The structural biology of HIV-1: mechanistic and therapeutic insights

Abstract

Three-dimensional molecular structures can provide detailed information on biological mechanisms and, for cases in which the molecular function affects human health, can significantly aid in the development of therapeutic interventions. For almost 25 years, key components of the lentivirus HIV-1, including the envelope glycoproteins, the capsid and the replication enzymes reverse transcriptase, integrase and protease, have been scrutinized to near atomic-scale resolution. Moreover, structural analyses of the interactions between viral and host cell components have yielded key insights into the mechanisms of viral entry, chromosomal integration, transcription and egress from cells. Here, we review recent advances in HIV-1 structural biology, focusing on the molecular mechanisms of viral replication and on the development of new therapeutics.

Figure 1

Schematic overview of the HIV-1 replication cycle. The infection begins when envelope glycoprotein spikes engage the CD4 receptor and the membrane spanning co-receptor (step 1; cell proteins discussed in text are indicated in green type), which leads to viral–cell membrane fusion and entry of the virus particle into the cell (step 2). Partial core shell uncoating (step 3) facilitates reverse transcription (step 4), which in turn yields the preintegration complex (PIC). Following import into the cell nucleus (step 5), PIC-associated IN orchestrates formation of the integrated provirus (step 6). Proviral transcription (step 7) yields different sizes of viral mRNAs (not shown), the larger of which require energy-dependent export to leave the nucleus (step 8). Genome-length mRNAs serve as a template for protein production (step 9) or viral particle assembly with protein components (step 10). ESCRT-mediated viral particle budding (step 11) and release (step 12) from the cell is accompanied or followed shortly thereafter by PR-mediated maturation (step 13) to create an infectious viral particle. Each step in the HIV-1 lifecycle is a potential target for antiviral intervention ; the sites of action of clinical inhibitors (boxed) and cellular restriction factors are indicated with red and green block signs, respectively. CRI, CCR5 inhibitor; FI, fusion inhibitor; RTC, reverse transcription complex.

Figure 2

CD4 and CD4-mimicking antibody binding to the gp120 core. (a) Structure of HIV-1 gp120 (outer domain is shown in yellow and inner domain in gray) in complex with CD4 (green; pdb code 3JWD). Only immunoglobulin-like domain 1 (D1) of CD4 is shown; the Phe43 side-chain is depicted as sticks. (b) VRC01 antibody–gp120 co-crystal structure (pdb code 3NGB, heavy chain shown in green and light chain in cyan) oriented as in panel a. Only the variable domains of the heavy (VH) and light (VL) chains of the antibody are shown.

Figure 3

HIV-1 capsid structures. Crystal structures of the hexameric (a, pdb code 3H47) and pentameric (b, pdb code 3P05) full-length HIV-1 CA assemblies. Individual subunits are coloured by chain. (c) The model for the complete HIV-1 capsid, based on the crystal structures . NTDs of the hexameric and pentameric CA units are shown in blue and yellow, respectively; CTDs are green. (d) HIV-1 CA NTD in complex with PF-3450074 (PF, pdb code 2XDE). The orientation is related to that of the blue NTD in panel a by an ~100° rotation, as shown. Residues critical forPF -3450074 binding as revealed by resistance mutations are indicated.

Figure 4

Structural analyses of HIV-1 RT function and its inhibition by small molecules. (a) Overview of the HIV-1 RT-template-primer complex (pdb code 1RTD). The protein and DNA chains are shown as cartoons. The subdomains of the active RT subunit are indicated and colour-coded; the inactive (p51) subunit is shown in gray. The structure contains a bound molecule of dTTP in the active site (pink). Grey spheres are Mg atoms. (b) Close-up of the polymerase active site (pdb code 1RTD) and DNA polymerization. The 3′-hydroxyl, absent in the original structure , is added for illustration purposes. The direction of nucleophilic attack is indicated by a dashed arrow. The catalytic residues, Met184 and the leaving pyrophosphate group (P–P) are shown as sticks and indicated. RT chain colours are conserved from panel a. (c) Stereo view of ATP-binding pocket in AZT-resistant HIV-1 RT (pdb code 3KLE). The excision product (AZTpppp A′) is shown as sticks with carbon atoms in light blue. Protein chains are shown as cartoons with semitransparent surfaces (colouring as in panel a); residues implicated in AZT resistance are indicated. (d) TCM278 bound to HIV-1 RT (pdb code 2ZD1). RTresidues forming the NNRTI-binding pocket are indicated.

Figure 5

Retroviral intasome structures and mechanism of IN catalysis. (a) Overview of the PFV intasome structure (pdb code 3OY9). The active (inner) IN chains are shown as green and yellow cartoons; catalytically inactive (outer) chains are gray. The transferred and non-transferred viral DNA strands are shown in dark and light magenta, respectively. Active site carboxylates are shown as sticks and divalent metal ions as gray spheres. (b) The PFV intasome in complex with a host DNA mimic (light and dark blue; pdb code 3OS2). IN chains are shown in space-fill mode conserving colours from panel a. (c) DNA strand transfer. The model is based on structures of the Mn²⁺-bound intasome and target capture complex (see for details). IN is shown as cartoons with D, D-35-E active site residues as sticks. DNA is shown as sticks; the invariant viral dA and dC nucleotides are indicated. Colours are conserved from panel a. Residue numbering corresponds to the HIV-1 IN sequence. Direction of nucleophilic attack is indicated by a red dashed arrow.

Figure 6

Higher-order Tat and Rev structures. (a) Crystal structure of HIV-1 Tat in complex with ATP-bound P-TEFb (pdb code 3MIA). The protein chains are shown as cartoons (left) or in space-fill mode (right). The N-lobe of Cdk9 is shown in yellow, C-lobe in green, and the T-loop in orange; Cyclin T1 is in blue, and HIV-1 Tat is shown in magenta. ATP bound to the active site of Cdk9 is shown as sticks and indicated. Gray spheres are Zn atoms. (b) Left: dimeric assemblies of HIV-1 Rev core observed in crystals (pdb codes 2X7L and 3LPH). Rev monomers are shown as cartoons and colored by chain, expect for the ARM motifs, which are blue. The crystal structures elucidate two types of Rev-Rev hydrophobic interfaces, one involving Leu12 and Leu60 and the other Leu18 and Ile55. Right: model of the Rev hexamer based on the dimeric structures, shown in space-fill mode. The oligomer projects RNA-binding ARM domains (blue) on one side, with CRM1-binding nuclear export signals (not resolved in the current structures) emanating from the other side.

Figure 7

Virus-cell interactions and HIV-1 budding. The structure of the UEV domain of TSG101 bound to the PT(S)AP domain of HIV-1 p6 protein (pdb code 3OBU). TSG101 is shown as green ribbon (left) or space-fill (right) cartoons. P6 (residues 5–12; PEPTAPPEE) is shown as sticks; the carbon atoms of the core L domain PTAP and the flanking regions are orange and yellow, respectively. Some of the key TSG101 residues involved in the interaction are indicated on the right panel.