Characterization of protein secondary structure from NMR chemical shifts

Physicochemical Characterization of Complex Drug Substances: Evaluation of Structural Similarities and Differences of Protamine Sulfate from Various Sources

“…This chemical shift range observed for the backbone amide protons (see insert in Fig. 6) is consistent with a predominately random coil conformation for protamine at pH 4 in solution (24,26). Thus, NMR spectroscopy further confirmed the results obtained in FTIR and CD spectroscopy that all the five protamine sulfate lots have very similar amino acid composition and are predominantly random coil conformation in solution.…”

Insights on Structure and Function of a Late Embryogenesis Abundant Protein from Amaranthus cruentus: An Intrinsically Disordered Protein Involved in Protection against Desiccation, Oxidant Conditions, and Osmotic Stress

“…Uni-dimensional 1 H-NMR spectrum provides general overviews of protein structure because chemical shifts values are strongly related with the presence of different elements of secondary structure (Wishart et al, 1991; Mielke and Krishnan, 2009). Particularly, H N amide protons are widespread from 6 to 11 ppm in proteins with a well-defined tri-dimensional folding with a high content of α-helix and β-strand.…”

DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure

“…These procedures bias the final predictions towards regions of Ramachandran space that are highly populated. In our hands both TALOS and PREDITOR are regularly inaccurate for residues in non-canonical structures, such as 3 10 helices and conformations with positive values of /, in part because neither approach can reliably handle glycine or residues that precede prolines. The recently updated TALOS+ package can make acceptable estimates for a greater proportion of residues [14], but all three methods return boundary ranges for / and w that typically fail to reflect the accuracy of the prediction.…”

“…Although isotropic chemical shift measurements promise to reveal much, their dependence on structure is not straightforward, complicated by the influence of many atoms in the protein system on the electronic environment around each nucleus. Recent advances have begun to elucidate the complex relationship between shift and conformation [2], from low resolution attempts to classify elements of secondary structure [3][4][5][6][7][8][9][10], through prediction of the backbone dihedral angles / and w [11][12][13][14], to the generation of high resolution protein structures solely from chemical shift and primary sequence information [15][16][17][18][19][20]. Blind determination of full three dimensional structures is currently restricted to smaller proteins (<150 amino acids), is less accurate than traditional NOE-based NMR methods [15][16][17] and can fail in regions where backbone chemical shift measurements are not available, for example due to the effects of conformational exchange broadening in exposed loops.…”