Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies

Abstract

The fusion peptide (FP) of HIV-1 envelope glycoprotein (Env) is essential for mediating viral entry. Detection of broadly neutralizing antibodies (bnAbs) that interact with the FP has revealed it as a site of vulnerability. We delineate X-ray and cryo-electron microscopy (cryo-EM) structures of bnAb ACS202, from an HIV-infected elite neutralizer, with an FP and with a soluble Env trimer (AMC011 SOSIP.v4.2) derived from the same patient. We show that ACS202 CDRH3 forms a "β strand" interaction with the exposed hydrophobic FP and recognizes a continuous region of gp120, including a conserved N-linked glycan at N88. A cryo-EM structure of another previously identified bnAb VRC34.01 with AMC011 SOSIP.v4.2 shows that it also penetrates through glycans to target the FP. We further demonstrate that the FP can twist and present different conformations for recognition by bnAbs, which enables approach to Env from diverse angles. The variable recognition of FP by bnAbs thus provides insights for vaccine design.

Keywords: ACS202; AMC011; HIV envelope glycoprotein; VRC34.01; X-ray crystallography; broadly neutralizing antibody; cryoelectron microscopy; fusion peptide.

Graphical abstract

Figure 1

Crystal Structure of ACS202 Fab in Complex with the HIV-1 Env Fusion Peptide (A) Expanded view of the variable domains of ACS202 Fab. CDR loops are highlighted (L1/H1 in green, L2/H2 in blue, L3 in yellow, and H3 in pink). The bound FP is not shown. (B) Surface representation of the variable domains of ACS202 Fab with the FP represented by a green tube. The light- and heavy-chain variable domains are colored light and dark gray, respectively. CDR loops that are involved in FP binding are highlighted (H2 in blue, L3 in yellow, and H3 in pink). No major conformational changes were observed in the Fab on FP binding. (C) Backbone interactions between the HIV-1 FP (green) and ACS202. Hydrogen bonds between the FP and CDRL3 (yellow), H2 (blue), and H3 (pink) are shown as black dashed lines. The FP forms an antiparallel β sheet with CDRH3 of ACS202. (D) Hydrophobic interactions between FP (green) and ACS202 (CDRL3 in yellow and CDRH3 in pink). Backbones are shown as tubes, and the side chains are highlighted as sticks. (E) The ACS202 antibody intimately interacts with the N-terminal A512 of the HIV-1 FP (green). The side chain of A512 is buried in a hydrophobic pocket formed by CDRL3-Y91, L94, F96, and CDRH3-Y100^K. Hydrogen bonds are shown as black dashed lines. (F) Stabilization of G516-A517 of the FP by ACS202. Hydrogen bonds are shown as black dashed lines. (G) Surface area of the FP. The pie chart shows that more than half of the surface area of the FP is buried by ACS202 Fab, with CDRH3 contributing to most of that interaction. Colors for each CDR loop correspond to the panels above. ASA, accessible surface area. Buried and accessible areas were calculated with PISA (Proteins, Interfaces, Structures, and Assemblies) (Krissinel and Henrick, 2007). (H) Surface area of each residue of the FP is shown in the bar chart, with buried surface area in gray and accessible area in white. Residues that form hydrogen-bond interactions with ACS202 are highlighted with “H” on top of each bar. Buried and accessible surface areas are calculated with PISA (Krissinel and Henrick, 2007). See also Figures S1 and S2 and Table S1.

Figure 2

Cryo-EM Reconstruction of Env Trimer AMC011 SOSIP.v4.2 in Complex with bnAb ACS202 (A) Reconstruction of Env trimer AMC011 SOSIP.v4.2 in complex with ACS202 Fab at ∼5.2 Å resolution, segmented to highlight densities corresponding to gp120 (yellow), gp41 (white), and ACS202 Fab (blue). (B) Model of Env trimer AMC011 SOSIP.v4.2 in complex with ACS202 Fab. Glycans are shown as green spheres. The FP is shown in yellow. Variable domains of ACS202 are shown in dark (heavy chain) and light (light chain) blue. (C) Crystal structure illustrating the interaction between ACS202 (blue) and synthetic FP fragment (green). (D) Cryo-EM structure shows that the interaction between ACS202 and the FP region (yellow) of Env trimer AMC011 SOSIP.v4.2 is similar to that with the synthetic FP, as shown in (C). The root-mean-square deviation (RMSD) (Cα) between the FPs is 1.7 Å. (E) Detailed interactions of Fab ACS202 recognition of AMC011 SOSIP.v4.2 Env trimer. Glycans are shown as green spheres. Side chains of the FP (yellow) are shown in sticks. Interactions between CDRH2 of ACS202 and the Env trimer are highlighted in the top right corner. See also Figure S4 and Table S3.

