Characterization of the effects of biosynthetically incorporated tryptophan analogues in rat parvalbumin F102W and structure-function studies of tryptophanyl-tRNA synthetase.
Bibliographic record
Abstract
Fluorescence spectroscopy of tryptophan residues is a valuable tool for dissecting the structure, function and dynamic behaviour of proteins. An important step in method development is the use of tryptophan analogues with unique photophysical properties that extend the utility of intrinsic protein fluorescence. Two difficulties limit the use of these analogues. Their structure, while similar to that of tryptophan, can perturb native protein structure resulting in misfolding or inactivity. There are also problems from an inability of tryptophanyl-tRNA synthetase (TrpRS) to use these analogues as a substrate in the tRNA charging reaction. The tryptophan residue in rat parvalbumin F102W is buried in the highly hydrophobic and conformationally restrained environment of the protein's core. Differences in hydrophobicity, size and hydrogen bonding capability of tryptophan analogues were expected to affect both the structure and stability of this protein once incorporated at position 102. All analogues were successfully incorporated. Incorporation of 5-hydroxytryptophan proved difficult and required an optimization of incubation temperature during induction. 7-azatryptophan and 5-hydroxytryptophan destabilized the protein while 4-fluorotryptophan, 5-fluorotryptophan and 6-fluorotryptophan stabilized the protein. Single tryptophan mutants of Bacillus stearothermophilis TrpRS showed large structural changes when forming the 4-fluorotryptophan-AMP intermediate. These changes were limited to the formation of the first intermediate. This is rationalized as a large global change occurring across both subunits that could affect substrate binding. H. sapien tryptophanyl-tRNA synthetase was expressed and found to be active when using tryptophan analogues as substrates. Differences in fluorescence properties of the intermediate suggest a unique environment at the active site.Dept. of Chemistry and Biochemistry. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2002 .A23. Source: Dissertation Abstracts International, Volume: 64-01, Section: B, page: 0183. Adviser: Arthur G. Szabo. Thesis (Ph.D.)--University of Windsor (Canada), 2002.
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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) | 0.000 | 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 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".