Molecular interactions of bacterial outer membrane proteins
Bibliographic record
Abstract
Transport of iron-siderophores and vitamin B12 across the outer membrane (OM) of Gram-negative bacteria requires energy from the proton motive force delivered by the TonB/ExbB/ExbD complex. TonB-dependent OM receptors such as FhuA, FepA, FecA and BtuB possess a Ton box: a conserved motif located proximal to their N-terminus that has been shown to interact with TonB. However, other sites on OM receptors have been proposed to participate in interactions with TonB. To identify novel sites of interactions with TonB, we selected TonB-binding peptides from a random library of peptides displayed on phages. Fifteen peptides displayed sequence similarities to known TonB-dependent OM receptors. Of the fifteen, eight were mapped to regions of FhuA, FepA and FecA for which crystal structures are available. DNA sequences for selected peptides were fused to malE and displayed at the N-terminus of the E. coli maltose binding protein (MBP) for further characterization. Surface plasmon resonance experiments revealed that when the peptides were monovalently displayed on MBP, they retained TonB-binding activity thereby permitting assessments of their binding characteristics. In vitro and in vivo assays demonstrated that only FhuA-mapping peptides could disrupt TonB-FhuA interactions, indicating that TonB selectively binds to multiple regions distinct for each OM receptor.
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".