The morphology of the immature HIV-1 virion

The evolution of catalytic function in the HIV-1 protease

The evolution of species is a complex phenomenon based on the optimization of a multidimensional function referred to as fitness. At the level of biomolecular evolution, the fitness function can be reduced to include physiochemical properties relevant to the biological function of a particular molecule. In this work, questions involving the physical-chemical mechanisms underlying the evolution of HIV-1 protease are addressed through molecular simulation and subsequent analysis of thermodynamic properties related to the activity of the enzyme. Specifically, the impact of 40 single amino acid mutations on the binding affinity toward the matrix/capsid (MA/CA) substrate and corresponding transition state intermediate has been characterized using a molecular mechanics Poisson-Boltzmann surface area approach. We demonstrate that this approach is capable of extracting statistically significant information relevant to experimentally determined catalytic activity. Further, no correlation was observed between the effect of mutations on substrate and transition state binding, suggesting independent evolutionary pathways toward optimizing substrate specificity and catalytic activity. In addition, a detailed analysis of calculated binding affinity data suggests that ground-state destabilization (reduced binding affinity for the substrate) could be a contributing factor in the evolutionary optimization of HIV-1 protease. A numerical model is developed to demonstrate that ground-state destabilization is a valid mechanism for activity optimization given the high concentrations of substrate experienced by the functional enzyme in vivo.

Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells

The major structural elements of retroviruses are contained in a single polyprotein, Gag, which in human immunodeficiency virus type 1 (HIV-1) comprises the MA, CA, spacer peptide 1 (SP1), NC, SP2, and p6 polypeptides. In the immature HIV-1 virion, the domains of Gag are arranged radially with the N-terminal MA domain at the membrane and C-terminal NC-SP2-p6 region nearest to the center. Here, we report the three-dimensional structures of individual immature HIV-1 virions, as obtained by electron cryotomography. The concentric shells of the Gag polyprotein are clearly visible, and radial projections of the different Gag layers reveal patches of hexagonal order within the CA and SP1 shells. Averaging well-ordered unit cells leads to a model in which each CA hexamer is stabilized by a bundle of six SP1 helices. This model suggests why the SP1 spacer is essential for assembly of the Gag lattice and how cleavage between SP1 and CA acts as a structural switch controlling maturation.

Effects of Gag mutation and processing on retroviral dimeric RNA maturation

After their release from host cells, most retroviral particles undergo a maturation process, which includes viral protein cleavage, core condensation, and increased stability of the viral RNA dimer. Inactivating the viral protease prevents protein cleavage; the resulting virions lack condensed cores and contain fragile RNA dimers. Therefore, protein cleavage is linked to virion morphological change and increased stability of the RNA dimer. However, it is unclear whether protein cleavage is sufficient for mediating virus RNA maturation. We have observed a novel phenotype in a murine leukemia virus capsid mutant, which has normal virion production, viral protein cleavage, and RNA packaging. However, this mutant also has immature virion morphology and contains a fragile RNA dimer, which is reminiscent of protease-deficient mutants. To our knowledge, this mutant provides the first evidence that Gag cleavage alone is not sufficient to promote RNA dimer maturation. To extend our study further, we examined a well-defined human immunodeficiency virus type 1 (HIV-1) Gag mutant that lacks a functional PTAP motif and produces immature virions without major defects in viral protein cleavage. We found that the viral RNA dimer in the PTAP mutant is more fragile and unstable compared with those from wild-type HIV-1. Based on the results of experiments using two different Gag mutants from two distinct retroviruses, we conclude that Gag cleavage is not sufficient for promoting RNA dimer maturation, and we propose that there is a link between the maturation of virion morphology and the viral RNA dimer.

The molecular basis of HIV capsid assembly--five years of progress

The assembly of HIV is relatively poorly investigated when compared with the process of virus entry. Yet a detailed understanding of the mechanism of assembly is fundamental to our knowledge of the complete life cycle of this virus and also has the potential to inform the development of new antiviral strategies. The repeated multiple interaction of the basic structural unit, Gag, might first appear to be little more than concentration dependent self-assembly but the precise mechanisms emerging for HIV are far from simple. Gag interacts not only with itself but also with host cell lipids and proteins in an ordered and stepwise manner. It binds both the genomic RNA and the virus envelope protein and must do this at an appropriate time and place within the infected cell. The assembled virus particle must successfully release from the cell surface and, whilst being robust enough for transmission between hosts, must nonetheless be primed for rapid disassembly when infection occurs. Our current understanding of these processes and the domains of Gag involved at each stage is the subject of this review.

