Chemical shift dispersion and secondary structure prediction in unfolded and partly folded proteins

Abstract

The intrinsic chemical shift dispersion for 15N, 1HN, 13C(alpha), 1H(alpha), 13C(beta) and 13CO resonances has been evaluated utilizing complete resonance assignment data for unfolded apomyoglobin, together with two other unfolded and five folded proteins, obtained from the literature. The dispersion of 13C(alpha), 1H(alpha), and 13C(beta) resonances for the unfolded proteins is poor, whereas the dispersion of 15N, 1HN and 13CO is much greater, reflecting the sensitivity of these nuclei to the nature of the neighboring amino acid in the primary sequence. By contrast, the dispersion of the 13C(alpha), 1H(alpha), and 13C(beta) nuclei are much greater in the folded proteins, reflecting the well-known dependence of the environments of these nuclei on secondary and tertiary structure. These differences in chemical shift dispersion dictate differences in strategies for resonance assignment in unfolded proteins compared with those most commonly used for folded proteins. Strategies utilizing the superior chemical shift dispersion of the 15N, 1HN and, in particular, the 13CO nuclei, are indicated for use with unfolded or partially folded proteins.