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Journal Articles

A Possible overestimation of the effect of acetylation on lysin residues in KQ mutant analysis

Fujimoto, Hirofumi*; Higuchi, Mariko; Koike, Manabu*; Ode, Hirotaka*; Pinak, M.; Kotulic Bunta, J.*; Nemoto, Toshiyuki*; Sakudo, Takashi*; Honda, Naoko*; Maekawa, Hideaki*; et al.

Journal of Computational Chemistry, 33(3), p.239 - 246, 2012/01

 Times Cited Count:29 Percentile:61.56(Chemistry, Multidisciplinary)

Lysine acetylation is one of the most common protein post transcriptional modifications. The acetylation effects of lysine residues on Ku protein were examined herein applying several computer simulation techniques. Acetylation of the lysine residues did not reduce the affinity between Ku and its substrate, DNA, in spite of the fact that the substitution of lysine with glutamine (KQ mutant) reduced the affinity of Ku for DNA, or the substitution of lysine with arginine (KR mutant) did not reduce it, as previously reported in experimental studies. These results suggest that the effects of in vivo acetylation may be overestimated when the KQ mutant is employed in mimicry of the acetylated protein.

Journal Articles

DNA strand break; Structural and electrostatic properties studied by molecular dynamics simulation

Kotulic Bunta, J.*; Laaksonen, A.*; Pinak, M.; Nemoto, Toshiyuki*

Computational Biology and Chemistry, 30(2), p.112 - 119, 2006/04

 Times Cited Count:3 Percentile:22.11(Biology)

Due to their lethal consequences, single and double strand breaks are among the most important and dangerous DNA lesions. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system, system with open valences of the atoms at the strand break ends as well as a system with filled valences was simulated. As for the results, the system with open valences is partly disrupted, and the system with filled valences is stabilized by forming new hydrogen bonds between two strand endings.

Oral presentation

Molecular dynamics and quantum simulations of conformational changes of dGTP and oxo-dGTP based on study of Dpo4 polymerase

Kotulic Bunta, J.*; Pinak, M.; Saito, Kimiaki

no journal, , 

DNA polymerase IV (Dpo4) is the crucial enzyme in the process of DNA recombination, being responsible for extending primer by incorporating new nucleotides. This study is focused on the incoming nucleotide which is primarily in a form of Guanosinetriphosphate (dGTP) molecule. Oxidation of the dGTP molecule to 8-OH-dGTP state can cause mutation in the process of recombination, enabled by precedent conformational change of 8-OH-dGTP molecule from -anti to -syn conformation. This work describes important aspects of this change as well as relation of the oxidized 8-OH-dGTP to surrounding amino acids in the polymerase.

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