Large scale MD simulation of 8-oxoguanine and AP site multiple lesioned DNA molecule combined with biomolecular visualization software

Abstract The visualization of a real picture and dynamical movements of biomolecules is an essential process for understanding their fundamental properties, although there are few systems that can be used in combination with existing dynamical computer codes. Presented here is the novel system, Fujitsu Bio Molecular Visualization System (F-BMVS), which enables to produce real pictures and an animation by arranging them along a time series of a large-scale simulation of biomolecules associated with a molecular dynamics (MD) simulation program. This animation system is used to study the results of MD code, AMBER, in order to find structural differences on the lesioned DNA comparing with non-damaged DNA. Compared with non-damaged DNA molecule, it was found that the lesioned one has two specific features—bending at the lesioned site and flipping out apurinic/apyrimidinic site. These results are supported by the dynamical analysis of structural properties of DNA molecules. Product of visualization also suggests that presented animation system has a great advantage for understanding certain properties of biomolecules in a dynamical mode.

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