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Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins

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 ana...

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Autores principales: Přerovská, Tereza, Pavlů, Anna, Hancharyk, Dzianis, Rodionova, Anna, Vavříková, Anna, Spiwok, Vojtěch
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8230119/
https://www.ncbi.nlm.nih.gov/pubmed/34179088
http://dx.doi.org/10.3389/fmolb.2021.682858
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author Přerovská, Tereza
Pavlů, Anna
Hancharyk, Dzianis
Rodionova, Anna
Vavříková, Anna
Spiwok, Vojtěch
author_facet Přerovská, Tereza
Pavlů, Anna
Hancharyk, Dzianis
Rodionova, Anna
Vavříková, Anna
Spiwok, Vojtěch
author_sort Přerovská, Tereza
collection PubMed
description 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.
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spelling pubmed-82301192021-06-26 Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins Přerovská, Tereza Pavlů, Anna Hancharyk, Dzianis Rodionova, Anna Vavříková, Anna Spiwok, Vojtěch Front Mol Biosci Molecular Biosciences 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. Frontiers Media S.A. 2021-06-07 /pmc/articles/PMC8230119/ /pubmed/34179088 http://dx.doi.org/10.3389/fmolb.2021.682858 Text en Copyright © 2021 Přerovská, Pavlů, Hancharyk, Rodionova, Vavříková and Spiwok. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Přerovská, Tereza
Pavlů, Anna
Hancharyk, Dzianis
Rodionova, Anna
Vavříková, Anna
Spiwok, Vojtěch
Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title_full Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title_fullStr Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title_full_unstemmed Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title_short Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins
title_sort structural basis of the function of yariv reagent—an important tool to study arabinogalactan proteins
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8230119/
https://www.ncbi.nlm.nih.gov/pubmed/34179088
http://dx.doi.org/10.3389/fmolb.2021.682858
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