified from the blood plasma and spit of HIV-seronegative topics cleaved gp120 more efficaciously than the more of course abundant IgG did, which had small or no consequence. To battle HIV, IgA could be administered in big doses as a drug to people already infected. Research workers are yet to do a vaccinum which stimulates the organic structure to increase its ain production of IgA.

NIH research published in Science studies the find of antibodies that bind 91 % of HIV-1 strains at the CD4bs part of gp120 potentially offering a curative and vaccine scheme.

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