Paramagnetic Systems in Biochemistry: Solution NMR Studies

Luchinat, Claudio; Parigi, Giacomo

doi:10.1002/9780470034590.emrstm1088

Cited by 4 publications

(2 citation statements)

References 43 publications

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“…While these analyses are invaluable for estimating the conformation of glycosidic linkages, it remains difficult to accurately describe the overall structures of oligosaccharides simply by accumulating such local conformational information. To obtain longer-distance information, paramagnetic effects, as a complementary to NOE or J coupling, have been applied in NMR structural and interaction analyses (11). Recently, paramagnetism-assisted methods have been used for oligosaccharide NMR analysis (12,13) and have validated the conformational dynamics of oligosaccharides originally established by MD simulations (3,9).…”

Section: B Paramagnetic Effects As a Source Of Conformational Informa...mentioning

confidence: 99%

Delineating the Dynamic Conformations of Oligosaccharides by Combining Molecular Simulation and NMR Spectroscopy

Yamaguchi

2020

TIGG

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Oligosaccharides are highly flexible molecules with significant degrees of freedom in their structures. To gain insights into the molecular basis of their biological functions, it is important to describe the conformational dynamics of oligosaccharides. The combination of molecular simulations and nuclear magnetic resonance (NMR) spectroscopy is an effective method for quantitatively interpreting the dynamic behaviors of oligosaccharides. In NMR analyses, paramagnetic-tagging of oligosaccharides provides information on their overall conformations; paramagnetism-assisted NMR methods can facilitate the validation of oligosaccharide dynamical structures originally derived from molecular dynamics simulations. Using this approach, the dynamic conformations of a series of sialyl oligosaccharides found in gangliosides and high-mannose-type oligosaccharides involved in the glycoprotein quality control system were revealed. The quantitative descriptions of their conformational spaces also provided the dynamic views of oligosaccharide-lectin interactions, which complemented static insights from crystallographic analyses. Understanding the oligosaccharidelectin binding process enables the design of oligosaccharides with enhanced affinity and specificity for target proteins.

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Section: B Paramagnetic Effects As a Source Of Conformational Informa...mentioning

confidence: 99%

Delineating the Dynamic Conformations of Oligosaccharides by Combining Molecular Simulation and NMR Spectroscopy

Yamaguchi

2020

TIGG

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“…Paramagnetism-assisted NMR approaches have recently been rekindled in the fields of NMR structural biology, including carbohydrate structural studies [12][13][14][15]. This revival has occurred in the context of the development of molecular biology-based sample preparation, in conjunction with the development of chemically designed paramagnetic probes as intelligence sources [16][17][18][19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides

Kato

Yamaguchi

2015

Glycoconj J

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Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques have recently been applied to a wide variety of biomolecular systems, using sophisticated immobilization methods to attach paramagnetic probes, such as spin labels and lanthanide-chelating groups, at specific sites of the target biomolecules. This is also true in the field of carbohydrate NMR spectroscopy. NMR analysis of oligosaccharides is often precluded by peak overlap resulting from the lack of variability of local chemical structures, by the insufficiency of conformational restraints from nuclear Overhauser effect (NOE) data due to low proton density, and moreover, by the inherently flexible nature of carbohydrate chains. Paramagnetic probes attached to the reducing ends of oligosaccharides cause paramagnetic relaxation enhancements (PREs) and/or pseudocontact shifts (PCSs) resolve the peak overlap problem. These spectral perturbations can be sources of long-range atomic distance information, which complements the local conformational information derived from J couplings and NOEs. Furthermore, paramagnetic NMR approaches, in conjunction with computational methods, have opened up possibilities for the description of dynamic conformational ensembles of oligosaccharides in solution. Several applications of paramagnetic NMR techniques are presented to demonstrate their utility for characterizing the conformational dynamics of oligosaccharides and for probing the carbohydrate-recognition modes of proteins. These techniques can be applied to the characterization of transient, non-stoichiometric interactions and will contribute to the visualization of dynamic biomolecular processes involving sugar chains.

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Paramagnetism-Assisted Nuclear Magnetic Resonance Analysis of Dynamic Conformations and Interactions of Oligosaccharides

Yamaguchi¹,

Kato²

2014

Glycoscience: Biology and Medicine

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Paramagnetic Systems in Biochemistry: Solution NMR Studies

Cited by 4 publications

References 43 publications

Delineating the Dynamic Conformations of Oligosaccharides by Combining Molecular Simulation and NMR Spectroscopy

Delineating the Dynamic Conformations of Oligosaccharides by Combining Molecular Simulation and NMR Spectroscopy

Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides

Paramagnetism-Assisted Nuclear Magnetic Resonance Analysis of Dynamic Conformations and Interactions of Oligosaccharides

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