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A system of linear equations for the identification of DNA binding affinity of zinc fingers

Open AccessPublished:January 01, 2019DOI:https://doi.org/10.1074/jbc.L118.006646
      In a recent article (
      • Hudson N.O.
      • Whitby F.G.
      • Buck-Koehntop B.A.
      Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
      ), the authors examined biophysical characteristics in the interaction between methylated DNA and ZBTB38 protein, which possesses five zinc finger domains (ZFs 6–10) in the C-terminal region. While the authors identified that ZFs 6–9 were minimal structural elements for high-affinity DNA binding, the role of ZF 10 remained inconclusive. Here, we show that the binding data shown in Fig. 1 of the paper can be used to predict the role of ZF 10 in regard to binding to methylated DNA with an algebraic technique of solving a system of linear equations (
      • Axler S.
      ).
      Fig. 1 of the paper reports dissociation constants (KD) of 5.3 nm, 5.0 nm, and 40.6 nm for ZFs 6–10, ZFs 6–9, and ZFs 7–10, respectively. From this information, a system of linear equations of binding affinity (ΔG0) with three unknowns can be established using the thermodynamic relation, ΔG0 = RT × ln KD (
      • Chang R.
      ), with an assumption of additivity in the binding (
      • Kang J.
      • Warren A.S.
      Thermodynamic analysis of additivity between the heavy and light chains in affinity maturation of an antibody.
      ).
      • ZFs 6–10: ΔG0(ZF 6) + ΔG0(ZFs 7–9) + ΔG0(ZF 10) = −46.7 kJ/mol
      • ZFs 6–9: ΔG0(ZF 6) + ΔG0(ZFs 7–9) = −46.9 kJ/mol
      • ZFs 7–10: ΔG0(ZFs 7–9) + ΔG0(ZF 10) = −41.7 kJ/mol
      By solving the three equations, we obtained that ΔG0(ZF 6) = −5.0 kJ/mol, ΔG0(ZF 7–9) = −41.9 kJ/mol, and ΔG0(ZF 10) = 0.2 kJ/mol. Our calculation clearly suggests that ZF 10 in ZBTB38 protein does not contribute to binding affinity in agreement with the speculation made in the paper (
      • Hudson N.O.
      • Whitby F.G.
      • Buck-Koehntop B.A.
      Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
      ).

      References

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        • Whitby F.G.
        • Buck-Koehntop B.A.
        Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
        J. Biol. Chem. 2018; 293 (30355731): 19835-19843
        • Axler S.
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        Physical Chemistry for the Chemical and Biological Science. University Science Books, Sausalito, CA2000
        • Kang J.
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        Thermodynamic analysis of additivity between the heavy and light chains in affinity maturation of an antibody.
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