Abstract
Arabinogalactan proteins are very abundant, heavily glycosylated plant cell wall proteins. They are intensively studied because of their crucial role in plant development as well as their function in plant defence. Research of these biomacromolecules is complicated by the lack of tools for their analysis and characterisation due to their extreme heterogeneity. One of the few available tools for detection, isolation, characterisation, and functional studies of arabinogalactan proteins is Yariv reagents. Yariv reagent is a synthetic aromatic glycoconjugate originally prepared as an antigen for immunization. Later, it was found that this compound can precipitate arabinogalactan proteins, namely, their ß-D-(1→3)-galactan structures. Even though this compound has been intensively used for decades, the structural basis of arabinogalactan protein precipitation by Yariv is not known. Multiple biophysical studies have been published, but none of them attempted to elucidate the three-dimensional structure of the Yariv-galactan complex. Here we use a series of molecular dynamics simulations of systems containing one or multiple molecules of ß-D-galactosyl Yariv reagent with or without oligo ß-D-(1→3)-galactan to predict the structure of the complex. According to our model of Yariv-galactan complexes, Yariv reagent forms stacked oligomers stabilized by π-π and CH/π interactions. These oligomers may contain irregularities. Galactan structures crosslink these Yariv oligomers. The results were compared with studies in literature.
Highlights
Arabinogalactan proteins (AGPs) represent an extremely heterogeneous group of plant cell wall proteoglycans, which together with moderately glycosylated extensins and minimally glycosylated proline-rich proteins belong to the superfamily of hydroxyproline-rich glycoproteins (HRGPs, Showalter et al, 2010)
AGPs contain signal sequences directing them to the extracellular location and often can be found anchored to the plasma membrane by the glycosylphosphatidylinositol (GPI) anchor (Seifert and Roberts, 2007)
AGPs are being extensively studied especially in higher plants because they have been shown to play an essential role in plant growth, development, reproduction, signaling, and stress responses (Nguema-Ona et al, 2012, Nguema-Ona et al, 2013; Lamport and Várnai 2013; Olmos et al, 2017; Ma et al, 2018; Su and Higashiyama 2018; Seifert 2020)
Summary
Arabinogalactan proteins (AGPs) represent an extremely heterogeneous group of plant cell wall proteoglycans, which together with moderately glycosylated extensins and minimally glycosylated proline-rich proteins belong to the superfamily of hydroxyproline-rich glycoproteins (HRGPs, Showalter et al, 2010). There are various tools to study these proteins including monoclonal antibodies, β-Yariv reagents, specific degradation of AGP sugar chains, chemical synthesis, and bioinformatics approach (Su and Higashiyama, 2018). Galactan trisaccharide was chosen as a minimal model oligosaccharide (Figure 1) This choice was driven by the fact that Yariv is selective for 1→3 linked oligomers, for which a trisaccharide is the smallest representative. Another oligosaccharide studied in this study is hexassacharide (Figure 1) because it was shown that oligosaccharides with more than five units form stable complexes with the Yariv reagent (Kitazawa et al, 2013)
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