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Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations

  • Takaki Tokiwa
    Takaki Tokiwa
    Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
    Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
  • Shogo Nakano*
    Shogo Nakano
    Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
    *Email: [email protected] (S.N.).
    More by Shogo Nakano
  • Yuta Yamamoto
    Yuta Yamamoto
    Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
  • Takeshi Ishikawa
    Takeshi Ishikawa
    Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
  • Sohei Ito
    Sohei Ito
    Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
    More by Sohei Ito
  • Vladimir Sladek
    Vladimir Sladek
    Institute of Chemistry−Centre for Glycomics, Dubravska cesta 9, 84538 Bratislava, Slovakia
  • Kaori Fukuzawa
    Kaori Fukuzawa
    School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-Ku, Tokyo 142-8501, Japan
    Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
  • Yuji Mochizuki
    Yuji Mochizuki
    Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
    Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
  • Hiroaki Tokiwa*
    Hiroaki Tokiwa
    Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
    *Email: [email protected] (H.T.)
  • Fuminori Misaizu
    Fuminori Misaizu
    Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
  • , and 
  • Yasuteru Shigeta*
    Yasuteru Shigeta
    Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
    Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
    *Email: [email protected] (Y.S.).
Cite this: J. Chem. Inf. Model. 2019, 59, 1, 25–30
Publication Date (Web):December 5, 2018
https://doi.org/10.1021/acs.jcim.8b00649
Copyright © 2018 American Chemical Society

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    Abstract

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    In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard. However, the physical complexity and the number of the interactions within a protein–ligand complex renders analysis of the results somewhat complicated. This situation prompted us to develop the 3D-visualization of interaction energies in protein (3D-VIEP) method; the toolkit AnalysisFMO, which should enable a more efficient and convenient workflow with FMO data generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate units, RbAnalysisFMO, and the PyMOL plugins. The former can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output files generated by the aforementioned quantum-chemical packages. The PyMOL plugins enable visualization of IFIEs or PIEs in the protein structure in PyMOL. We demonstrate the use of this tool on a lectin protein from Burkholderia cenocepacia in which FMO analysis revealed the existence of a new interaction between Gly84 and fucose. Moreover, we found that second-shell interactions are crucial in forming the sugar binding site. In the case of bilirubin oxidase from Myrothecium verrucaria (MvBO), we predict that interactions between Asp105 and three His residues (His401, His403, and His136) are essential for optimally positioning the His residues to coordinate Cu atoms to form one Type 2 and two Type 3 Cu ions.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jcim.8b00649.

    • List of analysisFMO toolkit and graphical user interface of the PyMOL plugins (PDF)

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    This article is cited by 15 publications.

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    13. Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson. Characterising GPCR–ligand interactions using a fragment molecular orbital-based approach. Current Opinion in Structural Biology 2019, 55 , 85-92. https://doi.org/10.1016/j.sbi.2019.03.021
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