Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
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 (1)H and (13)C 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 (15)N, the results do not agree with experimental values as well as (1)H and (13)C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for (13)C(α) atoms in proteins, and using the (1)H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.
State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062.
Tong
T
Zhu
Xiao
X
He
John Z H
JZ
Zhang
D001426:Bacterial Proteins / Q000737:chemistry*; D002247:Carbon Isotopes / Q000737:chemistry; D005740:Gases / Q000737:chemistry; D006801:Humans; D006859:Hydrogen / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009587:Nitrogen Isotopes / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry*
D001426:Bacterial Proteins; D002247:Carbon Isotopes; D005740:Gases; C034284:IgG Fc-binding protein, Streptococcus; D009587:Nitrogen Isotopes; D012997:Solvents; D025801:Ubiquitin; D006859:Hydrogen