Characterization of the DNA Binding Activity of the ZFY Zinc Finger Domain
Bibliographic record
Abstract
The ZFY protein is a member of one of the most interesting classes of polydactyl zinc finger proteins. It has a domain of 13 tandem zinc fingers that is organized with an internal repeat of odd-even finger pairs. It has been proposed that each finger pair interacts with six base pairs within a turn of the double helix, the downstream linker crossing the minor groove to place the next finger pair on the following turn of the DNA. Yet putative binding sites for the full-length ZFY protein appear to consist of a six-base AGGCCY consensus sequence that is present in one or two copies. In this study the equilibrium binding of two ZFY-derived zinc finger peptides to 4R DNA with tandem copies of the consensus sequence was investigated. The ZFY5 peptide contains fingers 5-13, including four odd-even finger pairs, and the ZFY11 peptide contains fingers 11-13 and has one odd-even finger pair. Both peptides bound to 4R DNA with equal affinities, forming a bimolecular complex that is mediated by the downstream AGGCCY motif. The additional odd-even finger pairs in ZFY5 made no measurable difference in the mechanism of DNA binding compared to ZFY11. The effects on the DNA-protein interaction of mutations in the 4R DNA and in the key alpha-helical residues of fingers 11-13 indicate that the binding of ZFY to DNA is mediated by the interaction of the GGCC core base pairs with fingers 12 and 13. These results demonstrate that the even-odd repeats in the ZFY zinc finger domain do not make significant contributions to DNA binding.
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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 | 0.000 |
| 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".