Figure 8

Docking studies predict direct interaction of DQBS with HIV-1 Nef. Molecular docking studies were performed with DQBS and the X-ray crystal structure of the Nef dimer (PDB: 1EFN). The most energetically favored sites for DQBS binding lie at the dimer interface (A; Site 1) and on the surface of each Nef monomer (B; Site 2). The location of each predicted binding site is shown on an overall view of the Nef dimer at the top with the individual Nef subunits colored in green and blue respectively. A close of up view of each binding site is shown below, highlighting the side chains of Nef residues within 4 Å of each ligand binding site. DQBS is predicted to make polar contacts with Asn126 in both binding sites, plus an additional contact with Thr138 in Site 2. For additional details of docking results, see Table 1.