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Abstract：
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 Ki and Ki 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.
摘要：
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至关重要。为了可视化具有1：1化学计量且没有协同性的结合反应的平衡和动力学，我们获得了二阶结合过程中蛋白质-配体复合物浓度与时间的精确关系，并对竞争结合过程进行了数值模拟。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和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]0如何影响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地估计表观IC50和IC50。使用估计的表观IC50，我们比较了通过使用Cheng-Prusoff方程计算的表观Ki和Ki，林-里格斯方程,和王群方程。我们还应用我们的工具来模拟高通量筛选，并比较实际实验的结果。用于模拟饱和度实验的可视化工具，结合和竞争结合的动力学实验，和抑制曲线，\"绑定曲线查看器,“可在www上获得。eplatton.net/binding-curve-viewer。
