(A) Principal component projection of the MD trajectories, with estimated free energy contours revealing a structured conformational landscape containing multiple low-energy basins. (B) Spectral clustering identifies six conformational substates (CSs), with representative centroids indicated as red points. (C) Root mean square fluctuation of the terminal loop nucleotides within each CS relative to its centroid, highlighting substate-specific flexibility. (D) Three-dimensional centroid structures, substate populations, and secondary structures annotated using the Leontis–Westhof nomenclature within each CS, where base-pairing and nucleobase stacking propensities are visualized via color intensity (darker tones indicate higher probability across the cluster ensemble).
