Data requirements for reliable chemical shift assignments in deuterated proteins

Abstract

The information required for chemical shift assignments in large deuterated proteins was investigated using a Monte Carlo approach (Hitchens et al., 2002). In particular, the consequences of missing amide resonances on the reliability of assignments derived from C_α and CO or from C_α and C_β chemical shifts was investigated. Missing amide resonances reduce both the number of correct assignments as well as the confidence in these assignments. More significantly, a number of undetectable errors can arise when as few as 9% of the amide resonances are missing from the spectra. However, the use of information from residue specific labeling as well as local and long-range distance constraints improves the reliability and extent of assignment. It is also shown that missing residues have only a minor effect on the assignment of protein-ligand complexes using C_α and CO chemical shifts and C_α inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process.