Conformational Dynamics of a Central Trisaccharide Fragment of the Le<sup>a</sup>Le<sup>x</sup> Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations
Bibliographic record
Abstract
Abstract Certain carbohydrate structures are recognized as cancer antigens, and identification of these and relevant epitopes are essential in fighting the disease. The trisaccharide β‐ D ‐Glc p NAc‐(1→3)‐β‐ D ‐Gal p ‐(1→4)‐β‐ D ‐Glc p NAc‐OMe represents a model for the central region of the Le a Le x hexasaccharide and it has herein been investigated by 1D 1 H, 1 H‐NOESY experiments to obtain effective interresidue proton–proton distances as well as by 2D J‐HMBC experiments to determine transglycosidic 3 J CH coupling constants. Molecular dynamics (MD) simulations using explicit water as solvent and three different carbohydrate force fields, namely, GLYCAM06, PARM22/SU01, and CHARMM2011, were employed for the interpretation of experimental data. Overall, the force field based MD simulations are able to reproduce the experimental data and the ψ torsion angle at the β‐(1→3)‐linkage is concluded to be flexible. In addition, different minor states were present for the three force fields with either anti‐ ψ or non‐ exo ‐anomeric conformations. Transitions between the exo ‐anomeric and the non‐ exo ‐anomeric conformations for the φ torsion angle at the β‐(1→4)‐linkage in one of the MD simulations were analyzed in detail. It was found that hydrogen‐bonding water molecules, interresidue hydrogen bonds and the transitions between antiperiplanar and synperiplanar conformations for the τ H torsion angle of an N‐acetyl group were all essential in the description of the glycosidic transition process. In particular, the transition of τ H may be a general way of regulating other transitions into less populated but biologically important conformational regions.
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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 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".