Fig. 4: Large conformational changes detected by MD and metadynamics simulations.

a An all-atom classical MD simulation of the AbnA-Conf2 crystal structure over 500 ns. The distance between Domain1 and Domain4 is plotted as a function of time. b The free energy landscape obtained by metadynamics for the conformational dynamics of AbnA as a function of (i) the distance between Domain1 and Domain4 and (ii) the dihedral angle between Domain1, Domain2, Domain3, and Domain4. Coloring corresponds to differences in energy values ranging from 0 (blue) to 15 kcal mol⁻¹ (red). Contour lines are contoured at 1.4 kcal mol⁻¹. Three energy minima are observed, as well as a small energy minimum shoulder located on an energetic plateau. The structural clusters, representative of each energy minimum, are presented, and the relative difference in energy between them is shown. Stars 1,2,3 indicate the locations of the AbnA-Conf1, AbnA-Conf2, and AbnA-Conf3 crystal structures on the energy landscape.