Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations
Figure 3
RMSd variation for the 300 ns long simulations of the GroEL subunit.
Black line corresponds to the RMSd with respect to the starting structure (t for A+C, and r″ for B+D), while the grey line corresponds the RMSd with respect to the opposite form (r″ for A+C, and t for B+D). Each plot corresponds to one specific MD simulation; (A) closed (t) unbound, (B) open (r″) unbound, (C) closed (t) ATP bound, and (D) open (r″) ADP bound. Black dashed line depicts the RMSd value between the open (r″) and closed (t) X-ray structure. Clustering analysis is performed on each of the 4 simulations, and the bar on the top of each RMSd plot is colored according to which cluster the corresponding frame belongs to.