Structural studies of the conjugative entry exclusion protein from the F and R100 plasmids, TraG
Bibliographic record
Abstract
Conjugative type IV secretion systems (T4SS) transmit mobile DNA elements in bacteria and are a significant contributor to the evolution of antibiotic resistance. Of the proteins produced from the F and R100 plasmids of Escherichia coli; the representative conjugative plasmids of gram-negative bacteria, TraG is among the largest and consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain denoted TraG*. Each domain has its own function, the membrane bound N-terminal domain is involved in pilus assembly while TraG* is bifunctional. In the donor cell, it interacts with TraN within the outer membrane to facilitate mating pair stabilisation. However, TraG* is also essential in preventing redundant DNA transfer through its interaction with a cognate TraS in the inner membrane of the recipient cell when the recipient carries the same plasmid. Thermofluor experiments showed N-terminal truncation mutants of TraG* displayed higher stability relative to full-length TraG*, and SEC MALS provides evidence of higher levels of aggregation in the full-length protein relative to the Nterminal truncation mutants. SEC-MALS-SAXS was performed to obtain low-resolution structural models to visualize the conformational changes resulting from the truncation, and crystal trials of TraG* mutants provide evidence of a higher propensity for the crystallisation of N-terminal truncations of TraG*. The 45 N-terminal residues of TraG* are predicted to be highly dynamic, possibly serving as a flexible linker between two independently functioning domains.
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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 | 0.000 | 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".