G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination.
A protocol for high-quality structure determination based on G-matrix Fourier transform (GFT) NMR is presented. Five through-bond chemical shift correlation experiments providing 4D and 5D spectral information at high digital resolution are performed for resonance assignment. These are combined with a newly implemented (4,3)D GFT NOESY experiment which encodes information of 4D 15N/15N-, 13C(alipahtic)/15N-, and 13C(aliphatic)/13C(aliphatic)-resolved [1H,1H]-NOESY in two subspectra, each containing one component of chemical shift doublets arising from 4D --> 3D projection at omega1:Omega(1H) +/- Omega(X) [X = 15N,13C(aliphatic)]. The peaks located at the centers of the doublets are obtained from simultaneous 3D 15N/13C(aliphatic)/13C(aromatic)-resolved [1H,1H]-NOESY, wherein NOEs detected on aromatic protons are also obtained. The protocol was applied for determining a high-quality structure of the 14 kDa Northeast Structural Genomics consortium target protein, YqfB (PDB ID ). Through-bond correlation and NOESY spectra were acquired, respectively, in 16.9 and 39 h (30 h for shift doublets, 9 h for central peaks) on a 600 MHz spectrometer equipped with a cryogenic probe. The rapidly collected highly resolved 4D NOESY information allows one to assign the majority of NOEs directly from chemical shifts, which yields accurate initial structures "within" approximately 2 angstroms of the final structure. Information theoretical "QUEEN" analysis of initial distance limit constraint networks revealed that, in contrast to structure-based protocols, such NOE assignment is not biased toward identifying additional constraints that tend to be redundant with respect to the available constraint network. The protocol enables rapid NMR data collection for robust high-quality structure determination of proteins up to approximately 20-25 kDa in high-throughput.
Shen
Yang
Y
Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, USA.
Atreya
Hanudatta S
HS
Liu
Gaohua
G
Szyperski
Thomas
T
D001426:Bacterial Proteins / Q000737:chemistry*; D002247:Carbon Isotopes; D004926:Escherichia coli / Q000737:chemistry; D005583:Fourier Analysis; D008970:Molecular Weight; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017434:Protein Structure, Tertiary
D001426:Bacterial Proteins; D002247:Carbon Isotopes; D009587:Nitrogen Isotopes