TY - JOUR
T1 - Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system
AU - Kurisaki, Ikuo
AU - Fukuzawa, Kaori
AU - Nakano, Tatsuya
AU - Mochizuki, Yuji
AU - Watanabe, Hirofumi
AU - Tanaka, Shigenori
N1 - Funding Information:
This work was supported by the Core Research for Evolutional Science and Technology (CREST) project of the Japan Science and Technology Agency (JST). We thank Prof. Kuniyoshi Ebina at Kobe University, Prof. Kei Yura at Ochanomizu University, Prof. Stuart M. Rothstein at Brock University, and Dr. Naoki Yamamoto at Kobe University for useful comments. One of the authors, I.K., also thanks the Japan Society for the support by the Research Fellowship from the Promotion of Science for Young Scientist. The molecular dynamics simulations were performed using Research Center for Computational Science, Okazaki, Japan.
Copyright:
Copyright 2010 Elsevier B.V., All rights reserved.
PY - 2010/12/30
Y1 - 2010/12/30
N2 - We report the molecular mechanism of protein-RNA complex stabilization based on the electronic state calculation. Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)-RNA complex system. The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation. The strength of inter-molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue-RNA base and residue-RNA backbone interactions. Under the influence of inter-molecular interactions, the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with intra-NOVA residue-residue interactions and the change of atomic charges by each residue. The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation.
AB - We report the molecular mechanism of protein-RNA complex stabilization based on the electronic state calculation. Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)-RNA complex system. The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation. The strength of inter-molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue-RNA base and residue-RNA backbone interactions. Under the influence of inter-molecular interactions, the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with intra-NOVA residue-residue interactions and the change of atomic charges by each residue. The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation.
KW - Ab initio fragment molecular orbital (FMO) method
KW - Neuro-oncological ventral antigen (NOVA)
KW - RNA-binding protein
KW - Sequence specific recognition
KW - Structure-function relationship
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U2 - 10.1016/j.theochem.2010.09.013
DO - 10.1016/j.theochem.2010.09.013
M3 - Article
AN - SCOPUS:78549252015
VL - 962
SP - 45
EP - 55
JO - Computational and Theoretical Chemistry
JF - Computational and Theoretical Chemistry
SN - 2210-271X
IS - 1-3
ER -