C alpha and C beta carbon-13 chemical shifts in proteins from an empirical database.

Abstract

We have constructed an extensive database of 13C C alpha and C beta chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical alpha-helix and beta-sheet geometries for C alpha, and of ca. 2 ppm for C beta. The side-chain dihedral angle chi 1 has an effect of up to 0.5 ppm on the C alpha shift, particularly for amino acids with branched side-chains at C beta. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main-chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different phi, psi shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and chi 1 angle, is 0.96 ppm for both C alpha and C beta. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention.