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all-atom force field amino acids approached the DNA arginines atoms of DNA beginning of MD beginning of simulation Biol catalytic center Chem complex enzyme-DNA complex stabile contact area crystal structure DNA molecule DNA surface electrostatic interaction energy enzymatic repair process enzyme and DNA enzyme and TD enzyme approaches enzyme T4 Endonuclease formation of complex formation of systems formed complex FUJITSU Gaussian charge distribution Gua-5 and Gua-8 Gua-5 and TD helix H1 JAERI JAERI Research keep stabile M.L. Dodson MD simulation Molecular Dynamics Morikawa N-glycosyl native DNA dodecamer Native thymines nucleotides Gua-5 Ohtsuka Particle Mesh Ewald phosphodiester bond Pinak potential energy proteins R.S. Lloyd recognition of TD recognition process role of electrostatic sequence side chains simulated annealing simulations were performed solute molecules solvated in water stabile afterwards stabile throughout system with native system with TD TD damaged TD lesioned DNA throughout the MD thymine dimer water molecules water-mediated hydrogen bonds