Structural, Functional and Dynamic Studies of F Plasmid T4SS Proteins
Bibliographic record
Abstract
The transfer of genetic material within a bacterial population through the process of conjugation distributes novel genetic elements for survival in unique environments. Bacterial conjugation is important to public health as the spread antibiotic resistance genes among bacteria results in multi-drug resistance. Indeed, approximately 70% of bacteria that cause hospital-acquired infections are resistant to at least one antibiotic. Conjugative systems, such as the F plasmid of Escherichia coli, consist of proteins that share similarities to type IV secretion systems (T4SS). T4SS proteins of the F plasmid form a membrane spanning protein complex and surface exposed pilus. The periplasmic T4SS proteins TraF, TraW and TrbC play important roles during the F pilus assembly and DNA transfer. Functional analysis of a series of TraF mutants has shown that modification to TraF abolishes pilus synthesis and in turn F plasmid conjugation. In addition, dynamic analysis of TraF using time-resolved hydrogen-deuterium exchange mass spectrometry has revealed a well structured C-terminal thioredoxin-like domain and a more dynamic N-terminal domain that is predicted to interact with companion T4SS protein TraH. In addition, interaction analysis of the putative pore forming proteins TraW and TrbC indicate that the C-terminal domain of TrbC is not required for interaction with TraW, unlike previous models of F T4SS assembly. Rather the C-terminal domain of TraW preferentially interacts with the N-terminal domain of TrbC. These studies are providing a clearer picture of the structures and interactions that occur within the F T4SS assembly during the conjugative process.
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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".