Fig. 2

Comparison of site-specific N-glycan processing of HIV-1 Env trimers. Site-specific analysis of glycan processing for a Env trimers from the JR-FL strain; b Env trimers from the BG505 strain; c Env trimers from the B41 strain. Shown for each glycosite were the proportion of peptides corresponding to unoccupied sites (grey), or sites containing high-mannose (green) and complex-type (purple) glycans. For glycosite numbers highlighted in yellow, proportions were assigned based on spectral hits since peak area did not reach the threshold. Sites with no number indicate the site was not present in the Env while sites with numbers and no bar graph indicate the site was not observed in LC/MS. Site-specific N-glycan processing of BG505 SOSIP is adapted with permission from ref. ¹⁴. The glycosylation profiles of JR-FL viral Env, BG505 ΔCT N332 Env, and B41 ΔCT Env were used as a reference for comparison with other Envs from the corresponding strain. Significant differences from reference samples are shown as colored bricks. Each recombinant Env was digested and analyzed in duplicate from two biological batches, while native trimers from infectious virus and pseudovirus were analyzed in duplicate from the same biological preparation (n = 6). Differences were assessed for the proportions of no glycan, high mannose and complex type at each glycosite. Differences of >10% were determined to be significant if the P value was <0.05 using a Mann–Whitney test. Mean ± s.e.m. were plotted