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

Abstract

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.

Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags

“…Comprehensive reviews on the physical background of paramagnetic effects in biomolecular NMR have been published by Bertini and co-workers [4,[15][16][17] and summarized in later reviews [18][19][20]. Reviews of applications in structural biology have been published with emphasis on metalloproteins [21][22][23][24][25], carbohydrates [26], solid state NMR [27][28][29], PREs for characterising transient, low-population states [30], protein-protein complexes [31], techniques for measuring PCSs [32], sparse protein labelling [33], paramagnetic tags [34][35][36][37] and paramagnetically induced residual dipolar couplings (RDC) and relaxation enhancements [18]. Additional reviews have focused on the use of PCSs and paramagnetically induced RDCs for structure analysis of flexible proteins [38] and comparisons of protein conformations in solution and in single crystals [39].…”

Recent Advances in NMR Studies of Carbohydrates

“…This approach can be applied also in carbohydrate elucidation, especially to simplify oligosaccharides analysis where signals are overlapping. Recently, Kato and Yamaguchi [42] reviewed the advantages and achievements on this field. Paramagnetic tagging of oligosaccharides has recently been proposed to their conformational analysis.…”

Conformational Analysis of a High‐Mannose‐Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR‐Validated Molecular Dynamics Simulation

“…[9,10] In this approach, ap aramagnetic lanthanide probe is chemically attached to the reducing terminuso ft he target oligosaccharide, in order to observe pseudo-contact shifts (PCSs) as sourceso fg eometricali nformation regarding spatiala rrangements of individual atoms with respectt oa n unpairede lectron. [9,10] In this approach, ap aramagnetic lanthanide probe is chemically attached to the reducing terminuso ft he target oligosaccharide, in order to observe pseudo-contact shifts (PCSs) as sourceso fg eometricali nformation regarding spatiala rrangements of individual atoms with respectt oa n unpairede lectron.…”

“…Recently,w epresented an approach that combines NMR spectroscopy and molecular dynamics (MD) simulations to characterise the conformational spaces of oligosaccharides in solution. [9,10] In this approach, ap aramagnetic lanthanide probe is chemically attached to the reducing terminuso ft he target oligosaccharide, in order to observe pseudo-contact shifts (PCSs) as sourceso fg eometricali nformation regarding spatiala rrangements of individual atoms with respectt oa n unpairede lectron. [9][10][11][12][13] The long-distancei nformation (up to 40 )f rom PCS measurements complements local conformational information provided by scalar coupling andt he nuclear Overhauser effect.…”

“…[9,10] In this approach, ap aramagnetic lanthanide probe is chemically attached to the reducing terminuso ft he target oligosaccharide, in order to observe pseudo-contact shifts (PCSs) as sourceso fg eometricali nformation regarding spatiala rrangements of individual atoms with respectt oa n unpairede lectron. [9][10][11][12][13] The long-distancei nformation (up to 40 )f rom PCS measurements complements local conformational information provided by scalar coupling andt he nuclear Overhauser effect. [14] We used PCS data for validating the conformational ensembles obtained by oligosaccharide MD simulation.T his approach was successfully applied to the exploration of conformational spaceso ccupied by as eries of gangliosidic sialo-oligosaccharides.…”