Density functional calculations of 15N chemical shifts in solvated dipeptides

Cai, Ling, Fushman, David, and Kosov, Daniel S. (2008) Density functional calculations of 15N chemical shifts in solvated dipeptides. Journal of Biomolecular NMR, 41 (2). pp. 77-88.

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Abstract

We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on 15N 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 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard β-sheet and α-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 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.

Item ID: 26208
Item Type: Article (Research - C1)
ISSN: 1573-5001
Keywords: chemical shielding tensor, chemical shift calculation, dipeptides, solvent effect, nitrogen-15, density-functional calculation
Date Deposited: 10 Apr 2013 02:13
FoR Codes: 02 PHYSICAL SCIENCES > 0299 Other Physical Sciences > 029901 Biological Physics @ 50%
03 CHEMICAL SCIENCES > 0307 Theoretical and Computational Chemistry > 030701 Quantum Chemistry @ 50%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970102 Expanding Knowledge in the Physical Sciences @ 100%
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