Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 41, Issue 2, Pages 77-88Publisher
SPRINGER
DOI: 10.1007/s10858-008-9241-7
Keywords
chemical shielding tensor; chemical shift calculation; dipeptides; solvent effect; nitrogen-15; density-functional calculation
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We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on N-15 chemical shielding in proteins. We used N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from protein GB3. The conducting polarizable continuum model was employed to include the effect of solvent in the density functional calculations. Our calculations for NMA show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic N-15 chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard beta-sheet and alpha-helical conformations ranges from 0.8 to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing > 6100 amino acid residues. The orientation of the N-15 chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.
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