Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation

Abstract

A server (CheShift) has been developed to predict (13)C(alpha) chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the phi, psi, omega, chi1 and chi2 torsional angles for all 20 naturally occurring amino acids. Their (13)C(alpha) chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted (13)C(alpha) chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 A or better resolution, for which sets of (13)C(alpha) chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 A. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed (13)C(alpha) chemical shifts are available. CheShift is available as a web server.

Fig. 1.

Plot of the χ1 torsional angles in degrees (as open-squares) from chain A versus chain B of the x-ray-determined structure of PDB ID 1RGE. We highlighted those residues showing differences greater than 2.0 ppm between predicted ¹³C^α chemical shifts from molecule A and B of 1RGE by CheShift with filled stars and filled circles. For details about the distribution of the black-filled symbols, see Protein 1RGE (Ribonuclease Sa).

Fig. 2.

Map of the differences in the computed ¹³C^α chemical shifts (in ppm according to the color scale) between an arbitrarily selected pair of side-chain torsional angles. The color indicates the difference in ¹³C^α chemical shifts (in ppm) for any pair of φ and ψ. (A) for Ser with χ1 = 160° and −180°, and a fixed χ2 = −180°; and panel (B) for Gln with χ2 = 65° and −65°, and a fixed χ1 = −60°.