Conformations of gas-phase ions of ubiquitin, cytochrome <i>c</i>, apomyoglobin, and <i>β</i>-lactoglobulin produced from two different solution conformations
Bibliographic record
Abstract
At low pH in solutions of 50% methanol, proteins form expanded denatured states (the "H" state). In 90% methanol, proteins form expanded helical denatured states with artificial alpha-helices (the "H(c)" state). Gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and native and disulfide-reduced beta-lactoglobulin were formed by electrospray ionization (ESI) of the proteins from the H and H(c) states in solution. Both states in solution produce the same charge states in ESI. The conformations of the ions were studied with cross section measurements and gas-phase H/D exchange experiments. The cross sections show that the ions retain considerable folded structure. For a given protein and given charge state, ions produced from the H and H(c) states showed the same cross sections (within approximately 1%). Ions of cytochrome c, apomyoglobin, and native and reduced beta-lactoglobulin of a given charge state showed no differences in H/D exchange level when produced from the H or H(c) state. However, ubiquitin ions produced from the H(c) state consistently exchange fewer ( approximately 13%) hydrogens than ions produced from the H state, suggesting that in this case the gas-phase protein ions retain some memory of their solution conformations.
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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".