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Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase.

Kirpota OO, Endutkin AV, Ponomarenko MP, Ponomarenko PM, Zharkov DO, Nevinsky GA - Nucleic Acids Res. (2011)

Bottom Line: Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k(cat) term instead; the rate increases by 6-7 orders of magnitude for cognate DNA as compared with non-cognate one.The k(cat) values for substrates of different sequences correlate with the DNA twist, while the K(M) values correlate with ΔG° of the DNA fragments surrounding the lesion (position from -6 to +6).The functions for predicting the K(M) and k(cat) values for different sequences containing oxoG were found.

View Article: PubMed Central - PubMed

Affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Department of Molecular Biology, Novosibirsk State University, 2 Pirogova Street and SB RAS Institute of Cytology and Genetics, 10 Lavrentieva Avenue, Novosibirsk 630090, Russia.

ABSTRACT
We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10-13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately -6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately -3.3 kcal/mol) together with other specific interactions (ΔG° approximately -0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k(cat) term instead; the rate increases by 6-7 orders of magnitude for cognate DNA as compared with non-cognate one. The k(cat) values for substrates of different sequences correlate with the DNA twist, while the K(M) values correlate with ΔG° of the DNA fragments surrounding the lesion (position from -6 to +6). The functions for predicting the K(M) and k(cat) values for different sequences containing oxoG were found.

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Dependencies of log Ki on the length (n) of ss (solid line) and ds (dashed line) d(pN)n inhibitors of oxoG excision from ds OG11 by OGG1. Triangles, d(pT)n; circles, d(pA)n; crosses, d(pC)n; squares, d(pT)n:d(pA)n.
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Figure 3: Dependencies of log Ki on the length (n) of ss (solid line) and ds (dashed line) d(pN)n inhibitors of oxoG excision from ds OG11 by OGG1. Triangles, d(pT)n; circles, d(pA)n; crosses, d(pC)n; squares, d(pT)n:d(pA)n.

Mentions: To assess whether the energy of interactions of OGG1 with ODNs is indeed additive in this manner, the data (Table 1) were analyzed as log dependences of Ki (directly proportional to ΔG°) for d(pN)n versus the number of mononucleotide units (n; Figure 3). The linear log dependences for ss d(pN)n (for 0 ≤ n ≤ 10; n = 0 corresponds to Pi) provide the evidence for the additivity of ΔG° values for the interaction of ten individual d(pN)n units with OGG1, consistent with our earlier observations that the protein globules of all relatively small DNA-dependent enzymes (30–40 kDa; the molecular mass of OGG1 is 39 kDa) interact with 9–11 nt units of DNA [reviewed in ref. (5)].Figure 3.


Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase.

Kirpota OO, Endutkin AV, Ponomarenko MP, Ponomarenko PM, Zharkov DO, Nevinsky GA - Nucleic Acids Res. (2011)

Dependencies of log Ki on the length (n) of ss (solid line) and ds (dashed line) d(pN)n inhibitors of oxoG excision from ds OG11 by OGG1. Triangles, d(pT)n; circles, d(pA)n; crosses, d(pC)n; squares, d(pT)n:d(pA)n.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113562&req=5

Figure 3: Dependencies of log Ki on the length (n) of ss (solid line) and ds (dashed line) d(pN)n inhibitors of oxoG excision from ds OG11 by OGG1. Triangles, d(pT)n; circles, d(pA)n; crosses, d(pC)n; squares, d(pT)n:d(pA)n.
Mentions: To assess whether the energy of interactions of OGG1 with ODNs is indeed additive in this manner, the data (Table 1) were analyzed as log dependences of Ki (directly proportional to ΔG°) for d(pN)n versus the number of mononucleotide units (n; Figure 3). The linear log dependences for ss d(pN)n (for 0 ≤ n ≤ 10; n = 0 corresponds to Pi) provide the evidence for the additivity of ΔG° values for the interaction of ten individual d(pN)n units with OGG1, consistent with our earlier observations that the protein globules of all relatively small DNA-dependent enzymes (30–40 kDa; the molecular mass of OGG1 is 39 kDa) interact with 9–11 nt units of DNA [reviewed in ref. (5)].Figure 3.

Bottom Line: Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k(cat) term instead; the rate increases by 6-7 orders of magnitude for cognate DNA as compared with non-cognate one.The k(cat) values for substrates of different sequences correlate with the DNA twist, while the K(M) values correlate with ΔG° of the DNA fragments surrounding the lesion (position from -6 to +6).The functions for predicting the K(M) and k(cat) values for different sequences containing oxoG were found.

View Article: PubMed Central - PubMed

Affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Department of Molecular Biology, Novosibirsk State University, 2 Pirogova Street and SB RAS Institute of Cytology and Genetics, 10 Lavrentieva Avenue, Novosibirsk 630090, Russia.

ABSTRACT
We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10-13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately -6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately -3.3 kcal/mol) together with other specific interactions (ΔG° approximately -0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k(cat) term instead; the rate increases by 6-7 orders of magnitude for cognate DNA as compared with non-cognate one. The k(cat) values for substrates of different sequences correlate with the DNA twist, while the K(M) values correlate with ΔG° of the DNA fragments surrounding the lesion (position from -6 to +6). The functions for predicting the K(M) and k(cat) values for different sequences containing oxoG were found.

Show MeSH