Catalyzing separation of carbon dioxide in thiamin diphosphate‐promoted decarboxylation
Bibliographic record
Abstract
Thiamin diphosphate-dependent decarboxylases form addition intermediates between thiamin diphosphate (ThDP) and 2-ketoacids. Although it appears that the intermediate should react without the intervention of catalysts, evidence has clearly shown that Brønsted acid catalysis occurs through a pre-associated system. This can promote separation of carbon dioxide from the residual carbanion by protonation of the carbanion. Proteins operate through pre-association and may readily promote the separation of carbon dioxide by protonating or oxidizing the nascent carbanion. Alternatively, a nucleophilic side chain may trap carbon dioxide as an unstable hemi-carbonate. Mutagenesis experiments by others have shown that enhanced activity due to the protein in the presence of thiamin diphosphate does not depend on the presence of any one proton donor, consistent with pooled activity within the active site. This form of catalysis has not been widely recognized, but should be considered an integral aspect of enzyme-promoted decarboxylation.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.006 |
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".