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    Emerging out of the “blur”: exploration, evaluation and significance of 3D N-glycans’ structure through molecular dynamic studies

    Harbison, Aoife M. (2021) Emerging out of the “blur”: exploration, evaluation and significance of 3D N-glycans’ structure through molecular dynamic studies. PhD thesis, National University of Ireland Maynooth.

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    Glycosylation is the most abundant and diverse post-translational modification of proteins, contributing to protein folding, trafficking, structural stability and dynamics, and function. Complex N-glycans are a class of glycans found in eukaryotes, sharing a common pentasaccharide core structure. The functionalization of the arms and the branching patterns are specific to different species, while the complexity of the cellular biosynthetic pathways contribute to the broad variety and to the heterogeneity of N-glycan sequences. By understanding at an atomistic level of detail the structural implications of glycan sequence, we can relate the glycan sequence to its function in a given glycoprotein environment. With this ultimate goal in mind I conducted, through conventional and enhanced molecular dynamics (MD) methods, a series of systematic studies of mammalian, plant and invertebrate glycosylation patterns, in order to characterize the intrinsic 3D architecture of different sets of commonly found and synthetic (non-natural) glycan structures. From these results, we were able to disentangle the complexity of N-glycans structure and dynamics through a new 3D representation, which describes N- glycans not only in terms of the monosaccharides sequence, but that also includes anomeric configurations and linkage specificity. Within this framework, we defined N-glycans as structured by specific groups of monosaccharide units, named “glycoblocks”. This formulation incorporates 3D structural information and uniquely dictates the overall conformational landscape of any given N - glycan. With this expanded viewpoint of sequence-to-structure dependencies in complex N-glycans, we applie d this knowledge to glycoproteins, where variation of glycan composition affects its functiona l capabilities. In the two cases presented in this thesis, we determined how changes in the sequence of the N-glycans in the Fc region of IgG1 antibodies affect its effector function, and discovered for the first time a unique functional role of the glycan shield in the SARS-CoV-2 spike protein. In both cases, we observed that the conformational equilibria of complex N-glycans change to promote conformers that can accommodate interactions with the glycoprotein environment, but this adaption does not interfere with the intrinsic 3D glycan architecture, shifting a paradigm commonly assumed in structural biology, where the protein dictates the glycan conformation by actively morphing it. The work presented in this thesis shows an alternative atomistic perspective of N-glycans structure and dynamics, where glycans play a starring role rather than a cameo as a simple protein “decoration”, while the knowledge and insight gained could inform the ad-hoc design and modulation of sequence-to- structure-to-function relationships of complex N-glycans, with applications in glycoengineering and therapeutic and diagnostic strategies.

    Item Type: Thesis (PhD)
    Keywords: exploration; evaluation; significance; 3D N-glycans’ structure; molecular dynamic studies;
    Academic Unit: Faculty of Science and Engineering > Chemistry
    Item ID: 14944
    Depositing User: IR eTheses
    Date Deposited: 19 Oct 2021 15:34
      Use Licence: This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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