Active Site Labeling of G8 in the Hairpin Ribozyme: Implications for Structure and Mechanism
Bibliographic record
Abstract
There is mounting evidence that suggests that general acid/base catalysis is operative in the hairpin ribozyme, with analogy to the protein enzyme RNaseA. Nevertheless, the extent of general base catalysis as well as the identity of the specific chemical groups responsible remains the subject of some controversy. An affinity label has previously been used to alkylate histidine 12 (His12), the active general base in RNaseA. To date, no such experiment has been applied to a ribozyme. We have synthesized the analogous affinity label for the hairpin ribozyme with an electrophilic 2'-bromoacetamide group in lieu of the 2'-hydroxyl (2'OH) at the substrate cleavage site and show that guanosine 8 (G8) of the hairpin ribozyme is specifically alkylated, most likely at the N1 position. This evidence strongly implicates N1 of G8 in active site chemistry. By direct analogy to RNase A, these findings could be consistent with the hypothesis that deprotonated G8 residue functions as a general base in the hairpin ribozyme. Other mechanistic possibilities for N1 of G8 such as indirect general base catalysis mediated by a water molecule or transition state stabilization could also be consistent with our findings.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".