Fig. 2: Protocol validation via comparison of the simulated and experimental mean squared displacement parameter of apoferritin and insulin.
a Mean squared displacement parameters extracted from simulated apoferritin (MSD(T), full symbols) and experimental (<u2(T)>, empty symbols) neutron scattering data. apo_h005 (red squares) and apo_h031 (green circles) denote lyophilised and hydrated apoferritin, respectively. The simulated MSD(T) values presented here were extracted from MD data generated from apoferritin models constructed using Protocol 2. Inset: simulated MSD(T) values predicted from model assemblies built using Protocol 1 for apo_h005 (full orange squares) and apo_h031 (full blue circles). Dotted lines are a guide to the eye. b Representative experimental data for hydrated apoferritin (0.31 g of D2O per g of protein) and associated fits at 10 (full purple triangles), 250 (empty green circles) and 290 (full blue squares) K. Data fitted using Eq. (2) (see Methods) from which the experimental <u2(T)> values shown in a) were extracted. c Protocol 2 validation via comparison of the simulated (full symbols) and experimental (empty symbols) mean squared displacement parameter of bovine insulin. ins_h005 (red squares) and ins_h025 (green circles) denote lyophilised and hydrated insulin, respectively. The simulated MSD(T) values were extracted from MD data generated from insulin models constructed using Protocol 2. MSD(T) values and errors are averages and standard deviations over 12 independent simulation replicas. Dotted lines are a guide to the eye. Errors, when not visible, are within symbol size.
