A Bittersweet Computational Journey among Glycosaminoglycans

Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiologi...

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Autores principales: Paiardi, Giulia, Milanesi, Maria, Wade, Rebecca C., D’Ursi, Pasqualina, Rusnati, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156566/
https://www.ncbi.nlm.nih.gov/pubmed/34063530
http://dx.doi.org/10.3390/biom11050739
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author Paiardi, Giulia
Milanesi, Maria
Wade, Rebecca C.
D’Ursi, Pasqualina
Rusnati, Marco
author_facet Paiardi, Giulia
Milanesi, Maria
Wade, Rebecca C.
D’Ursi, Pasqualina
Rusnati, Marco
author_sort Paiardi, Giulia
collection PubMed
description Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge.
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spelling pubmed-81565662021-05-28 A Bittersweet Computational Journey among Glycosaminoglycans Paiardi, Giulia Milanesi, Maria Wade, Rebecca C. D’Ursi, Pasqualina Rusnati, Marco Biomolecules Review Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge. MDPI 2021-05-15 /pmc/articles/PMC8156566/ /pubmed/34063530 http://dx.doi.org/10.3390/biom11050739 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Paiardi, Giulia
Milanesi, Maria
Wade, Rebecca C.
D’Ursi, Pasqualina
Rusnati, Marco
A Bittersweet Computational Journey among Glycosaminoglycans
title A Bittersweet Computational Journey among Glycosaminoglycans
title_full A Bittersweet Computational Journey among Glycosaminoglycans
title_fullStr A Bittersweet Computational Journey among Glycosaminoglycans
title_full_unstemmed A Bittersweet Computational Journey among Glycosaminoglycans
title_short A Bittersweet Computational Journey among Glycosaminoglycans
title_sort bittersweet computational journey among glycosaminoglycans
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156566/
https://www.ncbi.nlm.nih.gov/pubmed/34063530
http://dx.doi.org/10.3390/biom11050739
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