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. 2008 Sep 23;105(38):14389-94.
doi: 10.1073/pnas.0807105105. Epub 2008 Sep 11.

Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation

Jorge A Vila  1 , James M Aramini, Paolo Rossi, Alexandre Kuzin, Min Su, Jayaraman Seetharaman, Rong Xiao, Liang Tong, Gaetano T Montelione, Harold A Scheraga
Affiliations

Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation

Jorge A Vila et al. Proc Natl Acad Sci U S A. .

Abstract

A recently determined set of 20 NMR-derived conformations of a 48-residue all-alpha-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed (13)C(alpha) chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed (13)C(alpha) chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed (13)C(alpha) chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed (13)C(alpha) chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-A resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed (13)C(alpha) chemical shifts in solution than the 3BHP crystal structure. In addition, the (13)C(alpha)-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Bars indicate the rmsd between computed and observed 13Cα chemical shifts for each of the 10 conformations of YnzC[1–46] from Set-bt (red bars) and the 20 conformations from the ensemble of NMR structures retrieved from the PDB, 2JVD (blue bars). Horizontal lines designate the ca-rmsds computed for each of these two sets as described in Materials and Methods. Black and red horizontal lines designate the ca-rmsd computed for residues 1–48 of 2JVD and Set-bt (including the first two residues of the C-terminal purification tag), respectively.
Fig. 2.
Fig. 2.
Ribbon diagrams of the superposition of 10 conformations obtained in Set-bt (A), the superposition of 20 conformations of 2JVD (B), and the x-ray structure (three monomers in the asymmetric unit) (C).
Fig. 3.
Fig. 3.
Bars indicate the rmsd (ppm) between computed and observed 13Cα chemical shifts for each of the 10 conformations of YnzC [1–46] from Set-bt (red bars), the 20 conformations from 2JVD (blue bars), and for each of the three chains in the 2.0-Å crystal structure of YnzC [1–52], 3BHP, namely chains A, B, and C (black, yellow, and green bars). Horizontal lines designate the ca-rmsds computed for each of the two sets of NMR-derived conformations as described in Materials and Methods. Black and red horizontal lines designate the ca-rmsd computed for residues 1–46 of 2JVD and Set-bt, respectively.
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References

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