Superposition of chemical shifts in NMR spectra can be overcome to determine automatically the structure of a protein

[摘要] We are here addressing the problem of the automatic determination of a protein structure at atomic resolution, by using only the signal recorded on three spectra: 2D15N HSQC, 3D15N NOESY-HSQC and TOCSY-HSQC. A modified version of the neural network RESCUE (J.L. Pons and M.A. Delsuc,J. Biomol. NMR15(1999), 15−26), N15-RESCUE, is developed in order to predict the amino-acid type from only the15N, HN, Hαand Hβchemical shifts. The spatial distances between protein residues are estimated by automatic comparison of columns extracted from a 3D15N NOESY-HSQC spectrum, using the FIRE method (T.E. Malliavin, P. Barthe and M.A. Delsuc,Theor. Chem. Accts106(2001), 91−97). The predictions provided by both FIRE and N15-RESCUE methods are then used for the determination of a preliminary NMR structure of the protein p8. A mean RMSD value of 2.31±0.86 Å is observed between the coordinates of heavy atoms from helicesαI andαII, and theαIII helix is taking random orientations with respect to the other helices. This random orientation is a consequence of the lack of predicted proximities betweenαIII andαII, and is in agreement with other independent observations made on p8 structure.

[学科分类] 光谱学