Parameter optimization for calculation of proton chemical shift in protein

Abstract

The magnetic anisotropy effects of peptide group in structured protein on proton chemical shift have been investigated using trialanine modeling. The structure dependent part of chemical shift of CαH of the second amino acid residue was assumed to come purely from the magnetic anisotropy effects of C=O and C-N bonds of peptide in the direct neighborhood and thus to be dependent on Ø and Ψ angle of this depeptide. A set of dipeptide models with different Ø and Ψ angles were calculated using known algorithm to emphasize the role of parameters used in the equation. Comparison of sets of different parameters resulted in an optimized parameters which could reproduce the statistical chemical shift values observed in proteins with respect to the secondary conformation.