Figure 3

Cryo-EM Reconstruction of Env Trimer AMC011 SOSIP.v4.2 in Complex with bnAb VRC34.01 (A) Cryo-EM reconstruction of Env trimer AMC011 SOSIP.v4.2 in complex with VRC34.01 Fab at ∼4.5 Å resolution, segmented to highlight densities corresponding to gp120 (yellow), gp41 (white), and VRC34.01 Fab (pink). (B) Cryo-EM structure of the Env trimer AMC011 SOSIP.v4.2 in complex with VRC34.01 Fab. Glycan components of the epitope are shown as green spheres. The FP part of the epitope is shown in yellow. Variable domains of VRC34.01 are shown in dark (heavy chain) and light (light chain) purple. (C) Detailed interactions of VRC34.01 recognition of the FP and glycans N88 and N241. Glycans are shown as green spheres. Side chains of the FP (yellow) are shown in sticks. CDRH1 of VRC34.01 that interacts with the glycans at N241 is highlighted in blue. (D) Interactions between VRC34.01-CDRH1 (purple) with Env trimer AMC011 SOSIP.v4.2 (white). (E) Comparison between the different relative conformations of the ACS202-bound FP (green) and the VRC34.01-bound FP (yellow). gp41 molecules from the ACS202/Env complex and VRC34.01/Env complex structures were superimposed with PyMOL to show the different conformations and orientation of ACS202-bound and VRC34.01-bound FPs. (F) Comparison between the structures of VRC34.01 complexed with HIV-1 Env trimers AMC011 SOSIP.v4.2 (yellow) and BG505 SOSIP.664 (green). The epitopes on AMC011 SOSIP.v4.2 (including FP and glycans at N88 and N241), as well as the bound VRC34.01 Fab, are shown in yellow, and those of BG505 SOSIP.664 are in green, with the Env trimer in white. BG505 SOSIP.664 has serine at position 241 and thus lacks a glycan at this site. The slight angle shifts between the FPs, glycans, and Fabs of the two structures are highlighted with arrows. To measure the angle differences, Env protomers of AMC011 SOSIP.v4.2 and BG505 SOSIP.664 were aligned with PyMOL. The method to assess angle differences is shown in the right panel. See also Figures S2 and S3 and Table S3.

Figure 4

Neutralizing Antibodies Bind to HIV-1 Fusion Peptides with Different Angles of Approach (A) Cryo-EM reconstruction of Env trimer AMC011 SOSIP.v4.2 (white) in complex with ACS202 Fab (blue) shows a stoichiometry of three Fabs per trimer. The FP is shown in green. (B) Cryo-EM reconstruction of Env trimer AMC011 SOSIP.v4.2 (white) in complex with VRC34.01 Fab (purple) with a stoichiometry of three Fabs per trimer. The FP is shown in yellow. (C) Cryo-EM reconstruction of Env trimer JR-FL EnvΔCT (white) in complex with PGT151 Fab (cyan) with a stoichiometry of two Fabs per trimer (PDB: 5FUU) (Lee et al., 2016). The FP is shown in blue. (D) Cryo-EM reconstruction of Env trimer BG505 SOSIP (white) in complex with v16.02 Fab (green) with a stoichiometry of three Fabs per trimer (PDB: 6CDI) (Xu et al., 2018). The FP is shown in purple. (E) Cryo-EM reconstruction of Env trimer BG505 SOSIP (white) in complex with v20.0 Fab (blue) with a stoichiometry of three Fabs per trimer (PDB: 6CDE) (Xu et al., 2018). The FP is shown in orange. (F) Interface areas between anti-FP antibodies ACS202, VRC34.01, PGT151, vFP16.02, vFP20.01, and Env trimers. Interface area (Ų) with the FPs, other amino acids, and glycans are shown in orange, yellow, and green, respectively. The interface areas were calculated with PISA (Krissinel and Henrick, 2007). (G) Conformations of the FPs stabilized by ACS202 (green), VRC34.01 (yellow), PGT151 (blue), vFP16.02 (purple), and vFP20.01 (orange). Protomers of the antibody-bound Env proteins were superimposed with PyMOL, and the different conformations of the FP (A512–L520) are shown in the panel. The vFP16.02-bound and vFP20.01-bound FPs overlap with each other. (H) Comparison of the binding approaches of ACS202 (HC: dark blue, LC: light blue, bound FP: green), VRC34.01 (HC: dark red, LC: light red, bound FP: yellow), and PGT151 (HC: dark cyan, LC: light cyan, bound FP: blue) to the Env surface. See also Figure S3 and Table S2.