Conformational variability of HIV-1 Env trimer and viral vulnerability
- Department of Biological Sciences, Lehigh University, United States
Figures
Figure 1 with 2 supplements
Model structure of a fully glycosylated full-length HIV Env trimer embedded in a membrane.
(A) The model structure built by combining the cryo-electron microscopy (cryo-EM) structure of the ectodomain (yellow, Protein Data Bank [PDB] ID: 6B0N) with the nuclear magnetic resonance (NMR) structure of the membrane-proximal external region (MPER), transmembrane domain (TMD), and cytoplasmic tail (CT) (purple, PDB ID: 7LOI). The full-length model includes residues A31 to L856, while the CT-truncated (ΔCT) model includes residues A31 to S716. The missing loops in the PDB structures are highlighted in red, and the glycosylation sites are marked by cyan spheres. (B) Left: assignment of functional domains with boundary residue numbers, including signal peptide (SP), variable regions (V1-V5), fusion peptide (FP), heptad repeats (HR1 and HR2), MPER, TMD, and CT. Right: missing residues (red) and glycosylation sites (blue). The shaded region at the bottom marks CT residues excluded in the ΔCT model. (C) N-linked glycans shown as high-mannose (green) and complex (magenta) types. The full-length model is shown on the left and the ΔCT model on the right. (D) Env trimer embedded in a membrane. Lipid headgroups are highlighted by green spheres and glycans are omitted for visual clarity. The palmitoyl groups covalently attached to C764 and C837 are shown in cyan. Molecular illustrations were prepared using visual molecular dynamics (VMD) (Humphrey et al., 1996).
Figure 1—figure supplement 1
Steps in combining the structure of the ectodomain with the remaining domains.
(A) The original Protein Data Bank (PDB) structures (PDB IDs: 6B0N and 7LOI) with the common residues highlighted by orange spheres. The distance between the Cα of D664 is 39 Å in 6B0N and 16 Å in 7LOI. The broken ends of missing loops are shown in red, and the cleavage site in magenta. (B) Missing loops were grafted from a modeled structure generated by I-TASSER (red). The extra Gly and Ser residues from the 2xG4S linker introduced at the cleavage site in 6B0N were removed (magenta), and molecular dynamics (MD) simulations were performed to adjust distances between the common residues in two PDB structures. (C) The common residues were aligned, and two structures were merged.
Figure 1—figure supplement 2
Steps in building the uncleaved model.
(A) The cleaved model. (B) The cleavage site with the flanking loops in one protomer highlighted in dark magenta. If the flanking loops are connected along the blue dashed line, the protomer shown in yellow and cyan passes through the loop formed by the neighboring protomer in white, resulting in an entangled, knot-like topology. (C) The gap between the flanking loops is shorter in Protein Data Bank (PDB) structure 6B0N due to the presence of a 10-residue linker 508GGGGSGGGGS511, where the underlined residues are missing. (D) Molecular dynamics (MD) simulations were performed to adjust the length of the gap between the flanking loops to match that of the 508REKR511 cleavage site, and to reposition the flanking loops and the HR2 helix (red circle) to prevent the connected loop from forming a knot-like structure with the neighboring protomer. (E) 508REKR511 (blue) was modeled to connect the flanking loops.
Figure 2 with 13 supplements
Tilting motions of the ectodomain and transmembrane domain (TMD) are independent.
(A) Representative structures illustrating different ectodomain tilt angles and the schematic showing how tilt angles are calculated. (B) Probability densities of ectodomain and TMD tilt angles, calculated from cytoplasmic tail (CT)-truncated systems with various initial configurations.
Figure 2—figure supplement 1
Ectodomain tilt versus transmembrane domain (TMD) tilt, grouped by time intervals (cleaved cytoplasmic tail [CT]-truncated systems).
(A) Three trajectories starting from the ‘high’ TMD configuration. (B) Three trajectories starting from the ‘low’ TMD configuration. The 1 μs trajectory was divided into four intervals, with values from each interval shown in light gray, dark gray, black, and red, respectively.
