Conformation of Trisialic Acid Lactone: NMR Spectroscopic Analysis and Molecular Dynamics Simulation
Bibliographic record
Abstract
Abstract The conformation of the trisialic acid lactone α2,8‐(NeuAc)3 was analyzed by a combination of NMR spectroscopy, molecular modelling and molecular dynamic (MD) calculations. The interresidue NOEs provided 14 important distance restraints for the molecular simulation, and the final simulated structures showed a root mean square deviation of 0.78 for all superimposed structures. Because of the steric hindrance from the spirobicyclic δ‐lactone, the individual sialic acid pyranose rings are considered essential in the chair 5C2 conformation. In addition, lactone I close to the nonreducing end adopted a half‐chair A2HCB9 conformation, whereas lactone II, which is close to the reducing end adopted a skewed twist‐boat C2SC9 conformation. In the NMR solution structure and in the 1.0‐ns, in‐water MD calculation, the final simulated structures are in the exocyclic torsions (ω7, ω8) = (gauche–anti) surface of the energy adiabatic map, where the global minimum can be found. During the in‐water MD simulation, a slight fluctuation in the structure was observed, reflecting the steady conformation of the lactone and the middle residue of the trisaccharide. These data are consistent with a theoretical approach of polysialic acid (PSA) polylactone with torsions (ω7, ω8) = (65°, 175°) and (Φ, Ψ) = (75.8°, –112.4°). Thus, we conclude that the PSA polylactone is a right‐hand helix with a rotation angle, μ, of 240° and a repeating unit, n, of 1.5 residues. The structural properties of the PSA lactone discussed within this context differ from the helical epitope of G2+ PSA and may serve in future PSA‐related antigen designs. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
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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 | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".