Bibliographic record
Abstract
Rhomboid proteases are integral membrane serine proteases that catalyze peptide bond hydrolysis in biological membranes. Little is currently known about the interaction of enzyme and substrate. Coarse-grained molecular dynamics simulations in hydrated lipid bilayers are employed herein to study the interaction of the E. coli rhomboid protease GlpG (ecGlpG) with the transmembrane domain (TMD) of the substrate Spitz. Spitz does not associate with ecGlpG exclusively at the putative substrate gate near TMD 5. Instead, there are six prominent and stable interaction sites, including one between TMDs 1 and 3, with the closest enzyme-substrate proximity occurring at the ends of helical TMDs or in loops. Bilayer thinning is observed proximal to ecGlpG, but there is no evidence of additional thinning of the bilayer upon interaction with substrate. We suggest that the initial interaction between enzyme and substrate, or substrate capture event, is not limited to a single site on the enzyme, and may be driven by juxtamembrane electrostatic interactions. The findings are of additional interest because catalytically inactive rhomboids (iRhoms) are now known to interact with the substrates of their catalytically active counterparts and to antagonize the enzyme-driven pathways.
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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 | 0.000 | 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 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".