Structural Changes in the Nickel‐Responsive Regulator NikR from <i>Helicobacter pylori</i>
Bibliographic record
Abstract
Helicobacter pylori is a pathogenic bacterium estimated to infect 50% of the global population and causes peptic ulcers, gastritis, and gastric cancer. H. pylori is able to survive the fluctuating pH levels of the stomach mainly due to expression of two enzymes – urease and [NiFe]‐hydrogenase – that require nickel as an essential cofactor. Therefore, regulation of nickel concentration is crucial in order to avoid toxicity while maintaining an adequate supply. This is achieved by the nickel‐responsive transcription factor NikR (HpNikR), which maintains intracellular nickel homeostasis through binding the promoters of various genes, including those encoding nickel storage and import factors, and activating or repressing their transcription. HpNikR also plays a role in acid acclimation and there is evidence that its DNA‐binding activity can be modulated by changes in pH. It is therefore likely that there are promoter specific conformations exhibited by HpNikR that are sensitive to both nickel concentration and pH. However, the mechanisms by which nickel and pH activate DNA binding remain unclear. In this work, a series of mutants at key secondary structural elements were created as targets for labeling with a 19 F probe and 19 F‐NMR was used to uncover how nickel and pH influence the HpNikR conformational changes required for binding to different promoters. Support or Funding Information This work was supported in part by funding from the Canadian Institutes of Health Research.
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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 | 0.000 |
| 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".