Identification of N-terminal helix capping boxes by means of 13C chemical shifts.
We have examined the 13C alpha and 13C beta chemical shifts of a number of proteins and found that their values at the N-terminal end of a helix provide a good predictor for the presence of a capping box. A capping box consists of a hydrogen-bonded cycle of four amino acids in which the side chain of the N-cap residue forms a hydrogen bond with the backbone amide of the N3 residue, whose side chain in turn may accept a hydrogen bond from the amide of the N-cap residue. The N-cap residue exhibits characteristic values for its backbone torsion angles, with phi and psi clustering around 94 +/- 15 degrees and 167 +/- 5 degrees, respectively. This is manifested by a 1-2 ppm upfield shift of the 13 C alpha resonance and a 1-4 ppm downfield shift of the 13C beta resonance, relative to their random coil values, and is mainly associated with the unusually large value of psi. The residues following the N-cap residue exhibit downfield shifts of 1-3 ppm for the 13C alpha resonances and small upfield shifts for the 13C beta ones, typical of an alpha-helix.
Gronenborn
A M
AM
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.
Clore
G M
GM
D000595:Amino Acid Sequence; D000818:Animals; D002147:Calmodulin / Q000737:chemistry; D002247:Carbon Isotopes; D002417:Cattle; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D015847:Interleukin-4 / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012332:RNA, Heterogeneous Nuclear; D016914:Ribonuclease H / Q000737:chemistry; D012261:Ribonucleoproteins / Q000737:chemistry; D014359:Trypsin Inhibitor, Kazal Pancreatic / Q000737:chemistry
D002147:Calmodulin; D002247:Carbon Isotopes; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D011506:Proteins; D012332:RNA, Heterogeneous Nuclear; D012261:Ribonucleoproteins; D015847:Interleukin-4; D014359:Trypsin Inhibitor, Kazal Pancreatic; D016914:Ribonuclease H