Unraveling the Critical Role Played by <sub>Ado76</sub>2′OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase
Bibliographic record
Abstract
Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNA Thr that has been misaminoacylated with serine (i.e., Ser-tRNA Thr ) is hydrolytically cleaved to serine and tRNA Thr . It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNA Thr ( Ado76 2′OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNA Thr ester bond. We have performed a computational study, involving molecular dynamics (MD) and hybrid ONIOM quantum mechanics/molecular mechanics (QM/MM) methods, considering all possible editing mechanisms to gain an understanding of the role played by Ado76 2′OH group. More specifically, a range of concerted or stepwise mechanisms involving four-, six-, or eight-membered transition structures (total of seven mechanisms) were considered. In addition, these seven mechanisms were fully optimized using three different DFT functionals, namely, B3LYP, M06-2X, and M06-HF. The M06-HF functional gave the most feasible energy barriers followed by the M06-2X functional. The most favorable mechanism proceeds stepwise through two six-membered ring transition states in which the Ado76 2′OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic H 2 O to the bridging oxygen ( Ado76 3′O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the Ado76 2′-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C–O carb center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the Ado76 2′-OH group transfers its proton on the adjacent Ado76 3′-oxygen, cleaving the scissile C carb –O3′ Ado76 bond, while concomitantly accepting a proton from the previously formed C–O carb H group.
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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 | 0.000 | 0.000 |
| 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 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".