Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin - Fig 3

<p>Average number of residues showing each secondary structure element determined on the equilibrated period of the (A) MD and (B) REST2 simulations for each forcefield and starting structure. The pattern filled bars are representing the unfolded runs while the solid filled bars with the same colour are the folded runs.</p

Total simulation times collected for each forcefield employed and respective water models.

<p>Convergence of the REST2 simulations was determined using cluster analysis, whilst brute-force MD simulation was considered to reach equilibrium when the system energies and backbone RMSD had plateaued. CHARMM22/CMAP is designated as CHARMM27.</p

Cartoon/licorice representation of the starting structures of human amylin used in this work.

<p>(A) NMR micelle bound structure PDB code 2L86.^[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186219#pone.0186219.ref015" target="_blank">¹⁵</a>^]. (B) Unfolded random coil conformation (taken from our preliminary assessment of amylin).</p

Aromatic ring orientation in apoC-II(60-70) and cyc(60

<p>–<b>70).</b> A histogram of the Tyr63 and Phe67 relative aromatic ring orientation (X-axis) obtained from the 2.8 µs ensemble trajectory. Typical structures illustrating the relative ring orientations of cyc(60–70) (red) and apoC-II(60–70) (blue) are represented as insets.</p

Most populated structures determined by clustering analysis.

<p>Ribbon and explicit aromatic ring representations of the four most populated clusters (green – Tyr63; purple – Phe67). The apoC-II(60–70) peptide is shown in blue and cyc(60–70) is shown in red.</p

Structural evolution of cyc(60–70) and apoC-II(60–70).

<p>(<b>A</b>) Ribbon and CPK representation of cyc(60–70) showing the persistent intra-molecular backbone hydrogen bonds in blue. The secondary structure evolution of (<b>B</b>) cyc(60–70) and (<b>C</b>) apoC-II(60–70) over 2.8 µs of simulation. The secondary structure colour codes: cyan – turn; yellow – extended conformation; green – hydrogen bridge; white – coil; blue – 3-10 helix; red – π-helix.</p

Cyc(60–70) structure overlay of monomeric and heterodimeric state.

<p>Superimposition of the cyc(60–70) structures taken from the most populated cluster, c1 (red) and monomeric cyc(60–70) 2] (blue). The aromatic residues are also shown; Tyr63 in green and Phe67 in purple.</p

ApoC-II(60–70) structural characteristics in free and cyc(60–70) bound states.

<p>End-to-end distance with respect to the radius of gyration of apoC-II(60–70) peptide in its monomeric state (red data points 10]) and as a heterodimer bound to cyc(60–70) (blue data points). Ribbon representations of the peptides corresponding to the indicated regions of sampled conformational space are shown as insets. The positions of the cluster representative structures are illustrated with coloured circles: c1 (green), c2 (orange), c3 (dark blue) and c4 (tan).</p

ApoC-II(60-70) binding preference sites on cyc(60-70).

<p>Surface representations showing the binding preference sites for structures: (<b>A</b>) c1 and (<b>B</b>) c4. Cyc(60–70) hydrophobic face is shown in red and the hydrophilic face in blue, while the apoC-II(60–70) peptide is coloured grey.</p

Conceptual association pathway for apoC-II(60–70) interacting with cyc(60–70).

<p>The four most populated clusters are shown with respect to their relative interaction enthalpies, PMF dissociation free energies (for clusters c1 and c4 only) and hydrophobic contact area. The respective cluster populations are also shown below each representative complex with dots indicating multiple possible structures. The connecting dashed lines demonstrate possible pathways, while the arrows point in the direction of stronger bound complexes. The hydrophobic residues of cyc(60–70) are represented as red surface, and hydrophilic residues in blue. The cyc(60–70) structure is shown with its hydrophobic face on the right and hydrophilic face on the left. The apoC-II(60–70) and cyc(60–70) conformation is shown in ribbon representation in grey and black, respectively.</p