Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method

Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi, Tadashi Maruyama

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number107650
JournalJournal of Molecular Graphics and Modelling
Volume100
DOIs
Publication statusPublished - 2020 Nov

Keywords

  • Fragment molecular orbital method (FMO)
  • Inter-fragment interaction energy (IFIE)
  • Measles virus (MV)
  • Protein-protein interaction (PPI)
  • Singular value decomposition (SVD)

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

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