Data and script for "General Model of the Catalytic Core Structural Rearrangements during Splicing"

General Model of the Catalytic Core Structural Rearrangements during Splicing

(A) Rearrangements within the U6 core between the catalytic and inactive conformations, facilitated by Prp16. We propose that upon destabilization of the lower U6-ISL stem, the catalytic center adopts the optimal geometry for catalysis. Conversely, stabilization of pairing interactions within the lower stem promotes the Prp16-dependent transition out of the first-step conformation. (B) Consensus sequence and secondary structure diagram for U6-ISL based on the Rfam alignment. (C–E) Structural features of (C) U6-ISL, (D) U6atac-ISL, and (E) group II introns domain V. Sequences and secondary structures are shown for group representatives. (F) The free energy plot. For each representative, free energy of the lower (in blue) and upper segment (in black) is shown. The upper stem free energy shared by all U6-ISL (-12.75 kcal/mol) is shown as a black line. For group II introns, the free energies for the representative sequence (O. iheyensis) are shown as dots, and distributions of free energies for all (n = 92) diverse segments taken from the Rfam alignment are shown as violin plots. Statistical significance of differences between free energies was determined by the non-parametric Mann-Whitney test (p value = 7.85e-20). Free energies of destabilizing yeast lower ISL mutants (n = 18) are shown as purple dots.