Spassov V, Bashford D
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Protein Sci. 1998 Sep;7(9):2012-25. doi: 10.1002/pro.5560070918.
This paper describes an alternative mechanism for the cooperative binding of charged ligands to proteins. The ligand-binding sites are electrostatically coupled to protein side chains that can undergo protonation and deprotonation. The binding of one ligand alters the protein's protonation equilibrium in a manner that makes the the binding of the second ligand more favorable. This mechanism requires no conformational change to produce a cooperative effect, although it is not exclusive of conformational change. We present a theoretical description of the mechanism, and calculations on three kinds of systems: A model system containing one protonation site and two ligand-binding sites; a model system containing two protonation sites and two ligand-binding sites; and calbindin D9k, which contains two Ca2+-binding sites and 30 protonation sites. For the one-protonation-site model, it is shown that the influence of the protonation site can only be cooperative. The competition of this effect with the anticooperative effect of ligand-ligand repulsion is studied in detail. For the two-protonation site model, the effect can be either cooperative or, in special cases, anticooperative. For calbindin D9k, the calculations predict that six protonation sites in or near the ligand-binding sites make a cooperative contribution that approximately cancels the anticooperative effect of Ca2+-Ca2+ repulsion, accounting for more than half of the total cooperative effect that is needed to overcome repulsion and produce the net cooperativity observed experimentally. We argue that cooperative mechanisms of the kind described here are likely when there is more than one ligand-binding site in a protein domain.
本文描述了带电荷配体与蛋白质协同结合的另一种机制。配体结合位点通过静电作用与可发生质子化和去质子化的蛋白质侧链相连。一个配体的结合会改变蛋白质的质子化平衡，使得第二个配体的结合更有利。这种机制产生协同效应无需构象变化，尽管它并不排除构象变化。我们给出了该机制的理论描述，并对三种系统进行了计算：一个包含一个质子化位点和两个配体结合位点的模型系统；一个包含两个质子化位点和两个配体结合位点的模型系统；以及钙结合蛋白D9k，它包含两个Ca2+结合位点和30个质子化位点。对于单质子化位点模型，结果表明质子化位点的影响只能是协同的。详细研究了这种效应与配体 - 配体排斥的反协同效应之间的竞争。对于双质子化位点模型，这种效应可以是协同的，或者在特殊情况下是反协同的。对于钙结合蛋白D9k，计算预测配体结合位点内或附近的六个质子化位点产生协同作用，大约抵消了Ca2+ - Ca2+排斥的反协同效应，占克服排斥并产生实验观察到的净协同性所需的总协同效应的一半以上。我们认为，当蛋白质结构域中有多个配体结合位点时，这里描述的这种协同机制很可能存在。
