Journal of Chemical Information and Modeling
Journal of Chemical Information and Modeling
4 years ago

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes
Chris Oostenbrink, Aysegül Turupcu
In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing in N- and O-glycosylated proteins using a bottom up approach. We report the conformational free-energy landscapes of all relevant glycosidic linkages as obtained from local elevation simulations and subsequent umbrella sampling. To the best of our knowledge, this represents the first complete conformational library for the construction of N- and O-glycan structures. Next, we systematically study the effect of neighboring residues, by extensively simulating all relevant trisaccharides and one tetrasaccharide. This allows for an unprecedented comparison of disaccharide linkages in large oligosaccharides. With a small number of exceptions, the conformational preferences in the larger structures are very similar as in the disaccharides. This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples.

Publisher URL: http://dx.doi.org/10.1021/acs.jcim.7b00351

DOI: 10.1021/acs.jcim.7b00351

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