Mutagenesis of the substrate binding site of protein disulfide isomerase
Bibliographic record
Abstract
Protein disulfide isomerase (PDI) is the most abundant and best characterized member of the extensive PDI family of proteins found in the endoplasmic reticulum. PDI plays an important role in protein folding. It is composed of four thioredoxin-like domains denoted as a-b-b'-a'. Recent studies have identified a hydrophobic surface on the b' domain as the main binding site for the unfolded protein substrates of PDI. Here, the main hydrophobic residues of the b' domain were mutated in a bb' construct and tested for their ability to bind to the 14-residue mastoparan peptide. Most of the mutants had a significant effect on the binding affinity. In reverse experiments the mastoparan peptide was mutated and NMR titrations used to determine the orientation of the peptide on the bb' binding surface. Finally, the catalytic a and a' domains were individually tested for binding to unfolded RNaseA by NMR. Neither catalytic domain exhibited any direct interaction with the unfolded substrate.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".