Deletion of the P5abc Peripheral Element Accelerates Early and Late Folding Steps of the Tetrahymena Group I Ribozyme

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Abstract
The P5abc peripheral element stabilizes the Tetrahymena group I ribozyme and enhances its catalytic activity. Despite its beneficial effects on the native structure, prior studies have shown that early formation of P5abc structure during folding can slow later folding steps. Here we use a P5abc deletion variant (EΔP5abc) to systematically probe the role of P5abc throughout tertiary folding. Time-resolved hydroxyl radical footprinting shows that EΔP5abc forms its earliest stable tertiary structure on the millisecond time scale, ∼5-fold faster than the wild-type ribozyme, and stable structure spreads throughout EΔP5abc in seconds. Nevertheless, activity measurements show that the earliest detectable formation of native EΔP5abc ribozyme is much slower (∼0.6 min-1), in a manner similar to that of the wild type. Also similar, only a small fraction of EΔP5abc attains the native state on this time scale under standard conditions at 25 °C, whereas the remainder misfolds; footprinting experiments show that the misfolded conformer shares structural features with the long-lived misfolded conformer of the wild-type ribozyme. Thus, P5abc does not have a large overall effect on the rate-limiting step(s) along this pathway. However, once misfolded, EΔP5abc refolds to the native state 80-fold faster than the wild-type ribozyme and is less accelerated by urea, indicating that P5abc stabilizes the misfolded structure relative to the less-ordered transition state for refolding. Together, the results suggest that, under these conditions, even the earliest tertiary folding intermediates of the wild-type ribozyme represent misfolded species and that P5abc is principally a liability during the tertiary folding process.