Details

Autor(en) / Beteiligte

• Vila, Jorge A.
• Arnautova, Yelena A.
• Martin, Osvaldo A.
• Scheraga, Harold A.

Titel

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

Ist Teil von

• Proceedings of the National Academy of Sciences - PNAS, 2009-10, Vol.106 (40), p.16972-16977

Ort / Verlag

National Acad Sciences

Erscheinungsjahr

2009

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• A server ( Che Shift) has been developed to predict 13 C α chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13 C α 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 Che Shift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted 13 C α chemical shifts, was carried out for 3 sets of conformations: ( i ) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13 C α 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 Å. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that Che Shift 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 α chemical shifts are available. Che Shift is available as a web server.