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Statistical and thermodynamic analysis of the binding of trans-activation response–binding proteins to HIV-1 TAR RNA

Open AccessPublished:December 07, 2020DOI:https://doi.org/10.1016/j.jbc.2020.100067

      Abbreviations:

      TAR (trans-activation response), TBP (TAR-binding protein)
      In a recent article (
      • Chavali S.S.
      • Mali S.M.
      • Jenkins J.L.
      • Fasan R.
      • Wedekind J.E.
      Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.
      ), the authors examine the binding of lab-evolved trans-activation response (TAR)–binding proteins (TBPs) to HIV-1 TAR RNA. Here, we show our analysis of the thermodynamic data of the binding that identifies three quantitative features of the binding, which may provide further insight into the interactions.
      • (1)
        The binding of TBPs to HIV-1 TAR RNA exhibits enthalpy–entropy compensation (
        • Fox J.M.
        • Zhao M.
        • Fink M.J.
        • Kang K.
        • Whitesides G.M.
        The molecular origin of enthalpy/entropy compensation in biomolecular recognition.
        ,
        • Kang J.
        • Auerbach J.D.
        Thermodynamic characterization of dissociation rate variations of human leukocyte antigen and peptide complexes.
        ), which suggests that the bindings of the six TBPs follow a common mechanism in the binding (Fig. 1A).
        Figure thumbnail gr1
        Figure 1Statistical and thermodynamic analysis of the binding of TBPs to HIV-1 TAR RNA. A, enthalpy–entropy compensation in the binding. The solid line is the best fit to the data without two outliers (Tat ARM and TB-CP-6.9a), ΔH° = 343.3 × ΔS° – 36.6 (R2 = 0.9972), and the dotted line is its extrapolation. B, the β2-β3 loop sequence of the lab-evolved TBPs. X indicates two positions of mutation, leading to 400 possible variations of the sequence. All statistical analyses were conducted using SigmaPlot (version 11; Systat Software). TAR, trans-activation response; TBP, TAR-binding protein.
      • (2)
        Two other variants of TBPs do not fit the linear regression (Fig. 1A), according to a regression diagnostic test using studentized deleted residuals (
        • Pardoe I.
        Applied Regression Modeling.
        ). This suggests that the rest structure of TBPs other than the TAR-binding β2-β3 loop, which is absent in the two outliers, contributes to the binding.
      • (3)
        The ΔG° values of the six TBPs at 310.15 K calculated using Equation 1 are normally distributed, according to the Shapiro–Wilk normality test (W = 0.933, p = 0.607):
      ΔG°=ΔH°TΔS°
      (1)


      where ΔH° and ΔS° are experimentally measured values reported in the original paper (
      • Chavali S.S.
      • Mali S.M.
      • Jenkins J.L.
      • Fasan R.
      • Wedekind J.E.
      Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.
      ). Based on the statistical parameters, probability density of the ΔG° can be generated using Equation 2:
      p(ΔG°)=1σ2π×exp(12×(ΔG°ΔG°meanσ)2)
      (2)


      where σ = 1.9407 kJ/mol and ΔG°mean = –41.3 kJ/mol. The distribution allows one to relate the probability to find a TBP variant to its binding affinity. For example, statistically expected maximum ΔG° of the highest-affinity variant of TBPs (Fig. 1B) is obtained by solving Equation 3 for x to be –46.8 kJ/mol:
      1xp(ΔG°)dΔG°=1400
      (3)


      Conflict of interest

      The authors declare that they have no conflicts of interest with the contents of this article.

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        • Mali S.M.
        • Jenkins J.L.
        • Fasan R.
        • Wedekind J.E.
        Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.
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        The molecular origin of enthalpy/entropy compensation in biomolecular recognition.
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        Thermodynamic characterization of dissociation rate variations of human leukocyte antigen and peptide complexes.
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