화학공학소재연구정보센터
Journal of the American Chemical Society, Vol.119, No.49, 11941-11950, 1997
Predicting chemical shifts in proteins: Structure refinement of valine residues by using ab initio and empirical geometry optimizations
We have investigated the carbon-13 solution nuclear magnetic resonance (NMR) chemical shifts of C-alpha, C-beta, and C-gamma carbons of 19 valine residues in a vertebrate calmodulin, a nuclease from Staphylococcus aureus, and a ubiquitin. Using empirical chemical shift surfaces to predict C-alpha, C-beta shifts from known, X-ray phi,psi 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 chi(1) 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 similar to 0.90), the observed slopes of similar to -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 C-alpha (slope = -1.1, R-2 = 0.91) and C-beta (slope -0.93, R-2 = 0.89), as well as giving moderately good results for C-gamma. 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-1 beta 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 chi(1) conformer together with X-ray phi,psi values enables the successful prediction of both C-alpha and C-beta 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 sidechain conformers are those having the lowest (computationally determined) energy, as evidenced by the ability to predict essentially all C-alpha, C-beta chemical shifts in calmodulin, SNase, and ubiquitin, as well as moderate accord for C-gamma. 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.