8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: a molecular dynamics study.
The molecular dynamics (MD) simulation of DNA mutagenic oxidative lesion, 7,8-dihydro-8-oxoguanine (8-oxoG), complexed with the repair enzyme, human oxoguanine glycosylase 1 (hOGG1), was performed for 1 nanosecond (ns) in order to describe the dynamical process of DNA-enzyme complex formation. After 900 picoseconds of MD the lesioned DNA and enzyme formed a complex that lasted until the end of the simulation at 1 ns. The complex was mainly represented by the overlapping van der Waals surfaces of DNA and enzyme molecules. The amino group of arginine 324 was located close to the phosphodiester bond of the nucleotide with 8-oxoG enabling chemical reactions between amino acid and lesion. The broken hydrogen bonds resulting in locally collapsed B-DNA structure were observed at the lesion site. The phosphodiester bond at C5' of 8-oxoG was displaced to the position close to the amino group of arginine 324. The water-mediated hydrogen bond network was formed in each contact area between DNA and enzyme, further enhancing the stability of the complex. In the background simulation of the identical molecular system with the native DNA, neither the complex nor the water- mediated hydrogen bond network was observed.
Pinak
Miroslav
M
Japan Atomic Energy Research Institute, Radiation Risk Analysis Laboratory, Shirakata, Shirane 2-4, 319-1195 Tokai, Ibaraki, Japan. pinak@ismws001.tokai.jaeri.go.jp
D000465:Algorithms; D001120:Arginine / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D045647:DNA Glycosylases / Q000378:metabolism*; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D013997:Time Factors
C453560:7,8-dihydro-8-oxoguanine; D006147:Guanine; D004247:DNA; D001120:Arginine; D045647:DNA Glycosylases; C479058:oxoguanine glycosylase 1, human