Development of superagonist ligands for the vitamin D nuclear receptor, AMCR277A, -B and 2MeAMCR
Bibliographic record
Abstract
Phytochromes of plants, fungi, algae and bacteria are the photoreceptors that bind linear tetrapyrroles and show reversible photoconversion between red-absorbing form (Pr) and far-redabsorbing form.Cyanobacteriochromes with various spectral properties are the recently emerged photoreceptors that are distinctive relative of the phytochromes.Among them, AnPixJ-GAF2 from cyanobacterium Anabaena sp.PCC 7120 is a novel photoreceptor that covalently binds phycocyanobilin and shows green/red reversible photoconversion.It is suggested that the Pr form of AnPixJ-GAF2, which corresponds to that of phytochrome, is photoconverted to unusual blue-shifted green-absorbing form (Pg) via phytochromelike intermediate states.To get structural insights into this unique photoconversion mechanism, we tried to crystallize AnPixJ-GAF2 in both forms.As a result, we obtained blue crystals of the Pr form by hanging-drop vapor diffusion method.The crystals belong to space group P43212 and contain one monomer in an asymmetric unit.The crystal structure was solved at 1.8 Å resolution by iodide-SAD method.The overall structure and the chromophore structure of the Pr form are very similar to those of the Pr forms of bacterial phytochromes, although relative position of the chromophore to the apoprotein is significantly deviated.In correspondence with the deviation, amino acid residues surrounding the chromophore are quite diverged.Nevertheless, we can point out a common structural feature conserved between the two Pr forms.Moreover, some residues unique to AnPixJ-GAF2 are suggested to be crucial for the formation of the unusual Pg form.These results shed light on the universal and unique aspects of photosensory mechanism of phytochromes and cyanobacteriochromes.
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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 | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".