Structural biology of energy-transducting proteins from «Escherichia coli»
Bibliographic record
Abstract
The cell envelope of Gram-negative bacteria such as Escherichia coli is composed of an outer (OM) and cytoplasmic membrane (CM), which enclose a space known as the periplasm. For acquisition of essential nutrients, bacteria must transport molecules across both membranes. The import of certain scarce nutrients, such as iron and vitamin B12, requires the input of energy; however, the OM is devoid of any source of energy. To drive the transport of scarce nutrients across the OM, bacteria use the proton motive force of the CM. The TonB–ExbB–ExbD protein complex located within the CM is responsible for harnessing the energy of this proton gradient and transducing it to OM receptors. While the existence and the role of this complex has been investigated many years ago by genetic means and by in vivo crosslinking experiments, structural and functional aspects remain largely unknown. To date, only partial structures of periplasmic domains of TonB and ExbD are known. Additionally, information on the structure of the complex as well as stoichiometry has not been deduced. We have therefore designed a strategy for the co-expression and co-purification of ExbB and ExbD in complex. Here we produced milligram amounts of pure ExbB–ExbD; size-exclusion chromatography revealed that our samples were homogenous and monodisperse. Observation of our samples by negative-staining electron microscopy revealed uniform particles from which 2D reconstructions were generated. These reconstructions suggested a pentameric and perhaps cylindrical arrangement for the complex. In parallel, crystallization trials have identified promising leads. Our optimization efforts have led to the successful detergent exchange of the protein complex from dodecyl maltoside to decyl maltoside, to GNG-12 and to MNG-28; the latter two amphiphiles are proprietary and of undisclosed structure. We also adopted an NMR detergent quantitation method to standardize amounts of detergent in samples bound for crystalliz
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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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 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 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".