Influence of β-Sheet Structure on the Susceptibility of Proteins to Backbone Oxidative Damage: Preference for <sup>α</sup>C-Centered Radical Formation at Glycine Residues of Antiparallel β-Sheets
Bibliographic record
Abstract
Ab initio calculations at the B3LYP/6-31G(d) level of theory were carried out on selected cyclic hydrogen-bonded (H-bonded) dimers of glycine and alanine as models for β-sheets and on the α C-centered radicals derived from them. The structures mirrored the cycles found in the H-bonded network of parallel and antiparallel β-sheet secondary structure, and were otimized both with and without enforcement of constraints on the Φ,Ψ torsion angles. Transition structures for the migration of an H atom from an α C site to another α C site or to an S atom were located. It was found that the presence of a H-bonded strand of a β-sheet has little effect on the α C−H bond dissociation enthalpy (BDE) of glycine but raises the BDE of other residues by a significant amount. The parallel β-sheet structure and Φ,Ψ angles lead to a significant increase in BDE, relative to the random coil structure, due to loss of captodative stabilization. The antiparallel β-sheet structure and Φ,Ψ angles do not lead to a significant increase in BDE. All residues incorporated in β-sheet secondary structure, with the exception of glycine, are protected from oxidative damage because the α C−H bond is internal to the sheet and inaccessible to oxidizing radicals. Glycine is susceptible to oxidative damage because it has a second α C−H bond which is exposed. Among residues in secondary structures, only glycine is susceptible to damage by weak oxidants such as thiyl radicals and superoxide, provided it is in an antiparallel β-sheet. Radical damage may propagate readily from one strand to another above the β-sheet, but not within the β-sheet. β-Sheet structure narrows the difference between the glycyl α C−H BDE and S−H BDE and facilitates interstrand H atom transfer between the glycyl α C site and the S atom of cysteine.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".