Protein chemical shift analysis: a practical guide

Proper protein chemical shift analysis requires careful experimental measur ements and the implementation of standardized referencing procedures. In th is article we outline the steps necessary to ensure proper chemical shift r eferencing and the selection criteria for choosing appropriate "random coil " amino acid chemical shift values for predicting, comparing, and assigning H-1, C-13, and N-15 resonances in proteins. By making use of these standar dized conditions we demonstrate how several recently developed methods, nam ely homologous assignment techniques and empirical chemical shift contour m aps (or hypersurfaces), can significantly improve the accuracy of chemical shift prediction for H-1, C-13, and N-15 nuclei. In addition to illustratin g the potential utility of chemical shift prediction, we also outline proce dures for identifying secondary structure elements through heteronuclear ch emical shift analysis and further demonstrate how empirical shift contour m aps can actually be used to refine, and more importantly generate, reasonab ly good three-dimensional protein structures.