Probing the conformational dynamics of an OTU deubiquitinase enzyme active site
Bibliographic record
Abstract
Enzymes are fundamental to cell function. Despite this, exactly how they work remains unclear. Enzymes exist as 3D folded structures determined by their amino acid sequence, and these structures are necessary for function. However, enzymes change their 3D conformation frequently during the course of a reaction, and an understanding of these dynamic motions is necessary for a complete understanding of enzyme function. As a model for enzyme dynamics, we have studied the catalytic domain of Otu1, an ovarian tumour domain-containing deubiquitinase from yeast Saccharomyces cerevisiae. Deubiquitinases catalyze the breakdown of ubiquitin, and play an important role in regulating cell functions including immune response and signal transduction. We have probed the structural dynamics of the catalytic domain of Otu1 using the cysteine-labelling molecule 4,4’-dithiodipyridine (DTDP). The labelling reaction kinetics have been followed using stopped-flow fluorescence spectroscopy methods and have revealed the presence of a conformational change with a frequency of 127 ± 7 s-1. This conformational change may potentially play a role in the enzyme’s catalytic mechanism.
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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 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".