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Figure 6 | Retrovirology

Figure 6

From: Overlapping effector interfaces define the multiple functions of the HIV-1 Nef polyproline helix

Figure 6

Organization of effector interfaces on the surface of Nef associated with the polyproline helix. (A) Left, Function, The colored residues are grouped into proposed effector interfaces and presented on the three dimensional surface of Nef. The core of the SH3 domain binding interface that includes P72, Q73, V74, P75, L76, and R77 is indicated by “PQVPLR, Blue.” A proposed interaction interface important for MHCI downregulation that includes P78 and D123 is indicated by “D123, Pink”. Two residues near P78 and D123 that are 99% conserved, T80 and F121, are also pink. A second proposed interaction region important for MHCI downregulation is indicated as “MHCI, Brown.” Brown residues include E62-65 (tetra-glutamate), G67, and F68. The hydrophobic pocket that enhances the affinity of Hck binding includes L87, F90, W113, T117 and Q118 and is indicated with “Hydrophobic Pocket, Gold.” Note: T117 is obscured in this view. GFP/F is a proposed interface that overlaps “MHCI, Brown” and “Hydrophobic Pocket, Gold.” PQVPLR and GFP/F act in concert for Nef/activated PAK2 complex formation. GFP/F includes G67 and F68 (brown), P69 (tan), and F90 (gold). “PAK2, Tan” indicates P69 that is not part of the “MHCI, Brown” interface. White residues remain uncharacterized. (B) Right, Conservation, The same view of Nef as in (A) but the residues that are conserved at 99% in subtype B Nefs are green and labeled. The tetra-glutamate segment (amino acids 62–65) is conserved in the sense of being a negatively charged patch on the surface of Nef, but none of the positions is 99% glutamate. Amino acid 87 that is part of the hydrophobic pocket is 96% leucine, 2% isoleucine and 1% methionine [32]. The modified BH10 Nef (PDB: 2NEF) presented has a truncated N-terminal arm (amino acids 1–55) and has a deletion of the flexible internal loop (amino acids 159–173). These modifications are not visible as amino acids 56, 158, and 174 are on the backside of this view. All images were created using Pymol (www.pymol.org).

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