A Molecular\nDynamics Examination on Mutation-Induced\nCatalase Activity in Coral Allene Oxide Synthase
Bibliographic record
Abstract
Coral\nallene oxide synthase (cAOS) catalyzes the formation of allene\noxides from fatty acid hydroperoxides. Interestingly, its active site\ndiffers from that of catalase by only a single residue yet is incapable\nof catalase activity. That is, it is unable to catalyze the decomposition\nof hydrogen peroxide to molecular oxygen and water. However, the single\nactive-site mutation T66V allows cAOS to exhibit catalase activity.\nWe have performed a series of molecular dynamics (MD) simulations\nin order to gain insights into the differences in substrate (8<i>R</i>-hydroperoxyeicosatetraenoic) and H<sub>2</sub>O<sub>2</sub> active site binding between wild-type cAOS and the T66V mutant cAOS.\nIt is observed that in wild-type cAOS the active site Thr66 residue\nconsistently forms a strong hydrogen-bonding interaction with H<sub>2</sub>O<sub>2</sub> (catalase substrate) and, importantly, with\nthe aid of His67 helps to pull H<sub>2</sub>O<sub>2</sub> away from\nthe heme Fe center. In contrast, in the T66V-cAOS mutant the H<sub>2</sub>O<sub>2</sub> is much closer to the heme’s Fe center\nand now forms a consistent Fe···O<sub>2</sub>H<sub>2</sub> interaction. In addition, the His67···H<sub>2</sub>O<sub>2</sub> distance shortens considerably, increasing the\nlikelihood of a Cpd I intermediate and hence exhibiting catalase activity.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| 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) | 0.047 | 0.002 |
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; both teacher heads agree on what is shown here.
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".