An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations.
BACKGROUND
The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts.


METHODS
We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1).


RESULTS
Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data.


CONCLUSIONS
The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces.


CONCLUSIONS
The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.
Moriya
Jun
J
Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
Sakakura
Masayoshi
M
Tokunaga
Yuji
Y
Prosser
R Scott
RS
Shimada
Ichio
I
D001665:Binding Sites; D002247:Carbon Isotopes; D018360:Crystallography, X-Ray; D003497:Cyclic N-Oxides / Q000494:pharmacology*; D010450:Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D011485:Protein Binding / Q000187:drug effects; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D013113:Spin Labels; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism
D002247:Carbon Isotopes; D003497:Cyclic N-Oxides; D029701:Saccharomyces cerevisiae Proteins; D013113:Spin Labels; D025801:Ubiquitin; D010450:Endopeptidases; C059237:ubiquitin-Nalpha-protein hydrolase; C001803:tempol