Using the chemical shift anisotropy tensor of carbonyl backbone nuclei as a probe of secondary structure in proteins.

This study seeks to establish that the chemical shift anisotropy (CSA) tensor of the backbone carbonyl ((13)C') nucleus is a useful indicator of secondary structure elements in proteins. The CSA tensors of protein backbone nuclei in different secondary structures were computed for experimentally determined dihedral angles using ab initio methods and by calculating the CSA tensor for a model peptide over the entire dihedral angle space. It is shown that 2D and 3D cluster plots of CSA tensor parameters for (13)C' nuclei are able to distinguish between different secondary structure elements with little to no overlap. As evidenced by multinuclear 2D plots, the CSA of the (13)C' nucleus when correlated with different CSA parameters of the other backbone nuclei (such as C(alpha) or (1)H(alpha)) is also useful in secondary structure identification. The differentiation of alpha-helix versus beta-sheet motifs (the most populated regions of the Ramachandran map) for experimentally determined values of the carbonyl CSA tensor for proteins ubiquitin and binase (obtained from the literature) agrees well with the quantum chemical predictions.

Mapping NMR chemical shift anisotropy parameters of backbone nuclei onto secondary structure elements in proteins.

There has been much recent progress in using NMR chemical shift anisotropy (CSA) parameters to gain information about secondary structure content in proteins. This paper focuses on the comparison of CSA tensors of different backbone nuclei (namely 13C(a), 13C', 15N, 1H(a), 1H(N)) of all twenty amino acids appearing in well- defined secondary structures such as helices and sheets. Dihedral angle information of these backbone nuclei in different secondary structure elements has been extracted from experimentally determined structures of proteins deposited in the protein databank. The CSA tensors of these backbone nuclei have been computed for the corresponding dihedral angles using ab initio quantum chemical methods. It is shown that 2D correlated plots of a novel set of CSA parameters (r,t), that define the magnitude and shape of the anisotropy, are extremely useful in identifying secondary structure content. Further, multinuclear correlations between these CSA parameters can clearly distinguish between various secondary structure elements such as helices and sheets.