Understanding the thermodynamics and kinetics of the protein–ligand interaction is essential for biologists and pharmacologists. To visualize the equilibrium and kinetics of the binding reaction with 1:1 stoichiometry and no cooperativity, we obtained the exact relationship of the concentration of the protein–ligand complex and the time in the second-order binding process and numerically simulated the process of competitive binding. First, two common concerns in measuring protein–ligand interactions were focused on how to avoid the titration regime and how to establish the appropriate incubation time. Then, we gave examples of how the commonly used experimental conditions of [L]₀ ≫ [P]₀ and [I]₀ ≫ [P]₀ affected the estimation of the kinetic and thermodynamic properties. Theoretical inhibition curves were calculated, and the apparent IC₅₀ and IC₅₀ were estimated accordingly under predefined conditions. Using the estimated apparent IC₅₀, we compared the apparent K_i and K_i calculated by using the Cheng–Prusoff equation, Lin–Riggs equation, and Wang’s group equation. We also applied our tools to simulate high-throughput screening and compare the results of real experiments. The visualization tool for simulating the saturation experiment, kinetic experiments of binding and competitive binding, and inhibition curve, “Binding Curve Viewer,” is available at www.eplatton.net/binding-curve-viewer.

中文翻译：

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结合曲线查看器：可视化蛋白质-配体结合和竞争性结合的平衡和动力学


了解蛋白质-配体相互作用的热力学和动力学对于生物学家和药理学家来说至关重要。为了可视化 1:1 化学计量且无协同性的结合反应的平衡和动力学，我们获得了蛋白质-配体复合物的浓度与二级结合过程中的时间的精确关系，并数值模拟了竞争性过程。捆绑。首先，测量蛋白质-配体相互作用的两个常见问题集中在如何避免滴定方案以及如何建立适当的孵育时间。然后，我们举例说明了常用的实验条件 [L] ₀ ≫ [P] ₀ 和 [I] ₀ ≫ [P] < b3>影响了动力学和热力学性质的估计。计算理论抑制曲线，并在预定条件下相应估计表观IC ₅₀ 和IC ₅₀ 。使用估计的表观 IC ₅₀ ，我们比较了表观 K 和使用 Cheng-Prusoff 方程、Lin-Riggs 方程和 Wang 群方程计算的 K。我们还应用我们的工具来模拟高通量筛选并比较真实实验的结果。用于模拟饱和实验、结合和竞争性结合动力学实验以及抑制曲线的可视化工具“Binding Curve Viewer”可在 www.eplatton.net/binding-curve-viewer 上获取。