Carbon Monoxide Binding to Copper-Containing Nitrite Reductase from <i>Alcaligenes faecalis</i>
Bibliographic record
Abstract
To probe the active site of copper-containing nitrite reductase (NiR), the carbonyl derivatives of the wild-type enzyme and the Asp98Asn variant were studied by Fourier transform infrared (FTIR) spectroscopy. CO bound to wild-type NiR exhibits a single absorption band at 2050 cm -1 (Δν = ∼11 cm -1 ) arising from the C−O stretching mode. This band is not significantly affected by pH change (pH ≤ 8.0) or by H/D exchange. Interestingly, CO bound to the Asp98Asn variant exhibits two C−O stretching frequencies, one located at 2060 cm -1 (A 1 ) and the other at 2041 cm -1 (A 2 ). These two bands are both temperature and pH dependent, and the equilibrium constant K 298 (1.01), Δ H ° (−14(1) kJ/mol), and Δ S ° (−45(4) J/mol) for the A 1 ⇌ A 2 equilibrium (pH 7.0) were determined. In addition, H/D exchange results in a ∼2 cm -1 shift of CO to the red for A 2 but not A 1 . On the basis of these results and the X-ray crystal structure of NiR, we conclude that the single band at 2050 cm -1 observed in wild-type NiR is a single, non-hydrogen-bonded C−O stretching mode. The doublet band observed in the Asp98Asn variant indicates that the bound CO occupies two orientations and suggests that the orientation corresponding to band A 2 participates in hydrogen bonding. These results indicate a role for Asp98 in controlling the orientation and dynamics of ligand binding to the copper center. Implications concerning previous mechanistic arguments arising from analysis of the three-dimensional structure of the enzyme are discussed.
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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 | 0.000 |
| 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 | 0.001 | 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 teacher head, 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".