Functional discoveries from crystal structures of proteins from<i>M. tuberculosis</i>
Bibliographic record
Abstract
Genomic-DNA analysis on number of organisms is now accomplished.Using these information, comprehensive structure analysis of transcription factors for their structure-based functional understanding is in progress.Our research target is transcription factors including putative ones from hyper-thermophilic archaeon P.horikoshii, mesophilic bacteria C.glutamicum and vertebrates H.sapience.Target proteins were cloned, over-expressed, purified and purified proteins were tried crystallization for X-ray crystal structure analysis.We had already succeeded in structure analysis of three of them, PH1161 [1] and PH1932 from P.horikoshii and CGL2612 from C.glutamicum.PH1161 protein is a homologue of bacterial transcriptional activator TenA, and PH1932 and CGL2612 are homologue of transcriptional repressor protein ArsR and QacR, respectively.As a further functional analysis, recognition DNA sequences of PH1932 and CGL2612 proteins were analyzed using the SELEX (Systematic Evolution of Ligand by EXponential enrichment) method.The SELEX suggested several consensus sequence of DNA recognized by these proteins, providing indispensable information to reveal their biological functions.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".