HIV-1 negative factor binding to human thioesterase 8: insights from computational biology

HIV-1 Negative factor (Nef) is a protein essential for the metabolism of the virus. Here we investigate the interactions of Nef with one of its targets on infected human cells, the human thioesterase 8 (hTE8) enzyme. Homology modeling, virtual protein-protein docking and Molecular Dynamics Simulation experiments are carried out on the structural models of the enzyme and the complex respectively, with the aim of characterizing the putative interaction region. A plausible, albeit approximate, binding region is identified. The latter help interpret existing site directed mutagenesis data. Our calculations suggest also that the system largescale dynamics change upon complex formation.