Flavin binding site in Vibrio harveyi Luciferase
Bibliographic record
Abstract
Luciferase catalyzes the emission of blue-green light and is the central feature of bacterial bioluminescence. The three-dimensional structure of the bacterial luciferase apo-enzyme determined by X-ray crystallography has revealed the detailed landscape of the enzyme active site, however, the absence of a structure with bound substrate has impeded the understanding of the enzyme mechanism by which luciferase interacts with substrates and catalyzes their conversion into light emission. This thesis describes three research projects that focus on the molecular conformation of flavin in the active site of bacterial luciferase. Based on available structure-activity data as guidance, the first project deduces the binding conformation of the luciferase bound flavin by computer modeling. The second research project investigates the binding microenvironment of flavin, and assigns specific functions to the structural modules (amino acid residues), which coordinate flavin in the proposed model. The third project verifies the validity of the proposed model with mutational analysis of the binding site residues, and points out the possibility of altering the visible emission color of bacterial bioluminescence by redesigning luciferase. The last chapter concludes the thesis with the discussion of the structural mechanism of luciferase catalysis, and the perspectives for the engineering of luciferase variants that emit different light colors.
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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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".