Bibliographic record
Abstract
The pH range for Compound I formation of horseradish peroxidase (2.5 to 11) is the largest for any known enzyme reaction. A key part of the reaction is proton transfer from hydrogen peroxide to distal His42. This proton is retained to complete formation of a water leaving group as the ferryl porphyrin π-cation radical is formed. How can the imidazolium side chain of His42 retain a proton at very high pH? And how can it give up the proton when required at very low pH? The answer is rearrangement of electronic charge through Electron Density Circuits (EDCs) in the protein matrix. An increase of at least 9 p Ka units, which occurs on the imidazole side chain of His42 as the Compound I reactive intermediate is formed, is facilitated by an EDC. A reverse EDC facilitates proton transfer to form the water leaving group. The pathway of the EDC involves the heme, its propionate side chains, Arg41, and His42. The occurrence of EDCs in chymotrypsin reactions reinforces the nucleophilic attack, and the subsequent electron and proton transfers. They also can shift p Ka values. The catalytic triad of chymotrypsin is Ser195, His57, and Asp102. The currently accepted one-proton transfer mechanism involves Ser195 and His57, with Asp102 being regarded as too acidic to accept a proton. A comparatively small shift in the p Ka value of Asp102 is all that is required to make it a proton acceptor from His57 so a two-proton mechanism may occur.
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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".