Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

Abstract

Synchrotron radiation is the most versatile way to explore biological materials in different states: monocrystalline, polycrystalline, solution, colloids and multiscale architectures. Steady improvements in instrumentation have made synchrotrons the most flexible intense X-ray source. The wide range of applications of synchrotron radiation is commensurate with the structural diversity and complexity of the molecules and macromolecules that form the collection of substrates investigated by glycoscience. The present review illustrates how synchrotron-based experiments have contributed to our understanding in the field of structural glycobiology. Structural characterization of protein–carbohydrate interactions of the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution.

CHARMM-GUIGlycan Modelerfor modeling and simulation of carbohydrates and glycoconjugates

“…Experimental methods such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have been widely used to provide the atomic details of biomolecular structural information (Wormald et al 2002). During last decades, X-ray crystallography has been improved substantially with recent advances such as the synchrotron radiation (Perez and de Sanctis 2017). However, despite these technical advances, solving the complex carbohydrate structures remains nontrivial.…”

“…However, despite these technical advances, solving the complex carbohydrate structures remains nontrivial. For example, during the crystallization of glycoproteins, heterogeneity of glycans on the protein surface hinders the crystal packing, and the electron density maps of these glycans are not often fully resolved because of their high flexibility (Perez and de Sanctis 2017). NMR spectroscopy also has been advanced in terms of the labeling strategies such as labeled glycans with stable NMR-active isotopes.…”

Multifaceted Computational Modeling in Glycoscience

“…They offer a variety of data covering oligosaccharides, polysaccharides, glycoproteins, and protein–carbohydrate complexes. These data are associated with experimentally resolved structures, NMR, X-ray and neutron crystallography, cryoEM, and small angle X-ray scattering. Some other databases contain data derived from molecular mechanics or molecular dynamics simulations.…”

Glycans and glycosaminoglycans in neurobiology: key regulators of neuronal cell function and fate

“…While the structural complexity of glycan structures is a daunting subject to investigate [7][8][9][10] powerful analytics have been developed to assist in these investigations. These new methodologies include ion-mobility mass spectrometry [11,12], application of synchtrotron radiation for glycan structural analysis [13], application of high throughput automated N-glycopeptide glycoproteomic identification systems and orbitrap mass spectrometry [14][15][16], integrated systems glycobiology methodology incorporating glycogenomics, glycoproteomics and glycomics [17], fully automated chipelectrospray mass spectrometric analysis for the determination of CS/DS fine structure [18]. GAG microarrays for the analysis of GAG-protein interactions [19][20][21] have also been applied to profiling the sulphation patterns of GAGs to determine growth factor interactive sequences [22,23] and have also identified CS-E tetrasaccharides motifs which act as TNF antagonists [24].…”