Molecular dynamic of P. lutzii TRR1 model.
(A) Secondary structure elements evolution of the TRR1 model along MD trajectory; α-helices and β-sheets are shown in pink and yellow, respectively. (B) Evolution of the volume cavity of TRR1 model along MD trajectory. (C) RMSd (Root Mean Square Deviation) values plot of atoms from 500 conformations of TRR1 3-D model along MD trajectory. Each point on the graph represents the RMSd between the conformations, and the lowest RMSd values are close to the diagonal line. (D) 3D model of the four most probable conformations overlapped shown by colored lines.