Figure 7. Comparison between the catalytically active “open” conformation of HIV-1 reverse transcriptase and the “extended” conformations obtained in the simulations.

Side-view (A) and “top”-view (B) of nucleic acid-bound reverse transcriptase (PDB: 2HMI) (Ding et al., 1998). Side-view (C and E) and “top”-view (D and F) of a typical ligand-bound structure obtained in our simulations. The highlighted distances can be used as “fingerprints” for the identification of catalytically competent conformations.