Combined use of 13C chemical shift and 1H alpha-13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement.
A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28 degrees C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable C alpha, 96% of the C beta, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C alpha chemical shifts for regions of regular beta-sheet structure. These assignments also provide the basis for interpreting 1H alpha-13C alpha heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high internal mobility, indicated by these 1H alpha-13C alpha HNOE measurements, correlate with locations of residues involved in the putative mEGF-receptor binding site. Using four families of mEGF structures obtained over the last few years, we demonstrate that standard deviations between experimental and back-calculated delta delta C alpha values can be used to monitor the refinement of this protein's structure, particularly for beta-sheet regions. Improved agreement between calculated and observed values of delta delta C alpha is correlated with other measures of structure quality, including lowered values of residual constraint violations and more negative values of conformational energy. These results support the view that experimental conformation-dependent chemical shifts, delta delta C alpha, can provide a reliable source of information for monitoring the process of protein structure refinement and are potentially useful restraints for driving the refinement.
Celda
B
B
Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854.
Biamonti
C
C
Arnau
M J
MJ
Tejero
R
R
Montelione
G T
GT
D000595:Amino Acid Sequence; D000818:Animals; D002247:Carbon Isotopes; D004815:Epidermal Growth Factor / Q000737:chemistry* / Q000235:genetics; D006859:Hydrogen / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D002247:Carbon Isotopes; D011506:Proteins; D004815:Epidermal Growth Factor; D006859:Hydrogen