Equivalency of Binding Sites in Protein−Ligand Complexes Revealed by Time-Resolved Tandem Mass Spectrometry
Bibliographic record
Abstract
Gas phase, time-resolved, thermal dissociation measurements are reported for three protein−ligand complexes, the homodimer α(1 → 3)galactosyltransferase (GTB) with its native disaccharide acceptor, α- l -Fuc p -(1 → 2)-β- d -Gal p, the homotetramer streptavidin and its specific ligand biotin, and the homodimer of wheat germ agglutinin (WGA) and the disaccharide β- d -GlcNAc p -(1 → 6)- d -Gal p . It is shown that protein−ligand interactions that are structurally and thermodynamically equivalent in solution exhibit identical kinetic and energetic stabilities in the gas phase. In contrast, nonequivalent interactions in solution give rise to kinetically nonequivalent interactions in the gas phase. The equivalency of the rate constants measured for the loss of ligand from multiple, equivalent binding sites within a given protein complex is compelling evidence that the binding sites are structurally equivalent in the gas phase. This is the first quantitative experimental evidence for the preservation of elements of structural equivalency within protein complexes upon transfer from solution to the gas phase. This important finding serves as the basis for a new assay, which employs time-resolved tandem mass spectrometry, for evaluating the equivalency of ligand binding sites within proteins and multiprotein complexes in solution.
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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 | 0.001 | 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 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".