@article {533,
	title = {A rapid, nonradioactive assay for measuring heparan sulfate C-5 epimerase activity using hydrogen/deuterium exchange-mass spectrometry.},
	journal = {Methods Mol Biol},
	volume = {1229},
	year = {2015},
	month = {2015},
	pages = {209-19},
	abstract = {<p>Heparin and heparan sulfate (HS) glycosaminoglycans have important roles in anticoagulation, human development, and human diseases. HS C5-epimerase, which catalyzes the epimerization of GlcA to IdoA, is a crucial enzyme involved in the biosynthesis of heparin-related biomolecules. Here, we describe a detailed method for measuring the total activity of HS C5-epimerase that involves the following steps: H/D exchange upon epimerization of the substrate with HS C5-epimerase, low-pH nitrous acid treatment of the substrate, the separation of low-pH nitrous acid-cleaved disaccharides using HPLC, and mass spectrometry analysis. This nonradioactive method is rapid and sensitive and, importantly, allows us to study the reversible nature of HS C5-epimerase.</p>
},
	keywords = {Animals, Biocatalysis, Carbohydrate Epimerases, Chromatography, Ion Exchange, Chromatography, Liquid, Deuterium Exchange Measurement, Disaccharides, Enzyme Assays, Glucuronic Acid, Heparitin Sulfate, Humans, Iduronic Acid, Mass Spectrometry, Sf9 Cells},
	issn = {1940-6029},
	doi = {10.1007/978-1-4939-1714-3_19},
	author = {Babu, Ponnusamy and Victor, Xylophone V and Raman, Karthik and Kuberan, Balagurunathan}
}
@article {718,
	title = {Development of the structural core and of conformational heterogeneity during the conversion of oligomers of the mouse prion protein to worm-like amyloid fibrils.},
	journal = {J Mol Biol},
	volume = {423},
	year = {2012},
	month = {2012 Oct 19},
	pages = {217-31},
	abstract = {<p>Understanding how structure develops during the course of amyloid fibril formation by the prion protein is important for understanding prion diseases. Determining how conformational heterogeneity manifests itself in the fibrillar and pre-fibrillar amyloid aggregates is critical for understanding prion strain phenotypes. In this study, the formation of worm-like amyloid fibrils by the mouse prion protein has been characterized structurally by hydrogen-deuterium exchange coupled to mass spectrometry. The structural cores of these fibrils and of the oligomer on the direct pathway of amyloid fibril formation have been defined, showing how structure develops during fibril formation. The structural core of the oligomer not on the direct pathway has also been defined, allowing the delineation of the structural features that make this off-pathway oligomer incompetent to directly form fibrils. Sequence segments that exhibit multiple local conformations in the three amyloid aggregates have been identified, and the development of structural heterogeneity during fibril formation has been characterized. It is shown that conformational heterogeneity is not restricted to only the C-terminal domain region, which forms the structural core of the aggregates; it manifests itself in the N-terminal domain of the protein as well. Importantly, all three amyloid aggregates are shown to be capable of disrupting lipid membrane structure, pointing to a mechanism by which they may be toxic.</p>
},
	keywords = {Amino Acid Sequence, Amyloid, Animals, Deuterium Exchange Measurement, Kinetics, Mice, Models, Molecular, Molecular Sequence Data, Prion Proteins, Prions, Protein Conformation, Protein Folding},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2012.06.040},
	author = {Singh, Jogender and Sabareesan, A T and Mathew, M K and Udgaonkar, Jayant B}
}
