Hydrogen bonds between NF and residue 30 of sB-PRs

<p>. Number (above) and average (below) of hydrogen bonds performed between the ligand Nelfinavir and the residue 30 of each subtype B (sB) protease (Chain A) along 50 ns of molecular dynamics simulation. The colors are given in black, red and green for the wild-type (sB-WT), D30N (sB-D30N) and D30V (sB-D30V), respectively.</p

Molecular dynamics of sC-PRs bound to NF.

<p>Root Mean Square Deviation (RMSD) of subtype C (sC) proteases bound to Nelfinavir (NF) along 50 ns of molecular dynamics simulation. The colors are given in black, red and green for the wild-type (sC-WT), D30V (sC-D30V) and V32E (sC-V32E), respectively. Note that the sC-V32E RMSD behavior points to an open conformation state of the protease within the first 20 ns, alternating between open and closed conformation along the simulated period. The sC-WT and sC-D30V PRs remained in a closed conformation along the entire simulation.</p

Conformational variability of Nelfinavir.

<p>Structural analysis of Nelfinavir in solution along 100(FES) of this simulation (top) indicates three “islands” of low energy conformations (i1, i2 and i3), from which different structures were recovered (NF-i1, NF-i2, NF-i3). The crystal structure of Nelfinavir (1OHR) was the input conformation, and Root Mean Square Deviation (RMSD) indicates that all conformations sampled during the simulation differ from original structure by at least 0.2 nm (down).</p

Short replicated simulations of sB-PRs bound to NF.

<p>Average and Standard Deviation of the Root Mean Square Deviation (RMSD) for five independent 10 ns simulations of four different subtype B proteases (sB-PRs) bound to Nelfinavir (NF). Greater divergence is observed for sB-V32E, since two of its replicates presented a change to an open conformation of the flaps. Equilibration stages (before 2,500 ps) are not represented. Independent trajectories of each simulation can be observed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087520#pone.0087520.s002" target="_blank">Figure S2</a>.</p

Structural analysis of sB-D30V.

<p>(A) Superposition of the structures of sB-WT PR at 2,500 ps of simulation (grey) and at 50,000 ps (black). (B–C) Superposition of sB-D30N (red) and sB-D30V (green) at 50,000 ps over the respective structures at 2,500 ps (grey). (D–F) Measure of the deviation of ILE50 residue from PR Chain A considering the same structures from A, B and C, indicating the extent of Chain A flap movement. (G) Plot of the variation of the ASP25-ILE50 distance (Chain A) along the simulation. The stipulated threshold for semiopen conformation (1.58 nm) is indicated in blue.</p

Open conformation of the sB-V32E protease.

<p>Comparison between two frames of a molecular dynamics of the sB-V32E PR complexed with NF. Protease structure at 2,500 ps (25 ns) is represented in white (<i>cartoon</i>) with Nelfinavir depicted in purple (<i>sticks</i>). Protease structure at 50,000 ps (50 ns), in an open conformation, is depicted in blue (<i>cartoon</i>).</p