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.
Elavarasi
S Begam
SB
Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India.
Kumari
Amrita
A
Dorai
Kavita
K
D016880:Anisotropy; D002244:Carbon / Q000737:chemistry*; D008954:Models, Biological; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
D011506:Proteins; D002244:Carbon