Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Tong Zhu, Xiao He, John Zhang

Research output: Contribution to journalArticle

Abstract

Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson-Boltzmann) model. Our calculated chemical shifts of 1H and 13C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of 15N, the results do not agree with experimental values as well as 1H and 13C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for 13C α atoms in proteins, and using the 1H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.

Original languageEnglish (US)
Pages (from-to)7837-7845
Number of pages9
JournalPhysical Chemistry Chemical Physics
Volume14
Issue number21
DOIs
StatePublished - Jun 7 2012

Fingerprint

Solvation
Chemical shift
Density functional theory
solvation
chemical equilibrium
Nuclear magnetic resonance
fragments
density functional theory
proteins
nuclear magnetic resonance
Molecular mechanics
Quantum theory
Proteins
quantum mechanics
fragmentation
decoys
Ubiquitin
Immunoglobulin G
Gases
inclusions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Physics and Astronomy(all)

Cite this

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. / Zhu, Tong; He, Xiao; Zhang, John.

In: Physical Chemistry Chemical Physics, Vol. 14, No. 21, 07.06.2012, p. 7837-7845.

Research output: Contribution to journalArticle

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