Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)–RNA complex system

We report the molecular mechanism of protein–RNA complex stabilization based on the electronic state calculation. Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)–RNA complex system. The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation. The strength of inter-molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue–RNA base and residue–RNA backbone interactions. Under the influence of inter-molecular interactions, the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with intra-NOVA residue–residue interactions and the change of atomic charges by each residue. The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation.