Orientation and Protein−Cofactor Interactions of Monosubstituted<i>n</i>-Alkyl Naphthoquinones in the A<sub>1</sub>Binding Site of Photosystem I
Bibliographic record
Abstract
1,4-Naphthoquinone (NQ) and its monosubstituted derivatives, 2-methyl, 2-ethyl, and 2-butyl-1,4-naphthoquinone, have been incorporated into the A 1 binding site of photosystem I (PS I) after organic solvent extraction of the native phylloquinone. The charge separated state P 700 + NQ - has been studied by multifrequency transient EPR. The Q-band (35 GHz) spectra of fully deuterated 2-methyl-1,4-NQ- d 8 and 2-ethyl-1,4-NQ- d 10 show sufficient spectral resolution for the orientation of the quinone g tensor and thus the headgroup of the molecule to be determined. All orientation parameters of the substituted NQs are found to be the same as those established for native phylloquinone in PS I. However, for 2-ethyl-1,4-NQ and 2-butyl-1,4-NQ the X- and Q-band spectra exhibit a well resolved 1:2:1 hyperfine splitting. From the fact that it is absent when the first methylene group of the side chain is selectively deuterated, the splitting is assigned to the hyperfine coupling of the methylene protons. The principal values of the axially symmetric hyperfine coupling tensor are determined to be | A xx | = 12.2 MHz, | A yy | = 16.8 MHz, | A zz | = 12.2 MHz, and a iso = 13.7 MHz. The large methylene proton hyperfine coupling arises from a high spin density on the ring carbon atom to which the alkyl tail is attached. This in turn suggests that only one of the carbonyl groups of 2-alkyl-1,4-NQ is H-bonded to the protein and that the alkyl tail must be in the ortho position relative to the carbonyl group with the H bond. This implies that the alkyl side chain of the substituted NQs resides in the space normally occupied by the methyl group of phylloquinone and not that of the phytyl tail, which is meta to the H-bonded carbonyl group according to the X-ray structure. In addition, the hyperfine tensor indicates that the first two C−C bonds of the alkyl tail must be coplanar with the aromatic ring. However, the X-ray structure of PS I shows, for the native phylloquinone, that the phytyl tail is bent out of the quinone plane with the second C−C bond.
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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 | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".