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Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1.

Miroshnikova AD, Kuznetsova AA, Kuznetsov NA, Fedorova OS - Acta Naturae (2016 Jan-Mar)

Bottom Line: The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves.The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue.It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences. Prosp. Acad. Lavrent'eva, 8, Novosibirsk, 630090, Russia;

ABSTRACT
Apurinic/apyrimidinic (AP) endonucleases play an important role in DNA repair and initiation of AP site elimination. One of the most topical problems in the field of DNA repair is to understand the mechanism of the enzymatic process involving the human enzyme APE1 that provides recognition of AP sites and efficient cleavage of the 5'-phosphodiester bond. In this study, a thermodynamic analysis of the interaction between APE1 and a DNA substrate containing a stable AP site analog lacking the C1' hydroxyl group (F site) was performed. Based on stopped-flow kinetic data at different temperatures, the steps of DNA binding, catalysis, and DNA product release were characterized. The changes in the standard Gibbs energy, enthalpy, and entropy of sequential specific steps of the repair process were determined. The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves. The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue. It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step.

No MeSH data available.


Overall structures of free APE1 (pink, PDB ID 4LND) and APE1 associated withdamaged DNA (violet, PDB ID 1DE8).
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Figure 2: Overall structures of free APE1 (pink, PDB ID 4LND) and APE1 associated withdamaged DNA (violet, PDB ID 1DE8).

Mentions: According to the X-ray data, DNA binding leads only to minor structural rearrangements inAPE1 (Fig. 2). Comparisonof the structures of free APE1 (PDB ID 4LND) and a complex between APE1 and DNAcontaining the F site (PDB ID 1DE8) demonstrates that one of the seven tryptophanresidues of the enzyme molecule, Trp280, is located in the DNAbinding site andforms a hydrogen bond with a DNA phosphate group. Therefore, the observed changesin Trp fluorescence are likely related to enzyme conformational changes in theTrp280 region.


Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1.

Miroshnikova AD, Kuznetsova AA, Kuznetsov NA, Fedorova OS - Acta Naturae (2016 Jan-Mar)

Overall structures of free APE1 (pink, PDB ID 4LND) and APE1 associated withdamaged DNA (violet, PDB ID 1DE8).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837577&req=5

Figure 2: Overall structures of free APE1 (pink, PDB ID 4LND) and APE1 associated withdamaged DNA (violet, PDB ID 1DE8).
Mentions: According to the X-ray data, DNA binding leads only to minor structural rearrangements inAPE1 (Fig. 2). Comparisonof the structures of free APE1 (PDB ID 4LND) and a complex between APE1 and DNAcontaining the F site (PDB ID 1DE8) demonstrates that one of the seven tryptophanresidues of the enzyme molecule, Trp280, is located in the DNAbinding site andforms a hydrogen bond with a DNA phosphate group. Therefore, the observed changesin Trp fluorescence are likely related to enzyme conformational changes in theTrp280 region.

Bottom Line: The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves.The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue.It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences. Prosp. Acad. Lavrent'eva, 8, Novosibirsk, 630090, Russia;

ABSTRACT
Apurinic/apyrimidinic (AP) endonucleases play an important role in DNA repair and initiation of AP site elimination. One of the most topical problems in the field of DNA repair is to understand the mechanism of the enzymatic process involving the human enzyme APE1 that provides recognition of AP sites and efficient cleavage of the 5'-phosphodiester bond. In this study, a thermodynamic analysis of the interaction between APE1 and a DNA substrate containing a stable AP site analog lacking the C1' hydroxyl group (F site) was performed. Based on stopped-flow kinetic data at different temperatures, the steps of DNA binding, catalysis, and DNA product release were characterized. The changes in the standard Gibbs energy, enthalpy, and entropy of sequential specific steps of the repair process were determined. The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves. The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue. It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step.

No MeSH data available.