Is N-acetyl-d-glucosamine a rigid 4C1 chair?

摘要

Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure–activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid 4C₁ chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3–5 μs to reach a conformational equilibrium, which comprised a metastable 4C₁ chair that underwent 4C₁ ↔ 1C₄ transitions at a predicted forward rate of 0.8 μs−1 with an average 1C₄-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid 4C₁ chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 μs−1) and a more stable 4C₁ conformer (0.2 kcal mol−1), suggesting that pivotal 3D intermediates (particularly 2S_O, 1S₅ and B_2,5) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.