TY - JOUR
T1 - Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method
AU - Tanaka, Shigenori
AU - Watanabe, Chiduru
AU - Honma, Teruki
AU - Fukuzawa, Kaori
AU - Ohishi, Kazue
AU - Maruyama, Tadashi
N1 - Funding Information:
S.T. would like to acknowledge the Grants-in-Aid for Scientific Research (Nos. 17H06353 and 18K03825 ) from the Ministry of Education , Culture, Sports, Science and Technology ( MEXT ), Japan. C.W. acknowledges the JST PRESTO Grant Number JPMJPR18GD , Japan. This research was performed in the activities of the FMO drug design consortium (FMODD).
PY - 2020/11
Y1 - 2020/11
N2 - A theoretical scheme to systematically describe correlated (network-like) interactions between molecular fragments is proposed within the framework of the fragment molecular orbital (FMO) method. The method is mathematically based on the singular value decomposition (SVD) of the inter-fragment interaction energy (IFIE) matrix obtained by the FMO calculation, and can be applied to a comprehensive description of protein-protein interactions in the context of molecular recognition. In the present study we apply the proposed method to a complex of measles virus hemagglutinin and human SLAM receptor, thus finding a usefulness for efficiently eliciting the correlated interactions among the amino-acid residues involved in the two proteins. Additionally, collective interaction networks by amino-acid residues important for mutation experiments can be clearly visualized.
AB - A theoretical scheme to systematically describe correlated (network-like) interactions between molecular fragments is proposed within the framework of the fragment molecular orbital (FMO) method. The method is mathematically based on the singular value decomposition (SVD) of the inter-fragment interaction energy (IFIE) matrix obtained by the FMO calculation, and can be applied to a comprehensive description of protein-protein interactions in the context of molecular recognition. In the present study we apply the proposed method to a complex of measles virus hemagglutinin and human SLAM receptor, thus finding a usefulness for efficiently eliciting the correlated interactions among the amino-acid residues involved in the two proteins. Additionally, collective interaction networks by amino-acid residues important for mutation experiments can be clearly visualized.
KW - Fragment molecular orbital method (FMO)
KW - Inter-fragment interaction energy (IFIE)
KW - Measles virus (MV)
KW - Protein-protein interaction (PPI)
KW - Singular value decomposition (SVD)
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U2 - 10.1016/j.jmgm.2020.107650
DO - 10.1016/j.jmgm.2020.107650
M3 - Article
C2 - 32707520
AN - SCOPUS:85088136740
VL - 100
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
SN - 1093-3263
M1 - 107650
ER -