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

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: 2D 15 NH SQC, 3D 15 N 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 the 15 N, HN, Hα and Hβ chemical shifts. The spatial distances between protein residues are estimated by automatic comparison of columns extracted from a 3D 15 N 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 A is observed between the coordinates of heavy atoms from helices α Ia ndαII, and the αIII helix is taking random orientations with respect to the other helices. This random orientation is a consequence of the lack of predicted proximities between αIII and αII, and is in agreement with other independent observations made on p8 structure.