Figure 9

Three dimensional representations of the functional regions of Nef that interact with host cell proteins or represent putative dimerization domains. (A) left, Red and Orange, αB and flanking loop amino acids of the Nef/Nef interface in hexagonal crystals of PDB 1AVZ (amino acids D108, L112, Y115, H116, F121, P122, D123); Orange, residues that interact with human thioesterase (amino acids D108, L112, F121, P122, D123); Yellow, PQVPLR in the proline helix of the Nef SH3 binding domain (amino acids 72-77); Blue, residues that interact with the cytoplasmic tail of CD4 (amino acids W57, L58, E59, G95, L97, R106, L110); right, Image is rotated 180 degrees. Lilac and Magenta, C-terminal Nef/Nef interface seen in cubic crystals of PDB 1AVV (amino acids F139, R188, F191, H192, H193, R196, E197); Magenta and Purple, residues known to play a role in PAK-2 activation (amino acids H89, S187, R188, F191); Green, residues that form a hydrophobic pocket interacting with Ile96 of the RT loop of the Hck SH3 domain (amino acids L87, F90, W113, I114). (B) left, Cyan, critical residues identified in the protein-protein docking experiments, showcased in Figure 8. Only residues that interact in both the receptor and ligand in both the homodimeric and heterodimeric models are indicated (amino acids L100, I101, R105, R106, I109, L112, W113, H116); blue violet, one of two regions (region 2) of HIV-1Nef that is highly conserved in SIV Nef with 22 out of 27 identities (amino acids 122 to 148). right, Seafoam green, second of two regions (region 1) of HIV-1 Nef that is highly conserved in SIV Nef with 11 out of 12 identities (amino acids 88-99).