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

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

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.