The Sequence-Specific Association of the ETS Domain of Murine PU.1 with DNA Exhibits Unusual Energetics
Bibliographic record
Abstract
PU.1 belongs to the ETS family of transcription factors whose DNA-binding domains recognize purine-rich sequences containing the consensus 5'-GGAA/T-3'. We have characterized the sequence-specific association of the ETS domain of murine PU.1 to the lambdaB site of the Ig(lambda)2-4 enhancer as a function of temperature and pH by electrophoretic mobility shift, filter binding, and CD spectroscopy. From 0 to 25 degrees C, the dissociation equilibrium constant KD is, within experimental uncertainty, insensitive to temperature, and is only a weak function of temperature from 25 to 52 degrees C. van't Hoff analysis yielded a small value of DeltaCp = -2.1 kJ x mol(-1) x K(-1) in phosphate buffer, pH 7.4, containing 250 mM Na+. KD also shows a weak dependence at 25 degrees C on pH from 6.7 to 9.0 in phosphate, cacodylate, and Tris buffers that have disparate heats of ionization. The CD spectrum of the protein-DNA complex could be accounted for by a simple linear combination of the spectra of the free components throughout the binding temperature range. Structural calculations indicate that dehydration of solvent-accessible contact surfaces on the protein and DNA accounts for up to DeltaCp approximately -1 kJ x mol(-1) x K(-1). Taken together, these observations suggest that the hydrophobic effect and, in particular, coupled folding do not contribute significantly to the energetics of sequence-specific association. This is unusual with respect to other sequence-specific protein-DNA interactions for which significant enthalpic contributions and large negative heat capacities are commonly observed.
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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) | 0.001 | 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".