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Viruses 2018, 10(5), 236; https://doi.org/10.3390/v10050236

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

1
Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
2
Education Center on Computational Science and Engineering, Kobe University, 7-1-48, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
3
Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima, Yokosuka, Kanagawa 237-0061, Japan
4
Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 3173-25, Showa-machi, Kanazawa-ku, Yokohama, Kanagawa 236-0001, Japan
5
Faculty of Engineering, Tokyo Polytechnic University, 1583, Iiyama, Atsugi, Kanagawa 243-0297, Japan
*
Author to whom correspondence should be addressed.
Received: 7 February 2018 / Revised: 27 April 2018 / Accepted: 30 April 2018 / Published: 3 May 2018
(This article belongs to the Section Animal Viruses)
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Abstract

Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy. View Full-Text
Keywords: measles virus; hemagglutinin; receptors; molecular recognition; fragment molecular orbital (FMO) method; IFIE (inter-fragment interaction energy) measles virus; hemagglutinin; receptors; molecular recognition; fragment molecular orbital (FMO) method; IFIE (inter-fragment interaction energy)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Xu, F.; Tanaka, S.; Watanabe, H.; Shimane, Y.; Iwasawa, M.; Ohishi, K.; Maruyama, T. Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors. Viruses 2018, 10, 236.

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