Nuclear Magnetic Resonance Spectroscopy In Conjunction Research Articles

Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.

Oligosaccharides play pivotal roles in physiological and pathological contexts primarily through their interactions with proteins on cell surfaces and in intracellular environments. Although crystallographic approaches provide cumulative information about the atomic details of oligosaccharides complexed with proteins, quantitative characterization of the dynamic conformation of uncomplexed oligosaccharides is essential for better understanding of the energetics of carbohydrate–protein interactions. Nuclear magnetic resonance (NMR) spectroscopy is a potentially powerful tool for describing the conformational dynamics of oligosaccharides in solutions at an atomic resolution. However, methodological improvements are needed in applying NMR techniques to the analyses of the dynamic conformations of oligosaccharides during sample preparation, spectral observation, and data interpretation. This presentation outlines our recently developed method of dealing with dynamic conformational ensembles of oligosaccharides using paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics (MD) simulation. A key to this approach is the introduction of a paramagnetic lanthanide ion to the reducing end of oligosaccharides as the source of the atomic long-distance information. We successfully applied this method to the validation of MD-derived conformational spaces occupied by a series of sialyl oligosaccharide moieties of GM1, GM2, and GM3 gangliosides. The applicability of NMR is also revealed for characterizing the dynamic interactions of ganglioside clusters with intrinsically disordered proteins associated with neurodegenerative disorders using ganglioside-embedding small bicelles as nanoscale standardized membrane mimics.

Can pyrolysis-GC/MS be used to estimate the degree of thermal alteration of black carbon?

Very little is known about the macromolecular properties of biomass combustion residues referred to as black carbon (BC). Pyrolysis-gas chromatography–mass spectrometry (Py-GC/MS) was performed on: (i) peat from Spain at 400–1200 °C to investigate the effect of charring on pyrolysis fingerprint and (ii) natural charcoal from Laos in order to link molecular information to published chemical and reactivity parameters. Confirming earlier Py-GC/MS studies, the BC in the artificially charred peat and the natural charcoal produced predominantly benzene, toluene, C 2-benzenes, PAHs and benzonitriles. Furthermore, some charcoal samples produced significant amounts of phenols, methoxyphenols, carbohydrate markers, n-alkanes and n-alkenes upon pyrolysis, reflecting non-charred and weakly charred biomass. A series of pyrolysis product ratios related to the degree of dealkylation of the pyrolysis products (benzene/toluene, naphthalene/C 1-naphthalenes, C 1-naphthalenes/C 2-naphthalenes, benzofuran/C 1-benzofurans and benzonitrile/C 1-benzonitrile) increased with increasing artificial charring (peat) and, for the natural charcoal, these ratios were in accordance with established chemical and reactivity parameters related to charring intensity from other methods: proportion of aromatic C obtained from solid state 13C nuclear magnetic resonance spectroscopy (NMR), the proportion of charred material as estimated from NMR in conjunction with a molecular mixing model (NMR–MMM) and the resistance to acid dichromate oxidation. The alkyl side chains of aromatic pyrolysis products are probably inherited from short chain aliphatic C chains that cross link the predominantly aromatic building blocks of BC, and these linkages seem to disappear with increasing charring intensity. Thus, the degree of thermal alteration of BC can be discerned from the pyrolysis fragmentation pattern.

1H-[13C] NMR measurements of [4-13C]glutamate turnover in human brain.

A limitation of previous methods for studying human brain glucose metabolism, such as positron emission tomography, is that metabolic steps beyond glucose uptake cannot be studied. Nuclear magnetic resonance (NMR) has the advantage of allowing the nondestructive measurement of 13C distribution in specific carbon positions of metabolites. In this study 1H-[13C] NMR spectroscopy in conjunction with volume localization was used to measure the rate of incorporation of 13C isotope from infused enriched [1-13C]glucose to human brain [4-13C]glutamate. In three studies C4 glutamate turnover time constants of 25, 20, and 17 min were measured in a 21-cm3 volume centered in the region of the visual cortex. Based on an analysis of spectrometer sensitivity the spatial resolution of the method can be improved to < 4 cm3. In conjunction with metabolic modeling and other NMR measurements this method can provide a measure of regional rates of the brain tricarboxylic acid cycle and other metabolic pathways.

Self association of Streptomyces subtilisin inhibitor: sedimentation equilibrium and 1H NMR studies.

The self association of Streptomyces subtilisin inhibitor, a dimeric protein molecule of MW 23,000 in an aqueous environment has been investigated by the combined use of sedimentation equilibrium analysis and 1H nuclear magnetic resonance (NMR) spectroscopy. A significant degree of self association was found using the sedimentation equilibrium method in the concentration range between 5 and 20 mg/ml. Furthermore, the use of 1H NMR spectroscopy in conjunction with the sedimentation equilibrium method enabled us to study the self association in a much higher concentration range (up to 60 mg/ml or more). The self association reaction in the concentration range of 10-40 mg/ml fits reasonably well a "successive polymerization model" in which each step of the polymerization reaction consists of the addition of one intrinsic dimer of Streptomyces subtilisin inhibitor to the previously formed polymeric species, with an equilibrium constant common to all the steps of 400 M-1. The 1H NMR chemical shift and line broadening data show that the dimer-dimer interaction probably involves the reactive-site segment of this inhibitor without a significant conformational change in the major part of the protein structure.