Study of the Molecular Mechanism of W182 in the Bacteriorhodopsin Photocycle
Bibliographic record
Abstract
Bacteriorhodopsin (bR), a seven-transmembrane photoreceptor protein with retinal as the chromophore found in purple membrane of Halobacterium salinarum R1M1, functions as a proton pump. Tryptophan 182 (W182), one of the most conserved aromatic residues within the microbial rhodopsin family proteins, locates in the intracellular side of the retinal binding pocket and plays a very important role in affecting the photocycle and proton pumping activity of bR through the interaction with the retinal polyene chain. In this study, site-directed mutagenesis of W182F and W182A, in combination with in-situ UV-vis absorption spectroscopy, light-induced transient absorption change sepectroscopy, pH titration and molecular dynamics simulations, is employed to elaborate the molecular mechanism the functional role of W182 in the bR photocycle. Our results show that perturbation of W182F to the bR photocycle mainly originates from the disturbance of the retinal binding pocket, while the affect by the mutation of W182A mainly comes from the disruption of the intracellular half-channel of proton translocation pathway. The two mutations have different molecular mechanisms on the effect of proton transport on the extracellular half channel, resulting in a significant difference in the decay of M intermediate state.
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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 | 0.000 |
| 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".