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Modeling Repair System Kinetics: Effect of Oxoguanine Concentrations

Investigate repair system kinetics in living organisms by modeling the impact of varied initial levels of 8-oxoguanine on base excision repair. Explore the interactions of different DNA lesions, biochemical reactions, and enzyme activities. Analyze the time shift in intermediate DNA states and repair enzymes to unveil multi-turnover kinetics. Supervisor: Dr. Oleg Belov, Assistant: Svetlana Aksenova. Stochastic modeling and kinetic parameter estimation methods used in this theoretical exploration. Conclude with insights on Fpg protein and DNA ligase activities during base excision repair in Escherichia coli bacterial cells.

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Modeling Repair System Kinetics: Effect of Oxoguanine Concentrations

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  1. Project: “Mathematical modeling of repair systemsin living organisms” Theoretical investigation of the effect of different initial concentration of8-oxoguanine on the base excision repair kinetics Nyathi F. 1, Magonono F.A.1, Someketa M.A.2 1 University of Venda ,Thohoyandou, South Africa 2 University of Fort Hare, Alice, South Africa Supervisor: Dr. Oleg Belov Assistant: Svetlana Aksenova LRB, JINR

  2. Mathematical modeling of repair systems is a key approach to investigate details of the induced mutation process

  3. The objects of our research Base excision repair system Escherichia coli bacterial cells 8-oxoguanine (8-oxoG)

  4. 8-oxoguanine is a most common and stable product of oxidative DNA damage under influence of ionizing radiation (Dizdaroglu et al., 1993) (γ-radiation, 60Co) (γ-radiation,60Co, 55 Gy)

  5. Base excision repair Formamidopyrimidine-DNA-glycosilase (Fpg protein, MutM protein) Fpg-dependent base excision repair /Sugahara et al., 2000/

  6. Structural model of E. coli BER y1 /Belov, 2010 (in press)/ 8-oxoG e1 υ1 Fpg (GA) y2 AP site e1 e1 Fpg (EA) Fpg (LA) υ2 υ3 y4 y3 3'-nicked site 5'-nicked site υ4 e1 Fpg (PA) GA – glycosylase activity y5 ssDNA EA – endonuclease activity υ5 e2 PolI LA – lyase activity filled gap with two nicks y6 PA – phosphodiesterase activity e3 υ6 AP – apurinic/apyrimidinic site DNA ligase ssDNA – a single-stranded DNA repaired DNA adduct y7 Pol I – DNA polymerase I

  7. . Stochiometric model of Fpg dependent base excision repair in Escherichia coli bacterial cells /Belov, 2010 (in press)/

  8. Kinetic parameters estimation

  9. Kinetic parameters estimation

  10. Concentration-dependent kinetic parameters

  11. Modeling biochemical reactions (Gillespie, 1977)

  12. y1 8-oxoG e1 υ1 Fpg (GA) y2 AP site e1 Fpg (EA) e1 Fpg (LA) υ2 υ3 y4 y3 3'-nicked site 5'-nicked site υ4 e1 Fpg (PA) y5 ssDNA υ5 e2 PolI filled gap with two nicks y6 e3 υ6 DNA ligase y7 repaired DNA adduct Time, s

  13. [8-oxoG •Fpg] [8-oxoG] RESULTS N, nmol/L N, nmol/L Time, s Time, s Time,s 1µmol/L 2 µmol/L 4 µmol/L

  14. RESULTS for [AP site • Fpg] N, nmol/L N, nmol/L Time, s Time, s 1 µmol/L 2 µmol/L 4 µmol/L

  15. [5′-nicked site •Fpg] RESULTS [3′-nicked site•Fpg] N, nmol/L N, nmol/L Time, s Time, s 1 µmol/L 2 µmol/L 4 µmol/L

  16. 1 µmol/L 2 µmol/L RESULTS for [ssDNA • Pol I] N, nmol/L N, nmol/L Time, s Time, s Tim,s 4 µmol/L N, nmol/L Time, s

  17. [repaired DNA adduct] [filled gap•DNA ligase] RESULTS N, nmol/L N, nmol/L N, nmol/L Time, s Time, s 1 µmol/L 2 µmol/L 4 µmol/L

  18. [Fpg] [DNA ligase] RESULTS N, nmol/L N, nmol/L Time, s Time, s 1µmol/L 2 µmol/L 4 µmol/L

  19. RESULTS for [Pol I] 1 µmol/L 2 µmol/L N, nmol/L N, nmol/L 0 Time, s Time, s 0 0 Tim,s N, nmol/L 4 µmol/L Time, s

  20. Conclusion • The kinetics of base excision repair is modeled for different DNA lesion levels. • For the first time the kinetics of basic intermediate DNA states and BER enzymes are investigated under three different initial concentration of 8-oxoguanine. • For different initial concentrations of 8-oxoguanine, we obtained time shift in the kinetics of all intermediate DNA states and BER enzymes. • On the basis of the obtained results, it can be concluded that Fpg protein and DNA ligase demonstrate multi-turnover kinetics during BER.

  21. THANK YOU FOR YOUR ATTENTION! СПАСИБО ЗА ВНИМАНИЕ!

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