Sequence-dependent correction of random coil NMR chemical shifts

Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this tech nique is very reliable for folded proteins, application to unfolded protein s reveals significant deviations from measured random coil shifts for certa in nuclei. While some of these deviations can be ascribed to residual struc ture in the unfolded protein, others are clearly caused by local sequence e ffects. In particular, the amide nitrogen, amide proton, and carbonyl carbo n chemical shifts are highly sensitive to the local amino acid sequence. We present a detailed, quantitative analysis of the effect of the 20 naturall y occurring amino acids on the random coil shifts of N-15(H), H-1(N), and ( CO)-C-13 resonances of neighboring residues, utilizing complete resonance a ssignments for a set of five-residue peptides Ac-G-G-X-G-G-NH2. The work in cludes a validation of the concepts used to derive sequence-dependent corre ction factors for random coil chemical shifts, and a comprehensive tabulati on of sequence-dependent correction factors that can be applied for amino a cids up to two residues from a given position. This new set of correction f actors will have important applications to folded proteins as well as to sh ort, unstructured peptides and unfolded proteins.