User:Nathan Roy: Difference between revisions

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'''(LINK)'''. 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.   

Once Gag is localized to discreet sites on the plasma membrane, multimerization of Gag takes place quite quickly , driven by the CA domain, and more specifically our focus here, the C-terminal domain of CA (CTD). There are four helices that contribute to the interaction of CA CTD with it's partner. A side-by-side interaction has been proposed (Figure 3), but many believe the forces involved in the side-by-side model are not great enough to account for the organization and structural stability of assembled Gag. Also, helix 1 of the CA CTD contains a very conserved region of residues within many retroviruses called the MHR (major homology region)<scene name='User:Nathan_Roy/Mhr_side-by-side/1'>MHR region</scene>. In the side-by-side model, the MHR is not responsible for the dimer organization, yet mutations in the MHR region have a greater impact on ''in vivo''  Gag assembly than mutations in the residues responsible for structural stablility of the side-by-side model. This led researchers to seek a domain swapped structure of the CA CTD.  By making a single deletion of the Ala 177 residue (which lies in the loop between helix 1 and helix 2), the CA CTD domain adopts a domain-swapped conformation,<applet load='2ont_dimer.pdb' size='300' frame='true' align='right' caption='FIGURE 4. Domain swapped CA CTD' /> in which the MHR of helix 1 is extended to contact helices 2,3, and 4 of the adjacent CA CTD domain (Figure 4)(<scene name='User:Nathan_Roy/Mhr_domain_swapped/1'>MHR region</scene>). Keep in mind these are only models of Gag dimerization and subsequent multimerization, and that precise interactions that take place during Gag assembly are yet to be agreed upon.