Data requirements for reliable chemical shift assignments in deuterated proteins.
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 alpha and CO or from C alpha and C beta 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 alpha and CO chemical shifts and C alpha inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process.
Hitchens
T Kevin
TK
Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA 15213, USA.
McCallum
Scott A
SA
Rule
Gordon S
GS
D000577:Amides; D000595:Amino Acid Sequence; D003903:Deuterium; D029968:Escherichia coli Proteins; D008024:Ligands; D009010:Monte Carlo Method; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry; D017852:Phosphotransferases (Nitrogenous Group Acceptor) / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*
D000577:Amides; D029968:Escherichia coli Proteins; D008024:Ligands; D011506:Proteins; D003903:Deuterium; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; D017852:Phosphotransferases (Nitrogenous Group Acceptor); C022360:phosphoenolpyruvate-protein phosphotransferase