B-factor analysis suggests that <scp>L</scp>-lysine and <i>R</i>,<i>R</i>-bis-lysine allosterically inhibit Cj.DHDPS enzyme by decreasing its protein dynamics
Bibliographic record
Abstract
In Campylobacter jejuni (Cj.) , dihydrodipicolinate synthase (DHDPS) catalyzes the condensation of pyruvate (pyr) and (S)-aspartate--semi-aldehyde (ASA) to form dihydrodipicolinate. Cj.DHDPS regulates an essential step in the biosynthesis of L-lysine (Lys) and meso-diaminopimelate in bacterial cell wall synthesis. In our study, the normalized B-factors calculated from crystallographic data suggested that Lys and synthetic bisLys inhibitors allosterically inhibit the enzyme by reducing mobility in the regions that undergo transient conformational fluctuations to facilitate the diffusion of substrate Pyr in the active site for catalysis, consistent with published HDX-MS dynamics studies. The normalized B-factors also showed that bisLys allosterically inhibits DHDPS Y110F lysine insensitive mutant by rigidifying these flexible regions. The B-factor analysis suggest that flexibility in the regions (8, 9, 10, 11, L20, and 12) may be vital for substrate turn over and catalysis. Normalized Bfactors of DHDPS and its Y110F mutant with and without inhibitors in different space groups showed similar flexibility patterns, suggesting the reliability of our B-factors analysis.
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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) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
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".