Differential dependence of the infectivity of HIV-1 group O isolates on the cellular protein cyclophilin A

The cellular protein Cyclophilin A (Cyp A) is packaged into human immunodeficiency virus type 1 (HIV-1) particles through a specific interaction with the capsid domain of the Gag polyprotein. Inhibition of Cyp A incorporation by mutagenesis or cyclosporin treatment severely affects infectivity of all HIV-1 M subtypes tested. In contrast, the closely related lentiviruses HIV-2 and simian immunodeficiency virus (SIV) do not package Cyp A and are not inhibited by cyclosporin. For the HIV-1 group O isolate MVP5180, it was found that Cyp A incorporation and Cyp A dependence of infectivity did not correlate. This virus incorporates Cyp A but is not sensitive to treatment with cyclosporin A. For a more detailed study concerning the relationship between Cyp A incorporation and Cyp A dependence, we have analyzed five group O isolates for their ability to incorporate Cyp A and their sensitivity to cyclosporin treatment. All group O viruses incorporated Cyp A in comparable amounts as the M-group HIV-1 strain NL4-3. Furthermore, Cyp A incorporation was inhibited by cyclosporin in all cases. However, while isolate MVP 5180 was confirmed to replicate independent of Cyp A, three of the other four isolates were sensitive to cyclosporin treatment. Sequence analysis of the Cyp A binding regions revealed that the proline-rich motif, which is responsible for Cyp A incorporation, was conserved in all four isolates, while some sequence variations were detected in other positions close to this region. These results suggest that Cyp A dependence of replication is influenced by regions outside the Cyp-binding loop and may aid in determination of Cyp A function in HIV-1 replication.

Fusion of uninfected T-cells occurs with immature HIV-1 protease-mutant, but not morphologically similar protease inhibitor derived particles

Protease inhibitors are widely used in the treatment of human immunodeficiency virus type 1 (HIV-1)-infected individuals and show a drastic effect on the reduction of virus load. We previously reported that doughnut-shaped, protease-defective gp120-containing HIV-1 particles from an L-2 cell clone, carrying a provirus with mutations at the pol (protease), env (gp41) and nef genes, rapidly and more effectively induces virus particle-mediated syncytia formation of uninfected T-cells, than a parental wild-type laboratory strain of HIV-1 (LAI). In this study, we examined the possibility of whether enhanced syncytia formation is mediated by morphologically similar doughnut-shaped particles obtained after treatment of LAI-infected cells with the protease inhibitors L-689, 502, DMP-323, RO-31-8959, and KNI-272. Utilizing such protease inhibitor-induced particles and a clone of MOLT-4 cells, we could not detect any enhancement of syncytia formation, over that seen with wild-type LAI particles. This result should alleviate concerns of patients on highly active antiretroviral therapy (HAART), that protease inhibitors might accelerate progression of the disease through enhanced production of defective, 'immature'-appearing particles.

Cyclophilin A incorporation is not required for human immunodeficiency virus type 1 particle maturation and does not destabilize the mature capsid

The cellular protein cyclophilin A (CypA) is packaged into human immunodeficiency virus type 1 (HIV-1) virions through a specific interaction with the capsid (CA) domain of the Gag polyprotein. CypA is important for infectivity, but its role in viral replication is currently unknown. Previous reports suggested that CypA promotes uncoating or enhances maturation. We analyzed the morphology and capsid stability of HIV-1 variants defective in CypA binding and of virus grown in the presence of cyclosporin. Both cyclosporin treatment and alteration of Gly89 or Pro90 in the CypA-binding site of CA caused a 5- to 20-fold decrease in CypA incorporation. Virus produced from cyclosporin-treated cells and variants G89V and G89A were 10- to 100-fold less infectious but exhibited normal virion morphologies with regular cone-shaped capsids. Irregular capsid morphologies and lower infectivities were observed for some other variants in the CypA-binding region. Decreased CypA incorporation did not reduce the kinetics of intracellular polyprotein processing or of virus release. No increase in immature particles was observed. These results suggest that CypA does not promote virion maturation. Furthermore, detergent stripping of virus particles with various CypA contents revealed no difference in capsid stability. Based on these results and those reported in the accompanying paper, it appears likely that CypA also is not an uncoating factor. Alternative models for CypA function are discussed.

Quantitative intracellular kinetics of HIV type 1

Although our knowledge of HIV-1 growth, from a molecular mechanistic perspective, has rapidly increased, we do not yet know how the overall growth rate of HIV-1 depends on its constituent biochemical reactions. Such an understanding would be of fundamental importance and potentially useful for designing and evaluating anti-HIV strategies. As a first step toward addressing this need we formulate and implement here a global computer simulation for the intracellular growth of HIV-1 on a CD4+ T lymphocyte. Our simulation accounts for the kinetics of reverse transcription, integration of proviral DNA into the host genome, transcription, mRNA splicing and transport from the nucleus, translation, feedback of regulatory proteins to the nucleus, transport of viral proteins to the cell membrane, particle assembly, budding, and maturation. The simulation quantitatively captures the experimentally observed intracellular dynamics of viral DNA, mRNA, and proteins while employing no "fudge factors." Moreover, it provides an estimate of the intracellular growth rate of HIV-1 and enables evaluation of mono- and combined anti-HIV strategies.