Figure 2—figure supplement 2
Ectodomain tilt versus transmembrane domain (TMD) tilt, grouped by time intervals (uncleaved cytoplasmic tail [CT]-truncated systems).
Labeling and color coding are the same as in Figure 2—figure supplement 1.
Figure 2—figure supplement 3
Ectodomain tilt versus transmembrane domain (TMD) tilt, grouped by time intervals (cleaved full-length systems).
Labeling and color coding are the same as in Figure 2—figure supplement 1.
Figure 2—figure supplement 4
Ectodomain tilt versus transmembrane domain (TMD) tilt, grouped by time intervals (uncleaved full-length systems).
Labeling and color coding are the same as in Figure 2—figure supplement 1.
Figure 2—figure supplement 5
Temporal evolution of ectodomain and transmembrane domain (TMD) tilt angles (cleaved cytoplasmic tail [CT]-truncated systems).
Figure 2—figure supplement 6
Temporal evolution of ectodomain and transmembrane domain (TMD) tilt angles (uncleaved cytoplasmic tail [CT]-truncated systems).
Figure 2—figure supplement 7
Temporal evolution of ectodomain and transmembrane domain (TMD) tilt angles (cleaved full-length systems).
Figure 2—figure supplement 8
Temporal evolution of ectodomain and transmembrane domain (TMD) tilt angles (uncleaved full-length systems).
Figure 2—figure supplement 9
Probability densities of ectodomain and transmembrane domain (TMD) tilt angles (full-length systems).
Figure 2—figure supplement 10
Dynamic cross-correlation matrix of Cα atoms (cleaved cytoplasmic tail [CT]-truncated systems).
The x-axis (left to right) and the y-axis (top to bottom) correspond to residue indices ranging from 31 to 716 for each of the three protomers, where residues 31–664 compose the ectodomain. The transmembrane domain (TMD) (residues 684–705) is indicated by dashed boxes. Correlated and anti-correlated motions are color-coded from red to blue, respectively.
Figure 2—figure supplement 11
Dynamic cross-correlation matrix of Cα atoms (uncleaved cytoplasmic tail [CT]-truncated systems).
The x-axis (left to right) and the y-axis (top to bottom) correspond to residue indices ranging from 31 to 716 for each of the three protomers, where residues 31–664 compose the ectodomain. The transmembrane domain (TMD) (residues 684–705) is indicated by dashed boxes. Correlated and anti-correlated motions are color-coded from red to blue, respectively.
Figure 2—figure supplement 12
Dynamic cross-correlation matrix of Cα atoms (cleaved full-length systems).
The x-axis (left to right) and the y-axis (top to bottom) correspond to residue indices ranging from 31 to 716 for each of the three protomers. Residues 31–856 compose the ectodomain, and residues 706–856 compose the cytoplasmic tail (CT). The transmembrane domain (TMD) (residues 684–705) is indicated by dashed boxes. Correlated and anti-correlated motions are color-coded from red to blue, respectively.
Figure 2—figure supplement 13
Dynamic cross-correlation matrix of Cα atoms (uncleaved full-length systems).
The x-axis (left to right) and the y-axis (top to bottom) correspond to residue indices ranging from 31 to 716 for each of the three protomers. Residues 31–856 compose the ectodomain, and residues 706–856 compose the cytoplasmic tail (CT). The transmembrane domain (TMD) (residues 684–705) is indicated by dashed boxes. Correlated and anti-correlated motions are color-coded from red to blue, respectively.
Figure 3 with 1 supplement
Ectodomain is rigid, whereas the membrane-proximal external region (MPER) is highly flexible and adopts diverse conformations.
