Figure 2.
Protein structural variation during MD simulation at 300 K. (a) Dihedral angles and H bond angle/distance were analyzed. (b) Structure overlay of Ile60-Ile61 in snapshots at 200 ns in MD with Ile60ψ = 160° (green) and at 160 ns in MD with Ile60ψ = 113° (pink) indicates that the Cα position is unchanged while the N (blue) and carbonyl O (orange) move. (c) There is strong correlation between Ile61φ and Ile60ψ. Each scatter point represents one snapshot from MD simulation extracted every 10 ns. The correlation coefficient is −0.89. (d) The correlation plot of Ile60θ and Ile60ψ shows strong correlation between backbone torsion angle and H bond angle. The H bond angle θ is defined as the angle between the H bond (O---H) and C═O. Ile60 is located in a β-sheet structure, and its O forms a H bond with Met42 NH in MD simulation. The closest water molecule is ~7.5 Å away from the Ile60 O during the trajectory. The correlation between ψi+1, φi, and H bond angle θi is not unique for I60-I61, as shown in Figure S7.