Table 1.
Glycosidic linkage conformers for model N-linked oligosaccharides
| Torsion | Molecule (s) | SIM (ns) (ϕ, ψ)° | SIM (μs) (ϕ, ψ)° | NMR (ϕ, ψ)° | X-raya (ϕ, ψ)° |
|---|---|---|---|---|---|
| α(1–3) | |||||
| Man-Manb | 7, 8 | (70,−100) | (70,−100) (160,−80) | (80,−100) (60,180) | (72,−121) |
| Fuc-GlcNAcc | 2 | (−70,−100) | (−70,−100) (−150,−145) | (−72,−96) | (−72,−99) |
| Fuc-GlcNAc | 4 | (−70,−110) | (−75,−105) (−145,−140) (−80,75) | — | — |
| α(1–4) | |||||
| Fuc-GlcNAcd | 1 | (−70,135) | (−70,135) | (−77,142) | |
| α(1–6) | |||||
| Man-Manb | 7, 8 | (70,−160) | (70,−160) | (64,180) (64,60) | (67,179) (60,94) |
| α(2–3) | |||||
| NeuAc-Galc | 1, 2, 3 | (60,−120) | (60,−120) (−50,−140) | (60,−120) (−60,−120) (20,170) | (69,−125) |
| β(1–2) | |||||
| GlcNAc-Mane(1→3) | 8 | (−90,−70) | (−90,−70) (60,−90) | (−92,−83) | (−80,−98) (58,−87) |
| GlcNAc-Man (1→6) | 8 | (−90,−70) | (−90,−70) | — | — |
| β(1–3) | |||||
| Gal-GlcNAcd | 1 | (−70,−110) | (−70,−110) | (−70,−99) | (−74,−132) |
| β(1-4) | |||||
| Gal-GlcNAcc | 2 | (−70,130) | (−70,130) | (−74,138) | (−71,132) |
| Gal-GlcNAc | 3 | (−70,130) | (−70,130) (−70,−50) (−150,−100) | — | — |
Torsion states derived from the simulations (SIM) are from μs-simulations (μs) and the initial 100 ns of dynamics (ns) for 1–4, 7, and 8. All μs data are calculated from 10 μs simulations except 2 (25 μs). Prior refinements from solution NMR6, 30, 55, 56 and X-ray29 (in various environments) are tabulated.
a
Ref. 29.
b
Ref. 6.
c
Ref. 32.
d
Ref. 57.