FIGURE 15.

The domain mass center distance (DMCD) between the p66 fingers subdomain (residues 12–85 and 120–150) and the p66 thumb subdomain (residue 241–314) versus simulation time: (A) the CMD simulation and (B) the SMD simulation. The SMD simulation was followed by a CMD simulation for 1 ns after α-APA was completely pulled out from the inhibitor-binding pocket. The typical variation ranges of DMCDs in different types of HIV-1 RT structures. The structures of HIV-1 RT are denoted with their PDB entry codes as follows: structure in unliganded state, 1DLO (Hsiou et al., 1996), structures of HIV-1 RT in complexes of the template-primers, 2HMI (Ding et al., 1998) and 1RTD (Huang et al., 1998), and structures of HIV-1 RT bound with NNRTIs, 1HNI (Ding et al., 1995a), 1HNV (Ding et al., 1995b), and 1KLM (Esnouf et al., 1997).