Supplemental Data Assembly and Channel Opening in a Bacterial Drug Efflux Machine
Bibliographic record
Abstract
A putative chloride binding site in TolC. The C2 structure, viewed at the junction of the transmembrane and helical subdomains. The purple dotted sphere indicates a putative chloride that interacts with the exposed amide groups at the end of the α-helix. A water molecule is also found in the pocket (yellow dotted sphere) supported by interaction with a histidine imidazole. The mesh represents the 2Fo-Fc electron density map contoured at 1σ. Similar density in the corresponding position is observed in the P212121 form. Anion binding is likely to serve purely a structural role and appears to be a unique feature of the TolC channel, not present in the crystal structure of the homologous VceC and OprM outer membrane proteins. 1 Figure S2 Asymmetry of the TolC open state. Opening and asymmetry of the periplasmic end of the TolC channel as observed in the available crystal structures. The subunit non-equivalence in the crystal structure is most clearly seen in the inter-protomer distances. The outer rim of the TolC channel as defined by G365 is opening up in both novel crystal forms as compared with the closed state. The displacement of this residue also indicates clearly the asymmetric opening of the channel. 2 Figure S3 A docking model of the interaction of the AcrA hairpn (yellow) with TolC C2 structure. The residues highlighted in red include K383 and R390 from TolC and D149 from AcrA. The numbering of AcrA is according to the full-length sequence of the protein as represented in the 2F1M PDB entry. 3 Protein purification C41(DE3) and C43(DE3) cells were grown in 2xYT media at 37°C, induced at OD600 of roughly 0.6, and then were grown for 12 hours at 24 o C. Cells were harvested in lysis buffer (20 mM Tris-Cl pH 8.0, 150 mM NaCl, 20 mM MgCl2, complete EDTA free proteinase inhibitor cocktail (Roche), supplemented with DNase I and lysozyme), lysed using an Emulsiflex C5 cell homogenizer (Avestin, Canada) and cell pellet removed by centrifugation at 10,000 x g. The membrane fraction from the supernatant was pelleted by centrifugation at 100,000 x g for 3 hours. The membranes were
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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 | 0.002 | 0.007 |
| Meta-epidemiology (narrow) | 0.003 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.003 |
| Bibliometrics | 0.002 | 0.005 |
| Science and technology studies | 0.003 | 0.000 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.006 | 0.002 |
| Research integrity | 0.003 | 0.004 |
| Insufficient payload (model declined to judge) | 0.419 | 0.148 |
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".