Crystallographic and kinetic analysis of temperature-variant isozymes
Bibliographic record
Abstract
Biological catalysts have evolved to optimally work at a temperature regime at which their host organism thrives. The structural differences between homologous enzymes that work at temperature extremes can further our understanding of the underpinnings of enzyme function. In general, thermophilic enzymes have been described as "less-flexible" at room temperature, where their psychrophilic counterparts are "more flexible". The interplay between temperature, function, and dynamics is a relevant field of interest as it has impact upon the field of protein engineering. Our lab has a large host of structural and kinetic/functional data on our model enzyme, a mesophilic phosphoenolpyruvate carboxykinase (PEPCK), which must undergo a series of conformational changes to work optimally. Specifically, one dynamic element of PEPCK is a lid which transitions approximately 40 (tip-to-tip) to orient and protect substrates during catalysis. This lid is proposed to be sensitive to temperature fluctuations, where at lower temperatures it would become more rigid (closed) and at high temperatures more flexible (open). Both non-optimal conditions would impact its function, highlighting a delicate balance of dynamic motions. We have successfully crystallized a psychrophilic PEPCK which can be used to further investigate its dynamic properties. Structural and kinetic comparison of these variants can show us how an enzyme thermally adapts highly dynamic elements to maintain functional harmony.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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) | 0.002 | 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".