Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.
Laboratory of Physics and Modelling of Condensed Matter (UMR 5493), Grenoble Alpes University, CNRS, 38042 Grenoble, France.
Phys Rev E. 2017 Jul;96(1-1):012417. doi: 10.1103/PhysRevE.96.012417. Epub 2017 Jul 31.
Binding of ligands to macromolecules is central to many functional and regulatory biological processes. Key parameters characterizing ligand-macromolecule interactions are the stoichiometry, inducing the number of ligands per macromolecule binding site, and the dissociation constant, quantifying the ligand-binding site affinity. Both these parameters can be obtained from analyses of classical saturation experiments using the standard binding equation that offers the great advantage of mathematical simplicity but becomes an approximation for situations of interest when a ligand binds and covers more than one single binding site on the macromolecule. Using the framework of car-parking problem with latticelike macromolecules where each ligand can cover simultaneously several consecutive binding sites, we showed that employing the standard analysis leads to underestimation of binding parameters, i.e., ligands appear larger than they actually are and their affinity is also greater than it is. Therefore, we have derived expressions allowing to determine the ligand size and true binding parameters (stoichiometry and dissociation constant) as a function of apparent binding parameters retrieved from standard saturation experiments.
配体与生物大分子的结合是许多功能和调节生物过程的核心。描述配体-生物大分子相互作用的关键参数是计量学，即每个生物大分子结合位点结合的配体数量，以及解离常数，即配体结合位点亲和力的量化。这两个参数都可以通过使用标准结合方程对经典饱和实验的分析来获得，该方程具有数学简单的巨大优势，但当配体结合并覆盖生物大分子上的一个以上单个结合位点时，它成为了感兴趣情况下的一种近似。利用具有类晶格生物大分子的停车问题框架，其中每个配体可以同时覆盖几个连续的结合位点，我们表明，使用标准分析会导致结合参数的低估，即配体看起来比实际更大，它们的亲和力也比实际更大。因此，我们推导出了一些表达式，可以根据从标准饱和实验中获得的表观结合参数来确定配体大小和真实的结合参数（计量学和解离常数）。
