The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template

Andrabi, Raiees; Pallesen, Jesper; Allen, Joel D.; Song, Ge; Zhang, Jinsong; de Val, Natalia; Gegg, Gavin; Porter, Katelyn; Su, Ching-Yao; Pauthner, Matthias; Newman, Amanda; Bouton-Verville, Hilary; Garces, Fernando; Wilson, Ian A.; Crispin, Max; Hahn, Beatrice H.; Haynes, Barton F.; Verkoczy, Laurent; Ward, Andrew B.; Burton, Dennis R.

Binding of one of the V3-N332 epitope-specific bnAbs, PGT128, predominantly relies on the N332 glycan and a neighboring peptide motif 324 GDIR 327 at the base of the V3 loop (Figures 5B and S8) (Garces et al., 2014; Gristick et al., 2016; Kong et al., 2013; Pejchal et al., 2011; Sok et al., 2016b) . The lack of binding to the MT145K trimer by PGT128 and other bnAbs in this class can be explained by the absence of the N332 glycan on this Env. In contrast, three of the four core protein epitope residues 324 G-325 D-327 R are conserved on the MT145K trimer and, in fact, on other chimpanzee SIV Envs ( Figures 5B, S5, and S8 ). For the PGT128 class bnAbs, the interaction with glycan N332 can be substituted by the N295 glycan observed in some HIV isolates, but not by glycan N334 that is present on the MT145K trimer (Sok et al., 2014a) . In fact, the MT145K N334 glycan is positioned in a direction away from the V3-N332 epitope site, making it impossible to facilitate bnAb binding to this epitope. Strikingly, the majority of the known SIVcpz Env sequences possess an N334 glycan in place of the more common N332 glycan on the HIV Env, which appears to be a significant glycan shift upon species crossover as the virus established itself in humans ( Figure S5 ). In addition, the glycans at N442 in the gp120-C4 region and N412 in the gp120-V4 region of MT145K Env may obstruct PGT128 binding. The glycan at N442, unique (A) Site-specific glycoform quantification of the MT145K SOSIP soluble trimer. MT145K trimers from transiently transfected HEK293F cell expressed supernatants were affinity purified by the quaternary trimer-specific antibody, PGT145. The purified MT145K trimers were treated separately with three proteasestrypsin, chymotrypsin, and elastase-and the digests were enriched for glycopeptides and analyzed by liquid chromatography-electrospray ionization mass spectrometry (LC-ESI MS). The individual glycan compositions of the N-linked glycan sites (n = 26) are represented by bar graphs that indicate the relative abundance of each glycoform species and are derived from the mean of two analytical replicates. The pie charts summarize the proportion of glycoforms for each site and this information is color coded: oligomannose type in green and complex and/or hybrid glycans in pink. The glycoforms at N262 and N268 positions (indicated by ''*'') could not be separately determined by enzymatic digestion and the bars represent the average glycan compositions across both sites. (B) Hydrophilic interaction ultra-performance liquid chromatography (HILIC-UPLC) profiles of the total N-linked glycans released from the MT145K trimers. The proportions of oligomannose plus hybrid glycan contents and complex-type glycans are represented in green and pink colors, respectively. (C) Modeled glycan shields for the MT145K and BG505 SOSIP trimers. Man9GlcNAc2 oligomannose-type glycans were docked and rigid-body fitted at each of the corresponding Env glycan positions using the MT145K structure (determined in this study [PDB: 6OHY]) and the unliganded BG505 SOSIP.664 trimer structure (Kwon et al., 2015; PDB: 4ZMJ) . Top and side views of the trimers are shown and the individual glycan sites are labeled and color coded based on the content of oligomannose: green, 100%-80%; orange, 79%-20%; and pink, 19%-0%.