Gag protein from human immunodeficiency virus type 1 assembles in the absence of cyclophilin A

Human immunodeficiency virus type 1 (HIV-1) replication requires coordinated activities of host and viral factors. We reported previously that interactions of the host factor cyclophilin A with HIV-1 Gag polyproteins affected Gag processing and maturation of virus particles (Streblow et al., 1998. Virology 245, 197-202). We now use in vitro translation and physical analysis of Gag structures to refine our understanding of how cyclophilin A affects HIV-1 replication. Gag assembled into oligomeric structures in vitro in the presence or absence of cyclophilin A, and proteins synthesized under the two conditions were equally susceptible to cleavage by exogenous HIV-1 protease. These and previous data show that Cyclophilin A is required at a step between Gag assembly and Gag processing/virion morphogenesis. Cyclophilin A may be required for Gag conformational changes subsequent to assembly, that are required for efficient dimerization and activation of the viral protease.

Fusion between uninfected cells in retrovirus-induced fusion-from-within

We previously examined Moloney murine leukemia virus-induced fusion-from-within (FFWI) and fusion-from-without (FFWO) of SC-1 mouse cells. FFWI and FFWO can be distinguished by their stimulation by ionophores and polycations, respectively. FFWI is caused by infected cells. Normally, fusion between an infected cell and uninfected cells (heterofusions) is described, but we have surprisingly found that the infected cells also caused homofusion between uninfected cells in their vicinity (named neighbor homofusions). It was shown that neighbor homofusions were not induced by free virus particles (by FFWO). Transfectants expressing envelope proteins only induced heterofusions, indicating that virus production is necessary for the formation of neighbor homofusions. Both plasma membrane fragments and easily removable material from the surface of infected cells were able to induce fusion with the same stimulation pattern as FFWI and neighbor homofusion. These materials, especially the latter, have properties in common with virions, and it is discussed whether immature virions are involved in the formation of the neighbor homofusions.

The life-cycle of human immunodeficiency virus type 1

The life-cycle of human immunodeficiency virus type 1 (HIV-1) has been studied using several techniques including immunoelectron microscopy and cryomicroscopy. The HIV-1 particle consists of an envelope, a core and the region between the core and the envelope (matrix). Virus particles in the extracellular space are observed as having various profiles: a central or an eccentric round electron-dense core, a bar-shaped electron-dense core, and immature doughnut-shaped particle. HIV-1 particles in the hydrated state were observed by high-resolution electron cryomicroscopy to be spherical and the lipid membrane was clearly resolved as a bilayer. Projections around the circumference were seen to be knob-like. The shapes and sizes of the projections, especially the head parts, were found to vary with each projection. HIV-1 cores were isolated with a mixture of Nonidet P40 and glutaraldehyde, and were confirmed to consist of HIV-1 Gag p24 protein by immunogold labelling. On infection, the HIV-1 virus was found to enter the cell in two ways: membrane fusion and endocytosis. After viral entry, no structures resembling virus particles could be seen in the cytoplasm. In the infected cells, positive reactions by immunolabelling suggest that HIV-1 Gag is produced in membrane-bound structures and transported to the cell surface by the cytoskeletons. A crescent electron-dense layer is then formed underneath the cell membrane. Finally, the virus particle is released from the cell surface and found extracellularly to be a complete virus particle with an electron-dense core. However, several cell clones producing defective mature, doughnut-shaped (immature) or teardrop-shaped particles were found to be produced in the extracellular space. In the doughnut-shaped particles, Gag p17 and p24 proteins exist facing each other against an inner electron-dense ring, suggesting that the inner ring consists of a precursor Gag protein showing a defect at the viral proteinase.

Sequential steps in human immunodeficiency virus particle maturation revealed by alterations of individual Gag polyprotein cleavage sites

Retroviruses are produced as immature particles containing structural polyproteins, which are subsequently cleaved by the viral proteinase (PR). Extracellular maturation leads to condensation of the spherical core to a capsid shell formed by the capsid (CA) protein, which encases the genomic RNA complexed with nucleocapsid (NC) proteins. CA and NC are separated by a short spacer peptide (spacer peptide 1 [SP1]) on the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein and released by sequential PR-mediated cleavages. To assess the role of individual cleavages in maturation, we constructed point mutations abolishing cleavage at these sites, either alone or in combination. When all three sites between CA and NC were mutated, immature particles containing stable CA-NC were observed, with no apparent effect on other cleavages. Delayed maturation with irregular morphology of the ribonucleoprotein core was observed when cleavage of SP1 from NC was prevented. Blocking the release of SP1 from CA, on the other hand, yielded normal condensation of the ribonucleoprotein core but prevented capsid condensation. A thin, electron-dense layer near the viral membrane was observed in this case, and mutant capsids were significantly less stable against detergent treatment than wild-type HIV-1. We suggest that HIV maturation is a sequential process controlled by the rate of cleavage at individual sites. Initial rapid cleavage at the C terminus of SP1 releases the RNA-binding NC protein and leads to condensation of the ribonucleoprotein core. Subsequently, CA is separated from the membrane by cleavage between the matrix protein and CA, and late release of SP1 from CA is required for capsid condensation.