The Paired Domain of Pax3 Contains a Putative Homeodomain Interaction Pocket Defined by Cysteine Scanning Mutagenesis
Bibliographic record
Abstract
Pax3 is a transcription factor that plays an important regulatory role during neurogenesis, myogenesis, and formation of neural crest cell derived structures. Pax3 has two DNA binding domains, a paired domain (PD) and paired-type homeodomain (HD) that show complete interdependence for DNA binding, with mutations in one domain impairing DNA binding by the other domain. Cooperative interactions between the PD and HD of Pax3 suggest that the two domains may physically interact for DNA binding. Site-specific modification with thiol reagents in single cysteine Pax3 mutants was used to determine which segment of the PD may interact with the HD. Twenty-four single cysteine mutants were independently introduced in the second alpha-helix (alpha2, positions 59-80) and in the beta-hairpin structure (positions 40-41) at the amino terminal portion of the PD. These mutants were tested for their ability to bind to PD (P6CON, P3OPT) and HD-specific DNA targets (P2), and the effect of treatment with N-ethylmaleimide on these binding properties was established. In the PD, single cysteine mutants CL/Q40C, CL/I59C, CL/V60C, CL/P69C, CL/S70C, CL/I72C, CL/S73C, CL/L76C, CL/V78C, and CL/S79C displayed NEM sensitive DNA binding toward both PD and HD targets. Three PD mutants (CL/L41C, CL/A63C, and CL/H64C) showed unusual behavior, with DNA binding to PD targets being NEM insensitive while DNA binding by the HD was abrogated by NEM treatment. Three-dimensional modeling of the NEM sensitive PD cysteine mutants reveal that they are not randomly distributed, but rather that they cluster in a hydrophobic pocket. We propose that this hydrophobic pocket may serve as a docking site for the HD during DNA binding by the intact protein.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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".