Molecular dynamics simulations of hybrid and complex type oligosaccharides

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Conformational preferences of hybrid (G1cNAc 1Man 5GIcNAc 2) and complex (GlcNAc 1Man 3GlcNAc 2; GIcNAc 2Man 3GIcNAc 2) type asparagine-linked oligosaccharides and the corresponding bisected oligosaccharides have been studied by molecular dynamics simulations for 2.5 ns. The fluctuations of the core Man-α1,3-Man fragment are restricted to a region around (−30°,−30°) due to a ‘face-to-face’ arrangement of bisecting GIcNAc and the βl,2-GIcNAc on the 1,3-arm. However, conformations where such a ‘face-to-face’ arrangement is disrupted are also accessed occasionally. The orientation of the 1,6-arm is affected not only by changes in X, but also by changes in Φ and ψ around the core Man-αl,6-Man linkage. The conformation around the core Man-α1,6-Man linkage is different in the hybrid and the two complex types suggesting that the preferred values of Φ, ψ and χ are affected by the addition or deletion of saccharides to the a1,6-linked mannose. The conformational data are in agreement with the available experimental studies and also explain the branch specificity of galactosyltransferases.