(A) Top and side views of the ectodomain and MPER in the cleaved system, with root-mean-square fluctuation (RMSF) indicated by color. (B) Schematic illustrating the calculation of interchain distances and their distributions at the Cα atoms of G644, E654, D664, and F673. For each residue, the distribution from cleaved systems is shown in dark color (left), and that from uncleaved systems is shown in light color (right), represented by solid and transparent colors, respectively. The initial values of interchain distances are marked by purple stars. (C–F) Local structures of the ectodomain C-terminus and MPER. The HR2 helix and MPER in one protomer are highlighted in dark yellow, with the Cα atoms of four selected residues marked by blue, orange, green, and red spheres. (C) The initial conformation and (D) representative snapshot from simulations of the cleaved system. (E) The initial conformation and (F) representative snapshot from simulations of the uncleaved system.
Figure 3—figure supplement 1
Root-mean-square fluctuation (RMSF) and root-mean-square deviation (RMSD) of the ectodomain.
(A) Top and side views of the ectodomain and membrane-proximal external region (MPER) in the uncleaved system, with RMSF indicated by color. (B) RMSD relative to the initial model as a function of time, calculated from the trajectories of cytoplasmic tail (CT)-truncated systems.
Figure 4 with 8 supplements
R696 interacts with lipid headgroups and disrupts membrane integrity.
(A–C) Membrane-proximal external region (MPER) and transmembrane domain (TMD) in the cytoplasmic tail (CT)-truncated system with the ‘high’ TMD configuration. MPER-N, MPER-C, and TMD are shown in magenta, cyan, and white, respectively. Lipid headgroups, R696, and the residues anchored in the lipid headgroups (R683, R707, and R709) are shown in green, blue, and purple, respectively. Lipid headgroups and ions interacting with R696 are highlighted in orange and red, respectively. (A) Initial conformation. (B, C) Representative snapshots from different trajectories. (D–F) MPER and TMD in the CT-truncated system with the ‘low’ TMD configuration. (G) Two side views of the same snapshot where R696 of one protomer interacts with lipid headgroups in the exoplasmic leaflet and R696 of two protomers interact with lipid headgroups in the cytoplasmic leaflet. Lipid headgroups and tails are shown in green and gray, and water molecules in magenta. TMD of three protomers (i.e. chains A, B, and C) are shown in light yellow, dark yellow, and orange, respectively. (H) Frequency of TMD residues interacting with lipid headgroups, lipid tails, and water. For each combination of a TMD residue and an interacting component, the frequency represents the fraction of snapshots in which the heavy atoms of the TMD residue and the corresponding component are within 5 Å. Bar shading reflects this fraction, with fully filled bars indicating 100% and empty bars indicating 0%.
Figure 4—figure supplement 1
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (CHΔCT systems).
Three protomers of the TMD are shown in light yellow, purple, and pink; three protomers of the ectodomain in dark yellow, gray, and white; MPER-N and MPER-C in magenta and cyan, respectively; and lipid headgroups in green. Lipid headgroups interacting with R696 are highlighted in orange, and the ions interacting with R696 in red. MPER, membrane-proximal external region.
Figure 4—figure supplement 2
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (CLΔCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 1.
Figure 4—figure supplement 3
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (UHΔCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 1.
Figure 4—figure supplement 4
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (ULΔCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 1.
Figure 4—figure supplement 5
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (CHCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 1, with the cytoplasmic tail (CT) additionally shown in red.
Figure 4—figure supplement 6
Local conformation of the transmembrane domain (TMD) and global conformation of protein and membrane (CLCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 5.
Figure 4—figure supplement 7
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (UHCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 5.
Figure 4—figure supplement 8
Local conformations of the transmembrane domain (TMD) and global conformations of protein and membrane (ULCT systems).
Labeling and color coding are the same as in Figure 4—figure supplement 5.
Figure 5 with 1 supplement
Membrane-proximal external region (MPER) exhibits diverse conformations, and its exposure depends on both MPER and transmembrane domain (TMD).
(A) The initial structure of the CHΔCT system, where dF673 of two protomers equals 8.5 Å and 9.2 Å. Lipid headgroups are shown in green and R696 in blue. dF673 is defined as the distance from the Cɑ of F673 (red) to the highest among the adjacent lipid headgroups (orange and purple). (B) Distribution of dF673 in the CLΔCT and CHΔCT systems. The cyan dashed line indicates the mean dF673 of three protomers in the initial structure, and the blue solid line indicates the mean across all data sampled from simulations. (C, D) Representative snapshots illustrating the buried (C) and exposed (D) MPER. (E, F) The entire trimer structures corresponding to (C) and (D), respectively.
