Hiv-1 gag: Difference between revisions
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<StructureSection load='2H3I_mono1.pdb' size='450' side='right' scene='' caption=''> | <StructureSection load='2H3I_mono1.pdb' size='450' side='right' scene='' caption='HIV-1 gag protein complex with myristic acid (PDB code [[2h3i]])'> | ||
==HIV-1 Gag== | ==HIV-1 Gag== | ||
The HIV-1 Gag protein is the major structural protein required for virus assembly. It is synthesized as a polyprotein in the cytosol of an infected cell, and contains four functional segments; MA, CA (NTD and CTD), NC, and p6. The NC region is flanked by two "spacer" segments, denoted SP1 and SP2. The polyprotein is all alpha helical, except the NC region, which is composed of two RNA interacting zinc knuckle domains. Gag is often referred to as an "assembly machine" because expression of Gag alone is sufficient to produce budding virus-like particles (VLP's), due to multimerization of roughly 2000 Gag molecules per virion. Here, we will take a closer look at the MA, CA, and NC domains, and how the structural components of these domains aid in the assembly of virus particles. Viral particles can be classified as immature (pre-budding and non-infectious), and mature (post-budding and infectious), and this exchange is mediated by the HIV-1 protease. Upon viral budding, Gag is cleaved by the HIV-1 protease at multiple sites, thus possibly changing many of the structural interactions that make up the "immature" particle. For simplicity, we will only be discussing the immature formation of Gag on the plasma membrane of infected cells, as it coordinates organized viral budding. Also, it is thought that Gag forms a hexamer structure (deduced from electron microscopy studies) upon virus assembly, but because of the difficulties encountered by attempting to crystallize a multimeric structure, the exact formation of the hexamer is still up for debate. Current models predict that the MA and CA domains interact to form trimers, and these trimers conglomerate and display hexagonal symmetry. | The '''HIV-1 Gag''' protein is the major structural protein required for virus assembly. It is synthesized as a polyprotein in the cytosol of an infected cell, and contains four functional segments; MA, CA (NTD and CTD), NC, and p6. The NC region is flanked by two "spacer" segments, denoted SP1 and SP2. The polyprotein is all alpha helical, except the NC region, which is composed of two RNA interacting zinc knuckle domains. Gag is often referred to as an "assembly machine" because expression of Gag alone is sufficient to produce budding virus-like particles (VLP's), due to multimerization of roughly 2000 Gag molecules per virion. Here, we will take a closer look at the MA, CA, and NC domains, and how the structural components of these domains aid in the assembly of virus particles. Viral particles can be classified as immature (pre-budding and non-infectious), and mature (post-budding and infectious), and this exchange is mediated by the HIV-1 protease. Upon viral budding, Gag is cleaved by the HIV-1 protease at multiple sites, thus possibly changing many of the structural interactions that make up the "immature" particle. For simplicity, we will only be discussing the immature formation of Gag on the plasma membrane of infected cells, as it coordinates organized viral budding. Also, it is thought that Gag forms a hexamer structure (deduced from electron microscopy studies) upon virus assembly, but because of the difficulties encountered by attempting to crystallize a multimeric structure, the exact formation of the hexamer is still up for debate. Current models predict that the MA and CA domains interact to form trimers, and these trimers conglomerate and display hexagonal symmetry. | ||
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==Nucleocapsid (NC)== | ==Nucleocapsid (NC)== | ||
