Molecular dynamics simulations of the plant-specific insert dimer at pH 3.0
Bibliographic record
Abstract
This study examines the underlying mechanics driving tertiary structure and quaternary conformational changes in silico of the saposin-like domain, the plant-specific insert, of a potato (Solanum tuberosum) aspartic protease as a function of pH. Umbrella sampling was used to determine the free energy change of dissociation of the plant-specific insert at acidic and neutral pH and revealed that a lower barrier to dissociation exists at neutral pH as compared to acidic pH. Furthermore, principal component analysis was used to characterize tertiary structure conformational changes at active (pH4.5)and neutral pH of monomeric plant-specific insert. The results indicate that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin-fold at neutral pH and suggests a potential new structural motif among saposin-like proteins at pH 4.5.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.002 | 0.001 |
| 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".