Ribbon views of the NMR model of apolipophorin-III.

<p>NMR model 1 of this 164-residue, five-helix-bundle protein (PDB 1LS4) was used to start our simulations in the noted AMBER force fields. Bright green and black unstructured regions represent turn and random coil regions, respectively. Helices are colored from blue (helix 1) to green (helix 5). The bottom view is rotated toward the reader to provide an axial view down the helical bundle central core region.</p

Structural sampling of apolipophorin-III per residue.

<p>Probabilities of sampling helix (H), turn (T), random coil (C), and polyproline type II (P) states when simulated using the AMBER-94, AMBER-99φ, AMBER-03, and AMBER-99SB force fields are shown. The schematic at the top represents the NMR model that was used to initiate all simulations, with turns shown in green and coil regions shown in pink to match the color coded state sampling plots below, which show probability ranges from 0.0 (black) to 1.0 (color).</p

Free energy landscapes projected onto the Ramachandran map.

<p>These maps represent equilibrium sampling of the F_s peptide in the AMBER force fields evaluated, which have been ordered to match <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010056#pone-0010056-g001" target="_blank">Figure 1</a> in (a) through (d). Each map consists of backbone torsional values binned in 3° intervals for all residues, and contours represent <i>k</i>T units at 305 K, the midpoint temperature of the helical peptide.</p

Ensemble averaged equilibrium structural properties for the F_s and A₂₁ peptides.

<p>RMSD (all-atom root-mean-square deviation), R_g (radius of gyration), N_helix (number of α-helical residues), N₃₁₀ (number of 3₁₀-helical residues), N_seg (number of helical segments), and N_cont (length of helical segments).</p

Convergence of mean helical content for the (a) F_s and (b) A₂₁ ensembles.

<p>The AMBER-03 (red), AMBER-99SB (green), and AMBER-99φ (blue) potentials are shown, where helix> represents the number of helical residues averaged across all runs in a given ensemble of 1,000 simulations. Dotted and solid lines represent simulation ensembles initiated from the fully random coil and fully helical states, respectively. Other structural properties listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010056#pone-0010056-t002" target="_blank">Table 2</a> show similar convergence. Noise near the 100 ns regime is the result of a limited number of simulations reaching those times following the ensemble convergence that occurs prior to the 40 ns timepoint.</p

Simulated ensemble statistics for the F_s and A₂₁ peptides.

<p>*Each force field was sampled using 1,000 trajectories starting in the fully helical state (H) and 1,000 trajectories starting in the random coil state (C) with no structured residues.</p><p>Max (longest individual trajectory), Total time (total ensemble simulation time), and >EQ (total equilibrium simulation time) are shown for each data set.</p

Mean SASA^* for apolipophorin-III simulations.

<p>*SASA (solvent-accessible surface area) is in Ų and was calculated using VEGA (<a href="http://nova.colombo58.unimi.it" target="_blank">http://nova.colombo58.unimi.it</a>).</p>‡<p>All 21 NMR models were used to generate these means and standard deviations.</p