Propagation of Photoinduced Electric Field Changes Through Phytochrome and their Impact on Conformational Transitions
Bibliographic record
Abstract
In phytochromes, photoisomerization of the chromophore and subsequent structural relaxations lead to the functionally essential secondary structure transition of the tongue, a phytochrome-specific protein segment. The coupling mechanism between chromophore and protein structural changes is yet not understood, but electric field changes are discussed to play an important role. In this work, electric field changes in the chromophore binding pocket (CBP) are confirmed to propagate over long distances through the protein and alter the electric field in the tongue region. An experimental-theoretical approach to analyze local electric fields using Stark reporters has been further developed. These are nitrile groups introduced site-specifically into the protein via noncanonical amino acids. The functional integrity of the variants is checked by crystallography and various spectroscopies. For the first time, functionally intact variants with substitutions in the tongue are generated. Based on frequency shifts and relative intensities of the nitrile stretching modes, hydrogen-bonding and noncovalent electric field contributions are separated. The field changes originating in the CBP are transduced to the tongue along a pathway via Phe192. Given a proper direction of the net electric field vector in the tongue region, the magnitude of the field may be sufficient to destabilize the tongue structure.
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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".