Figure 6.

Two dominant folding pathways of the Tetrahymena ribozyme. The wild-type ribozyme and P3-weakening mutants fold primarily through the lower pathway (red) and the P3-strengthening mutants fold primarily through the upper pathway (green). All of the intermediates on the lower pathway are postulated to include the non-native topology, while those on the upper pathway have the native topology (indicated for intermediates with a superscript N). On the red pathway, the transition from I_trap to I_commitment (abbreviated I_commit) is shown as occurring in two substeps, with native tertiary structure being disrupted in the first substep and then non-native structure being resolved in the second substep. From I_commitment, folding can continue to the misfolded state (M) with the reformation of tertiary contacts, or P3 can be disrupted to allow an exchange of topology, and reformation of P3 gives the intermediate I_P3^N, which folds rapidly to the native state (N). The rate constants for the transitions from I_commitment are not known but a lower limit of X ≥ 5 was established from earlier work.^{19, 29} For the P3-strengthening mutants, incubation in buffer solution allows formation of P3, which is proposed to be coupled to formation of the native topology, giving the intermediate I₁^N (dashed box). Upon Mg²⁺ addition, folding proceeds by tertiary structure formation to an intermediate that has the non-native structural feature of I_trap but the native topology (I_trap^N). This intermediate is resolved in two substeps as described above, and reformation of tertiary contacts leads to formation of the native state.