FIGURE 9.

Effects of S304G mutation on molecular dynamics of V3 loop. Molecular models for 562 and 562 S304G V3 loops were constructed by homology modeling and subjected to MD simulations as described in section “Materials and Methods.” (A) Time course of RMSD between the initial model and models at given times of MD simulation. (B) Superposition of V3 structures obtained during 10–20 ns of MD simulations. (C) Distribution of RMSF in V3 loop. RMSF values that represent atomic fluctuations of the main chains of individual amino acids were calculated with 10,000 snapshots from 10 to 20 ns of each MD simulation. (D) Distributions of frequencies of β-sheet and turn structures in V3 loop that were formed during MD simulations. RMSD, RMSF, and frequencies were calculated using the ptraj module in Amber (Case et al., 2005). Red arrows in (B), (C), and (D) show the position of S304G mutation. Red and blue lines in (C) and (D) represent data on 562 and 562 S304G clones, respectively.