Ab initio studies of amide-¹⁵N chemical shifts in dipeptides: Applications to protein NMR spectroscopy

The results of calculations aimed at providing a better understanding of how protein structural parameters affect ¹⁵N nuclear magnetic resonance (NMR) chemical shifts, using ab initio quantum chemical methods, are reported. The results support previous empirical observations that the two backbone dihedral angles closest to the peptide group (ψ_i-1 and φ_i) have the largest effects on ¹⁵N chemical shifts, contributing a range of about 20 ppm. The adjacent torsion angles φ_i-1 and ψ_i have a smaller contribution, up to 8 ppm, but also need to be considered when predicting protein chemical shifts. Different side chain conformations produce chemical shift variations of up to ∼4 ppm. Hydrogen bonding to peptide carbonyl groups can also contribute to ¹⁵N shielding, as can longer range electrostatic field effects, but these effects are smaller than those due to torsions. Calculations of ¹⁵N chemical shifts of nonhelical alanine residues in a Staphylococcal nuclease, dihydrofolate reductase from Lactobacillus casei, and ferrocytochrome c₅₅₁ from Pseudomonas aeruginosa show a good correlation between experimental observation and ab initio prediction, but the shielding of helical residues is overestimated by ∼8 ppm, due most likely to electric field effects from the helix dipole. ¹⁵N NMR chemical shifts are very sensitive probes of protein conformation and have potential for structure validation, although at present they are less useful than are ¹³C shifts for prediction and refinement, because of their more complex dependence on multiple torsional, as well as electrostatic field, effects.