Pääkkönen Johan, Jänis Janne, Rouvinen Juha
Department of Chemistry, University of Eastern Finland, P.O. Box 111, 80101 Joensuu, Finland.
ACS Omega. 2022 Mar 16;7(12):10789-10795. doi: 10.1021/acsomega.2c00560. eCollection 2022 Mar 29.
A set of simulation applets has been developed for visualizing the behavior of the association and dissociation reactions in protein studies. These reactions are simple equilibrium reactions, and the equilibrium constants, most often dissociation constant , are useful measures of affinity. Equilibria, even in simple systems, may not behave intuitively, which can cause misconceptions and mistakes. These applets can be utilized for planning experiments, for verifying experimental results, and for visualization of the equilibria in education. The considered reactions include protein homodimerization, ligand binding to a receptor (or heterodimerization), and competitive ligand binding. The latter one can be considered as either a ligand binding to two receptors or a binding of two ligands to a single receptor. In general, the user is required to input the total concentrations of all proteins and ligands and the dissociation constants of all complexes, and the applets output the equilibrium concentrations of all protein species graphically as functions of concentration and as numerical values at a specified point. Also, a curve fitting tool is provided which roughly estimates the concentrations or the dissociation constants based on the experimental data. The applets are freely available online (URL: https://protsim.github.io/protsim) and readily hackable for custom purposes if necessary.
已经开发了一组模拟小程序，用于可视化蛋白质研究中缔合和解离反应的行为。这些反应是简单的平衡反应，平衡常数，最常见的是解离常数，是亲和力的有用度量。即使在简单系统中，平衡的表现也可能不符合直觉，这可能导致误解和错误。这些小程序可用于实验规划、验证实验结果以及在教育中可视化平衡。所考虑的反应包括蛋白质同二聚化、配体与受体结合（或异二聚化）以及竞争性配体结合。后者可以被视为一个配体与两个受体结合，或者两个配体与一个受体结合。一般来说，用户需要输入所有蛋白质和配体的总浓度以及所有复合物的解离常数，小程序会以图形方式输出所有蛋白质物种的平衡浓度，作为浓度函数以及在指定点的数值。此外，还提供了一个曲线拟合工具，可根据实验数据大致估算浓度或解离常数。这些小程序可在网上免费获取（网址：https://protsim.github.io/protsim），如有必要，还可方便地进行定制修改。
