Domain coupling in the ABC transporter system BtuCD/BtuF: molecular dynamics simulation, normal mode analysis and protein-protein docking
Bibliographic record
Abstract
ATP binding cassette (ABC) transporters form a large class of proteins that use energy from ATP to power transport across biological membranes against the thermodynamic gradient. They consist of two water-soluble domains that are responsible for ATP hydrolysis and two transmembrane domains that form the transport pathway. In addition, they often interact with auxiliary domains or proteins that may regulate the transport process or deliver substrates. Recent crystal structures have revealed the molecular architecture of ABC transporters. We are using a combination of computational techniques to study the dynamics of ABC transporters, the possible mechanism by which the energy of ATP hydrolysis is used for transport, and the interactions between the different domains. We present an overview of our current understanding of the interactions between the domains of the vitamin Bu importer BtuCD, new simulation results from the BtuCD protein, and two models of the interactions of BtuCD with its substrate binding protein BtuF.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".