Preface for the Special Issue on the Exploration of the Multifaceted Roles of Glycosaminoglycans: GAGs

Nikitovic, Dragana; Pérez, Serge

doi:10.3390/biom11111630

Cited by 5 publications

(1 citation statement)

References 19 publications

(20 reference statements)

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“…In addition, GAGs’ high flexibility and periodicity render these molecules profoundly challenging to analyze using experimental techniques only [ 30 – 31 ]. Thus, computational approaches could be efficiently used to gain insight into protein–GAG interactions that take place at single-molecule levels [ 32 ]. More than a complementary tool, computational approaches provide a better understanding of the role of individual interaction partners (including GAGs, solvent, and ions) by bringing often new and experimentally inaccessible details [ 33 – 34 ].…”

Section: Introductionmentioning

confidence: 99%

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Marcisz,

Anila,

Gaardløs

et al. 2023

Beilstein J. Org. Chem.

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In the past few decades, glycosaminoglycan (GAG) research has been crucial for gaining insights into various physiological, pathological, and therapeutic aspects mediated by the direct interactions between the GAG molecules and diverse proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is essential to explain their biological functions. In this study, the umbrella sampling (US) approach is used to pull away a GAG ligand from the binding site and then pull it back in. We analyze the binding interactions between GAGs of three types (heparin, desulfated heparan sulfate, and chondroitin sulfate) with three different proteins (basic fibroblast growth factor, acidic fibroblast growth factor, and cathepsin K). The main focus of our study was to evaluate whether the US approach is able to reproduce experimentally obtained structures, and how useful it can be for getting a deeper understanding of GAG properties, especially protein recognition specificity and multipose binding. We found that the binding free energy landscape in the proximity of the GAG native binding pose is complex and implies the co-existence of several binding poses. The sliding of a GAG chain along a protein surface could be a potential mechanism of GAG particular sequence recognition by proteins.

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Section: Introductionmentioning

confidence: 99%

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Marcisz,

Anila,

Gaardløs

et al. 2023

Beilstein J. Org. Chem.

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Modification of hyaluronic acid to enable click chemistry photo-crosslinking of hydrogels with tailorable degradation profiles

Buckley¹,

Montgomery

Szank³

et al. 2023

International Journal of Biological Macromolecules

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Multifaceted Computational Modeling in Glycoscience

Pérez

Makshakova

2022

Chem. Rev.

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Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate−carbohydrate interactions, glycolipids, and N-and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics. CONTENTS 5.1. N-and O-Linked Glycans 5.2. Structure and Dynamics of SARS-CoV-2 5.3. Structure, Function, and Dynamics of Glycolipids 6. Polysaccharides 6.1. Polysaccharides in Solution 6.2. Polysaccharides in the Solid-State 6.3. Lipolysaccharides in Membranes 7. Protein Carbohydrate Interactions 7.1. Presentation: Synopsis of the Protein Families 7.2. Insights into Glycosyltransferases 7.3. Insights into Glycosyl Hydrolases 7.4. Enzymatic Degradation of Polysaccharides in the Solid-State

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Preface for the Special Issue on the Exploration of the Multifaceted Roles of Glycosaminoglycans: GAGs

Abstract: Glycosaminoglycans (GAGs) are linear, anionic polysaccharides that consist of repeating disaccharides of hexosamine and hexuronic acid [...]

Cited by 5 publications

References 19 publications

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

Modification of hyaluronic acid to enable click chemistry photo-crosslinking of hydrogels with tailorable degradation profiles

Multifaceted Computational Modeling in Glycoscience

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