Fogarty, Carl A. (2023) Characterisation of structure-to-function relationships in free and protein-linked glycans by computer simulation techniques. PhD thesis, National University of Ireland Maynooth.

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Abstract

Complex carbohydrates (glycans) are the most abundant biopolymers in Nature. They functionalize proteins and lipids and form a thick coating on the surface of cells, which facilitates the cell’s movement and its interaction with toxins, viruses, and other cells. This is usually accomplished through a ”handshake” recognition between proteins and glycans. Many proteins have their surfaces decorated with glycans (or glycosylated). It is known that the type of glycans present can influence the protein’s function and stability. In my extensive research, I employed thorough molecular dynamics (MD) simulations to delve into the subtle yet crucial modifications affecting the N-glycan architecture in various biological contexts. I investigated modifications involving core α(1-3)-Fuc and β(1-2)-Xyl in standard N-glycoforms found in plants and invertebrates, known to be immunogenic in humans. MD simulations disclosed notable changes in the 3D structure and dynamics of N-glycans, underscoring their pivotal role in selective recognition by lectin receptors and antibodies. The detailed, atomistic-level analysis emphasised that these functionalizations predominantly impact the local spatial vicinity of the modified monosaccharide. Consequently, a novel approach was proposed that employs structural 3D units or glycoblocks to predict the architecture of N-glycans. My focus shifted to characterising human oligomannose N-glycans free and glycosylated on the CD16a Fc γ Receptor(FcγRIIIa). Through conventional MD simulations, I unraveled a complex architecture shaped by a network of transient hydrogen-bonding interactions. Specific glycoforms exhibited distinct sets of constraints, determining the accessibility for further functionalisation and shedding light on glycoform-specific interactions in modulating antibody-dependent cellular cytotoxicity (ADCC). Then I investigated the impact of SARS-CoV-2 S N-glycosylation variations on protein function. MD simulations revealed that altering the size of N-glycans at specific sites influenced the stability of receptor binding domain (RBD) conformations, providing insights into the structural dynamics of the virus and potential implications for viral infectivity. Comparative analysis of ancestral sequences suggested the contribution of changes in the topology of the glycan shield to the increased activity of SARS-CoV-2 relative to closely related coronaviruses. Lastly, I explore the role of C-mannosylation in Thrombospondin Type 1 Repeats (TSR) in proteins, focussing on TSR 1 in BAI1. MD simulations highlighted position-specific effects and the profound influence of the glycan type on stability. The transition between glycan types, including α-mannose, α-rhamnose, α-quinovose, and β-mannose, unveiled nuanced impacts on folding energy and structural dynamics, offering valuable insights for therapeutic protein engineering and drug development. These findings enhance our understanding of the intricate relationships between glycan dynamics and protein function, paving the way for novel approaches in glycoscience research and therapeutic interventions.

Item Type:	Thesis (PhD)
Keywords:	Characterisation; structure-to-function relationships; free and protein-linked glycans; computer simulation techniques;
Academic Unit:	Faculty of Science and Engineering > Chemistry
Item ID:	19037
Depositing User:	IR eTheses
Date Deposited:	15 Oct 2024 10:12
URI:
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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