Figure 8
Modeling the potential role of N283/T283 in various Env for gp120:CD4 interaction. Swiss PDB Viewer was used to change T283 (A) to N283 (B) in the HIV-1JR-FL gp120 crystal structure (2B4C) [95], as previously described [53]; potential hydrogen bonds are indicated by dotted lines and the estimated distance is shown, suggesting a greater likelihood for formation of a hydrogen bond with Q40 (shown in yellow) in CD4 (green) for N283 than for T283, in the HIV-1JR-FL gp120 background. DS17 and DS17(N283T) Env were modeled based on the HIV-1JR-FL gp120 crystal structure (C and D, respectively) using the Swiss Model Server, and the models showed that the distance between T283 and Q40 would be shorter than between N283 and Q40, although both would be larger than what it is usually accepted for the formation of a hydrogen bond (3.3Å). Finally, the SPL and SPL(T283N) Env were best modeled based on the HIV-1YU-2 gp120 crystal structure (E and F, respectively), and the models showed that both could potential make hydrogen bond contacts with Q40 in CD4, although the shorter distance in SPL(T283N) would suggest a greater likelihood for this to occur for mutated N283 than for wild-type T283. The brain-derived Env did not result in a good model with any of the published gp120 crystal structures.