Predicting Chemical Shifts in Proteins:  Structure Refinement of Valine Residues by Using ab Initio and Empirical Geometry Optimizations

Abstract

We have investigated the carbon-13 solution nuclear magnetic resonance (NMR) chemical shifts of Cα, Cβ, and Cγ carbons of 19 valine residues in a vertebrate calmodulin, a nuclease from Staphylococcus aureus, and a ubiquitin. Using empirical chemical shift surfaces to predict Cα, Cβ shifts from known, X-ray φ,ψ values, we find moderate accord between prediction and experiment. Ab initio calculations with coupled Hartree−Fock (HF) methods and X-ray structures yield poor agreement with experiment. There is an improvement in the ab initio results when the side chain χ1 torsion angles are adjusted to their lowest energy conformers, using either ab initio quantum chemical or empirical methods, and a further small improvement when the effects of peptide-backbone charge fields are introduced. However, although the theoretical and experimental results are highly correlated (R 2 ∼ 0.90), the observed slopes of ∼−0.6−0.8 are less than the ideal value of −1, even when large uniform basis sets are used. Use of density functional theory (DFT) methods improves the quality of the predictions for both Cα (slope = −1.1, R 2 = 0.91) and Cβ (slope = −0.93, R 2 = 0.89), as well as giving moderately good results for Cγ. This effect is thought to arise from a small, conformationally-sensitive contribution to shielding arising from electron correlation. Additional shielding calculations on model compounds reveal similar effects. Results for valine residues in interleukin-1β are less highly correlated, possibly due to larger crystal−solution structural differences. When taken together, these results for 19 valine residues in 3 proteins indicate that choosing the lowest energy χ1 conformer together with X-ray φ,ψ values enables the successful prediction of both Cα and Cβ shifts, with DFT giving close to ideal slopes and R 2 values between theory and experiment. These results strongly suggest that the most highly populated valine side-chain conformers are those having the lowest (computationally determined) energy, as evidenced by the ability to predict essentially all Cα, Cβ chemical shifts in calmodulin, SNase, and ubiquitin, as well as moderate accord for Cγ. These observations suggest a role for chemical shifts and energy minimization/geometry optimization in the refinement of protein structures in solution, and potentially in the solid state as well.

Toward Direct Determination of Conformations of Protein Building Units from Multidimensional NMR Experiments Part II: A Theoretical Case Study of Formyl-L-Valine Amide

“…This opens up the possibility of scaling of chemical shifts computed under rather different conditions. In a further study of relevance, [40] by using empirical chemical shift surfaces Pearson et al attempted to predict 13 C NMR shifts of valine residues in calmodulin, nuclease, and ubiquitin, utilizing their X-ray structures. Most RHF results and experimental values showed worse agreement than expected, which improved slightly by using density functional theory-type calculations.…”

Extracting structural information using time-frequency analysis of protein NMR data

“…Z can only influence the chemical shifts of atoms within a fixed radius [37]. When this radius can be estimated, upper bounds on the distance between temporally-correlated tracks can be calculated and applied quantitatively in a manner analogous to NOE's.…”

Prediction of protein 13Cα NMR chemical shifts using a combination scheme of statistical modeling and quantum-mechanical analysis

“…Then they also studied the factors that affect 13 C a -shielding [18], the results of this analysis was complementary to Xu and Case's research [19]. However, computation of the chemical shifts at the ab initio Hartree-Fock or density functional theory (DFT) level for protein structures cannot be accomplished unless some approximations are adopted [20][21][22], because their magnitudes are very sensitive to, and depend mainly on, the backbone torsional angles (u, w) [5], although the influence of the side-chain torsional angles v's cannot be disregarded [20][21][22][23][24].…”