Three-dimensional Structure and Function of Replication Protein A
Bibliographic record
Abstract
Replication protein A (RPA), the most abundant single-stranded DNA (ssDNA)-binding protein in eukaryotes, participates in nearly every aspect of DNA maintenance and is necessary for cell viability. RPA wasoriginally identified as an indispensable component ofDNA replication of simian virus 40 (SV40) (Wobbe et al.1987; Fairman and Stillman 1988; Wold and Kelly 1988).Later, it was also found to be involved in DNA recombination, and in the nucleotide excision, base excision, andrecombinational pathways of DNA repair (Wold 1997;Iftode et al. 1999). Although it is clear that RPA is essential in all of these processes, its exact role is not totally understood. RPA has no enzymatic activity; it binds tightlyto ssDNA in a defined orientation and establishes proteinprotein contacts with components of the DNA replication, recombination, and repair machinery. Since ssDNAis a common intermediate in DNA replication, recombination, and repair, one possible function that can be attributed to RPA is to protect ssDNA from nucleolyticdegradation or other modifications. RPA may also have amore active role of reducing the conformational entropyof ssDNA. Applying a mechanical tension on an ssDNAtemplate significantly increases the rate of DNA polymerization by decreasing the entropy of DNA and, consequently, the energetic cost of the work done by thepolymerase (Wuite et al. 2000). The applied tension onssDNA may mimic the effect of RPA binding. The ability of RPA to simultaneously bind ssDNA and mediateinteractions with multiple proteins may be necessary forthe ordered assembly of DNA replication and repaircomplexes if for no other reason than to establish the correct orientation of the first proteins in the pathway withrespect to the 5′-3′ polarity of DNA (de Laat et al. 1998;Iftode and Borowiec 2000). In fact, recent data suggestthat RPA participates not only in the initiation, but also inthe subsequent steps of the ordered assembly of replication and repair proteins by means of a competition-basedmechanism where proteins trade places for binding to acommon site on RPA (Yuzhakov et al. 1999; Kowalczykowski 2000; Mer et al. 2000b)...
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".