Fig. 25. Comparison of residue-wise dynamical properties measured by NMR and MD derived order parameter O² (y axis in the bottom panel). The backbone order parameter provides information on the amplitude of fluctuation of NH and CH bond vectors. The magenta shadowed area shows the residues with higher backbone flexibility (lower O² corresponds to higher flexibility). Experimental parameters can be calculated by T1, T2 and heteronuclear NOE relaxation experiments. Often short MD simulations are sufficient to produce O² which can capture motions in ps to ns timescale but for slower relaxation motions one needs longer simulations (μs to ms). Comparison of NMR and MD derived O² in PAPs can give insights into how flap flexibility varies between apo and ligand-bound conformations. See ref. 95 and 96 for comparison of conformational dynamics using MD and NMR. The figure was adapted from ref. 102.