Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
J Chem Phys. 2019 Mar 7;150(9):094104. doi: 10.1063/1.5079748.
The influence of diffusion on the kinetics of ligand binding to a macromolecule with two sites is considered for a simple model where, in the reaction-controlled limit, there is no cooperativity and hence the sites are independent. By applying our recently developed formalism to describe a network of coupled diffusion-influenced reactions, we show that the rate constants of chemical kinetics cannot just be renormalized. Rather a new reaction channel, which connects the two singly occupied states, must be introduced. The rate constants of this new channel depend on the committor or capture probability that a ligand that just dissociated from one site rebinds to the other. This result is rederived in an elementary way using the encounter complex model. Illustrative calculations are presented where the kinetics of the fractional saturation of one site is compared with that of a macromolecule that has only this site. If all sites are initially empty, then the second site slows down binding to the first due to competition between the sites. On the other hand, if the second site is initially occupied, the binding of the first site speeds up because of the direct diffusion-induced transitions between the two singly bound states.
考虑到扩散对具有两个结合位点的大分子上配体结合动力学的影响，我们研究了一个简单的模型，其中在反应控制极限下没有协同作用，因此各个位点是独立的。通过应用我们最近开发的形式来描述耦合扩散影响反应的网络，我们表明化学动力学的速率常数不能仅仅被重新归一化。相反，必须引入一个新的反应通道，该通道将两个单占据态连接起来。这个新通道的速率常数取决于配体从一个位点解离后重新结合到另一个位点的衔接子或捕获概率。使用遭遇复合物模型以基本的方式重新推导出这个结果。我们给出了说明性的计算，比较了一个位点的分数饱和动力学和只有这个位点的大分子的动力学。如果所有的位点最初都是空的，那么由于位点之间的竞争，第二个位点会减缓与第一个位点的结合。另一方面，如果第二个位点最初被占据，那么由于两个单结合态之间的直接扩散诱导跃迁，第一个位点的结合会加快。
