Visualizing the Gas Channel of a Monofunctional Carbon Monoxide Dehydrogenase
Bibliographic record
Abstract
Carbon monoxide dehydrogenase (CODH) plays an important role in the processing of one‐carbon gases carbon monoxide and carbon dioxide. In CODH enzymes, these gases are channeled to and from the Ni‐Fe‐S active sites using hydrophobic cavities. In this work, we investigate these gas channels in a monofunctional CODH from Desulfovibrio vulgaris , which is unusual among CODHs for its oxygen‐tolerance. Based on computational predictions, we expect that monofunctional D. vulgaris CODH will have gas channels different from those of bifunctional Moorella thermoacetica carbon monoxide dehydrogenase/acetyl‐CoA synthase (CODH/ACS). By pressurizing D. vulgaris CODH protein crystals with xenon and solving the structure to 2.04 Å resolution, we identify 12 xenon sites per CODH monomer, thereby elucidating hydrophobic channels used for CO transport. We find that D. vulgaris CODH has one CO channel that has not been experimentally validated previously in a CODH, and a second channel that is shared with Moorella thermoacetica carbon monoxide dehydrogenase/acetyl‐CoA synthase (CODH/ACS). This experimental visualization of D. vulgaris CODH gas channels lays groundwork for further exploration of factors contributing to oxygen‐tolerance in this CODH, as well as study of channels in other CODHs.
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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 | 0.001 |
| 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".