Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme

Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated...

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Bibliographic Details
Published in:The Journal of chemical physics 2014-11, Vol.141 (18), p.185101-185101
Main Authors: Kanematsu, Yusuke, Tachikawa, Masanori
Format: Article
Language:English
Subjects:
Bacterial Proteins - chemistry
Crystallography
Elongation
HYDROGEN
Hydrogen Bonding
Hydrogen bonds
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
Isotopes - chemistry
Light
LIQUIDS
Magnetic Resonance Imaging
Mathematical models
Models, Biological
Molecular orbitals
NEUTRON DIFFRACTION
NMR
NUCLEAR MAGNETIC RESONANCE
Photoreceptors, Microbial - chemistry
Physics
Protein Tyrosine Phosphatases - metabolism
PROTEINS
Quantum mechanics
Quantum Theory
Solvent effect
SOLVENTS
SPECTRAL SHIFT
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Summary:Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.4900987