By using molecular dynamics (MD) simulations we have further analyzed the conformational preferences of hybrid (GlcNAc1Man5GIcNAC2) and complex (GlcNAc1Man3GicNAC2; GlcNAC2Man3GlcNAC2) type asparagine-linked oligosaccharides and the corresponding bisected oligosaccharides that are the substrates for various Golgi glycosyltransferases and precursors in the biosynthesis of glycoproteins. The results of these simulations, which have been published in the International Journal of Biological Macromolecules (1996:18;101-14), show that the fluctuations of the core Man-alphal,3-Man fragment are restricted to a region around (-30degrees-30degrees) due to a 'face-to-face' arrangement of bisecting GlcNAc and the beta1,2-GlcNAc on the 1,3-arm and are in agreement with the conclusions drawn from NMR studies. However, occasionally conformations where such a 'face-to-face' arrangement is disrupted are also accessed. The orientation of the 1,6-arm is affected not only by changes in khi, but also by changes in phi and psi around the core Man-alphal,6-Man linkage, as was observed previously in the MD simulations of the heptasaccharide moiety of the Erythrina corallodendron lectin. The conformation around the core Man-alphal,6-Man linkage is different in the hybrid and the two complex types suggesting that the preferred values of phi, psi, and khi are affected by the addition or deletion of saccharides to the alphal,6-linked mannose. The conformational data are in agreement with the available experimental studies and also explain the branch specificity of galactosyltransferases. alpha-Lactalbumin, a protein that modifies the substrate specificity of beta-1,4-galactosyltransferase, does not bind any sugar even though it does show structural similarity with the A, B, C, D, E, & F sugar binding sites of lysozyme. Lysozyme binds a hexasaccharide, (-NAM-NAG-)3, in the A to F sites, where D-E is the catalytic site. Computer modeling methods are being used to address the question """"""""why alpha-lactalbumin does not bind any sugar while as its homologous protein c-type lysozyme, with which it has both sequence and structural homology, does bind and hydrolyse oligosaccharides""""""""? Computer modeling approach is being used to study the binding of monosaccharides to C, B and D sites of alpha-lactalbumin and lysozyme.

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National Cancer Institute (NCI)
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National Cancer Institute Division of Basic Sciences
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Schuyler, Adam D; Jernigan, Robert L; Qasba, Pradman K et al. (2009) Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins 74:760-76