Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method

Abstract In large biomolecular systems such as protein complexes, there are huge numbers of combinations inter-residue interactions whose comprehensive analyses often beyond the intuitive processing by researchers. Here we propose a computational method to allow for systematic analysis these based on fragment molecular orbital calculations, in which inter-fragment interaction energies comprehensively processed singular value decomposition. For trimer complex SARS-CoV-2 spike protein, three-body among residues belonging three chains analyzed elicit small number essential modes or networks crucial structural stability complex.