Abstract
HIV-1 has been the target of intensive research at the molecular and biochemical levels for >25 years. Collectively, this work has led to a detailed understanding of viral replication and the development of 24 approved drugs that have five different targets on various viral proteins and one cellular target (CCR5). Although most drugs target viral enzymatic activities, our detailed knowledge of so much of the viral life cycle is leading us into other types of inhibitors that can block or disrupt protein-protein interactions. Viruses have compact genomes and employ a strategy of using a small number of proteins that can form repeating structures to enclose space (i.e. condensing the viral genome inside of a protein shell), thus minimizing the need for a large protein coding capacity. This creates a relatively small number of critical protein-protein interactions that are essential for viral replication. For HIV-1, the Gag protein has the role of a polyprotein precursor that contains all of the structural proteins of the virion: matrix, capsid, spacer peptide 1, nucleocapsid, spacer peptide 2, and p6 (which contains protein-binding domains that interact with host proteins during budding). Similarly, the Gag-Pro-Pol precursor encodes most of the Gag protein but now includes the viral enzymes: protease, reverse transcriptase (with its associated RNase H activity), and integrase. Gag and Gag-Pro-Pol are the substrates of the viral protease, which is responsible for cleaving these precursors into their mature and fully active forms (see Fig. 1A).
Highlights
The Gag and Gag-Pro-Pol precursors assemble at the plasma membrane of the cell, with the membrane being pinched off from the cell surface to create a membrane-bound virion with a diameter of ϳ120 nm, representing a volume of ϳ0.9 attoliters (Fig. 1)
We examine outstanding issues surrounding the HIV-1 PR, the role of protein processing and rearrangement in the assembly pathway, the impact of PR inhibitor resistance on viral fitness and assembly, and the fact that all of this biochemistry takes place within the confines of a particle that is only 120 nm wide
The number of active enzyme molecules in a virus particle can be manipulated by titrating in an inhibitor, titrating in an inactive subunit through phenotypic mixing, or reducing enzymatic activity with mutations that confer a fitness loss
Summary
It has been difficult to observe processing events in released virions, and early activation of PR activity by creating a tethered dimer within a single Gag-Pro-Pol molecule or delay of particle formation relative to processing negatively impacts particle formation [40, 41]; these observations suggest that activation of the PR is delayed until later in the assembly process but that processing must be completed either during budding or relatively quickly after budding. Mutations in the active site can change the interaction with the inhibitor either by reducing a contact or creating a steric hindrance (Fig. 2A) (50 –55) Such changes are more tolerated if a side chain of the drug extends outside of the substrate envelope. Such fitness cost and pleiotropic effects of a virus with reduced PR activity may be the reason that patients with virus carrying PI resistance mutations (that lower fitness overall) can have slowed disease progression in the setting of drug failure [72]
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