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

Tong Zhu, John Z.H. Zhang, Xiao He

Research output: Contribution to journalArticlepeer-review

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 1H NMR chemical shifts, while the 13C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for 15N 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 13Cα NMR chemical shifts on the secondary structure of proteins, and the calculated 1H chemical shift can be utilized to discriminate the native structure of proteins from decoys.

Original languageEnglish (US)
Pages (from-to)49-70
Number of pages22
JournalAdvances in experimental medicine and biology
Volume827
DOIs
StatePublished - 2015

Keywords

  • Ab initio
  • Automated fragmentation QM/MM
  • Linear scaling
  • Protein NMR chemical shift
  • Solvent effect

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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