As we have seen, Gag is responsible for correct targeting of viral assembly to discreet sites on the plasma membrane, and viral capsid structure assembly into organized virus particles. However, Gag is also responsible for packaging of the viral RNA into budding virions, and this function is executed by the NC domain. The 5' LTR of HIV-1 genomic RNA contains a recognition element called the psi element. All retroviruses contain some type of psi element in order to get specific packaging of viral genomic RNA within the budding particles, and in the case of HIV-1, the psi element is 120 bases, and contains 4 stem-loop structures. Although the psi element can be quite variable, the SL3 loop is highly conserved within HIV-1 strains. <scene name='Hiv-1_gag/Cv/ | As we have seen, Gag is responsible for correct targeting of viral assembly to discreet sites on the plasma membrane, and viral capsid structure assembly into organized virus particles. However, Gag is also responsible for packaging of the viral RNA into budding virions, and this function is executed by the NC domain. The 5' LTR of HIV-1 genomic RNA contains a recognition element called the psi element. All retroviruses contain some type of psi element in order to get specific packaging of viral genomic RNA within the budding particles, and in the case of HIV-1, the psi element is 120 bases, and contains 4 stem-loop structures. Although the psi element can be quite variable, the SL3 loop is highly conserved within HIV-1 strains. <scene name='Hiv-1_gag/Cv/4'>The NC domain of HIV-1 NL4-3 in complex with the SL3 loop of the viral psi element is shown </scene>. | ||
There are two zinc knuckle domains, with the zinc ion held by three Cys residues and a His (<scene name='User:Nathan_Roy/Zinc_knuckle/1'>Knuckle</scene>). Notice that guanine210 and guanine212 of the RNA interact with the F2 and F1 CCHC zinc knuckles respectively. In the F1 knuckle, G9 fits into a hydrophobic cleft formed by Val13, Phe16, Ile24, and Ala 25. G9 satisfies Watson-Crick hydrogen bonding by interacting with the NH groups from Phe16 and Ala25 (<scene name='User:Nathan_Roy/F1_interaction/1'>Show residues</scene>), and also the CO group of Lys14 (<scene name='User:Nathan_Roy/F1_interaction/2'>Show</scene>). G7 interacts much the same with the F2 knuckle by hydrogen bonding with the NH groups of Trp37 and Met46, while also hydrogen bonding with the CO group of Gly35. The adenine211 nucleotide forms a hydrogen bond with a highly conserved Arg32 residue (<scene name='User:Nathan_Roy/F1_interaction/3'>Show</scene>). Also, residues 3 thru 10 form a 3.10 helix, which nestles into the RNA major groove (<scene name='User:Nathan_Roy/3-10_helix/1'>Show helix</scene>). These interactions allow viral RNA to be specifically packaged into virions. Also of note, it has been shown that NC binding of viral RNA increases the ability of Gag to multimerize, thus providing another mechanism to couple functional virion assembly to Gag multimerization and viral budding. | There are two zinc knuckle domains, with the zinc ion held by three Cys residues and a His (<scene name='User:Nathan_Roy/Zinc_knuckle/1'>Knuckle</scene>). Notice that guanine210 and guanine212 of the RNA interact with the F2 and F1 CCHC zinc knuckles respectively. In the F1 knuckle, G9 fits into a hydrophobic cleft formed by Val13, Phe16, Ile24, and Ala 25. G9 satisfies Watson-Crick hydrogen bonding by interacting with the NH groups from Phe16 and Ala25 (<scene name='User:Nathan_Roy/F1_interaction/1'>Show residues</scene>), and also the CO group of Lys14 (<scene name='User:Nathan_Roy/F1_interaction/2'>Show</scene>). G7 interacts much the same with the F2 knuckle by hydrogen bonding with the NH groups of Trp37 and Met46, while also hydrogen bonding with the CO group of Gly35. The adenine211 nucleotide forms a hydrogen bond with a highly conserved Arg32 residue (<scene name='User:Nathan_Roy/F1_interaction/3'>Show</scene>). Also, residues 3 thru 10 form a 3.10 helix, which nestles into the RNA major groove (<scene name='User:Nathan_Roy/3-10_helix/1'>Show helix</scene>). These interactions allow viral RNA to be specifically packaged into virions. Also of note, it has been shown that NC binding of viral RNA increases the ability of Gag to multimerize, thus providing another mechanism to couple functional virion assembly to Gag multimerization and viral budding. | ||