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 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.
Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan.
Yusuke
Y
Kanematsu
Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan.
Masanori
M
Tachikawa
D001426:Bacterial Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D007554:Isotopes / Q000737:chemistry; D008027:Light; D008279:Magnetic Resonance Imaging; D008954:Models, Biological; D020283:Photoreceptors, Microbial / Q000737:chemistry*; D017027:Protein Tyrosine Phosphatases / Q000378:metabolism; D011789:Quantum Theory
D001426:Bacterial Proteins; D007554:Isotopes; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria; D017027:Protein Tyrosine Phosphatases