Figure 5—figure supplement 1
Temporal evolution of the distance from the membrane-proximal external region (MPER) midpoint to the membrane surface.
The distance dF673, defined in Figure 5A, is shown as a function of simulation time for the CHΔCT and CLΔCT systems.
Figure 6 with 10 supplements
Antibody epitope accessibility.
(A) The frequency of accessibility. Each marker represents the epitope on one of the three protomers across all trajectories. For 35O22, red indicates the accessibility frequency without considering steric clashes with the membrane, while purple indicates the frequency accounting for clashes with the membrane. (B–D) Representative snapshots showing conformations with the epitope exposed (upper) and shielded (lower) for antibodies PGT128, 35O22, and 4E10, respectively. The antibody VH and VL domains are shown in surface representation, with lipid head groups in green spheres and glycans that may interfere with the antibody in distinct colors.
Figure 6—figure supplement 1
Shielding of antibody PGT128 epitope.
(Left) Variable domains of the heavy and light chains aligned onto our modeled structure. (Middle) Top view of the glycosylated trimeric protein, with the orange arrow indicating the epitope location. (Right) Part of the epitope in the antibody–epitope complex Protein Data Bank (PDB) structure was used for structural alignment and is highlighted in purple. Glycans capable of hindering antibody binding are shown in various colors.
Figure 6—figure supplement 2
Shielding of antibody PG9 epitope.
Labeling and color coding are the same as in Figure 6—figure supplement 1.
Figure 6—figure supplement 3
Shielding of antibody VRC01 epitope.
Labeling and color coding are the same as in Figure 6—figure supplement 1. (Middle) The glycosylated trimeric protein is shown in a side view instead of the top view.
Figure 6—figure supplement 4
Shielding of antibody 35O22 epitope.
Labeling and color coding are the same as in Figure 6—figure supplement 3. (Left) The dashed greens indicate the approximate location of the lipid headgroups.
Figure 6—figure supplement 5
Shielding of antibody 4E10 epitope.
Labeling and color coding are the same as in Figure 6—figure supplement 4.
Figure 6—figure supplement 6
Shielding of antibody 10E8 epitope.
Labeling and color coding are the same as in Figure 6—figure supplement 4.
Figure 6—figure supplement 7
Snapshots showing the membrane-proximal external region (MPER) of one protomer accessible to either 4E10 or 10E8.
(A) Snapshot in which the MPER of the white protomer is accessible to 4E10 (cyan transparent surface) but not to 10E8. (B) Snapshot in which the MPER of the white protomer is accessible to 10E8 (green transparent surface) but not to 4E10.
Figure 6—figure supplement 8
Snapshots showing the membrane-proximal external region (MPER) of two protomers are accessible to 4E10.
The MPER is accessible to 4E10, (A) exclusively in the yellow protomer, and (B) exclusively in the gray protomer.
Figure 6—figure supplement 9
Snapshots showing the membrane-proximal external region (MPER) of two protomers are accessible to 10E8.
The MPER is accessible to 4E10, (A) exclusively in the yellow protomer, and (B) exclusively in the white protomer.
Figure 6—figure supplement 10
Snapshots showing the membrane-proximal external region (MPER) of three protomers are accessible to 10E8.
The MPER is accessible to 4E10, (A) exclusively in the yellow protomer, (B) exclusively in the gray protomer, and (C) exclusively in the white protomer.
Additional files
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Supplementary file 1
Supplementary tables.
- https://cdn.elifesciences.org/articles/110107/elife-110107-supp1-v1.docx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/110107/elife-110107-mdarchecklist1-v1.docx
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Conformational variability of HIV-1 Env trimer and viral vulnerability
eLife 15:RP110107.
https://doi.org/10.7554/eLife.110107.4
