Abstract
The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: the full-length glycan composition, including linkage details for the glycosidic bonds. The developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.
Highlights
IntroductionThe attachment of carbohydrates to macromolecules extends the capabilities of cells to convey significantly more information than what is available through protein synthesis and the expression of the genetic code alone
Glycosylation is used as a switch to modulate protein activity [1]; glycosylation plays a crucial part in folding/unfolding pathways of some proteins in cells [2,3]; the level of N-glycan expression regulates the adhesiveness of a cell [4]; glycosylation plays a role in immune function [5] and cellular signalling [5,6]
Our newly developed computational bridge between structural biology and glycomics databases makes the detection of gross modelling errors easier, as demonstrated by the following examples
Summary
The attachment of carbohydrates to macromolecules extends the capabilities of cells to convey significantly more information than what is available through protein synthesis and the expression of the genetic code alone. Glycosylation is used as a switch to modulate protein activity [1]; glycosylation plays a crucial part in folding/unfolding pathways of some proteins in cells [2,3]; the level of N-glycan expression regulates the adhesiveness of a cell [4]; glycosylation plays a role in immune function [5] and cellular signalling [5,6]. The influenza virus uses the haemagglutinin glycoprotein to recognise and bind sialic acid decorations of human cells in the respiratory tract [7]. Glycosylation is used by pathogens to evade the host’s immune system via glycan shields [8,9,10], and thereby to delay
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