Protein chemical shift analysis: a practical guide

Proper protein chemical shift analysis requires careful experimental measurements and the implementation of standardized referencing procedures. In this article we outline the steps necessary to ensure proper chemical shift referencing and the selection criteria for choosing appropriate "random coil" amino acid chemical shift values for predicting, comparing, and assigning 1H, 13C, and 15N resonances in proteins. By making use of these standardized conditions we demonstrate how several recently developed methods, namely homologous assignment techniques and empirical chemical shift contour maps (or hypersurfaces), can significantly improve the accuracy of chemical shift prediction for 1H, 13C, and 15N nuclei. In addition to illustrating the potential utility of chemical shift prediction, we also outline procedures for identifying secondary structure elements through heteronuclear chemical shift analysis and further demonstrate how empirical shift contour maps can actually be used to refine, and more importantly generate, reasonably good three-dimensional protein structures.Key words: NMR, chemical shift, prediction, structure, protein.

The acidic specific capsular polysaccharide of Rhodococcusequi serotype 3. Structural elucidation and stereochemical analysis of the lactate ether and pyruvate acetal substituents

The specific capsular polysaccharide produced by Rhodococcusequi serotype 3 was found to be a high-molecular-weight acidic polymer composed of D-glucose, D-galactose, D-glucuronic acid, 4-O-[(S)-1-carboxyethyl]-D-mannose, and pyruvic acid in equal molar proportions. Structural analysis, employing a combination of chemical and nuclear magnetic resonance techniques, established that the polysaccharide is composed of linear repeating tetrasaccharide units,[Formula: see text]in which (R)-1-carboxyethylidene groups bridge the O-2 and O-3 positions of the β-D-glucuronic acid residues. The 1H and 13C NMR resonances of the native and depyruvulated serotype 3 polysaccharides were fully assigned by homo- and heteronuclear chemical shift correlation methods. The absolute configurations of the lactate-substituted mannopyranosyl residues and the pyruvate acetals were determined from 1H–1H NOE measurements on the intact polysaccharide. Unequivocal determination of the absolute chirality of the 4-O-[(S)-1-carboxyethyl]-β-D-mannopyranose residues was achieved by 1H–1H NOE measurements on an acetylated lactone derivative of the glycose.