Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
 

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.

Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.

Adv Exp Med Biol. 2015;827:49-70

Authors: Zhu T, Zhang JZ, He X

Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental (1)H NMR chemical shifts, while the (13)C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for (15)N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of (13)C? NMR chemical shifts on the secondary structure of proteins, and the calculated (1)H chemical shift can be utilized to discriminate the native structure of proteins from decoys.*


PMID: 25387959 [PubMed - in process]



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