Kim Jun Soo, Yethiraj Arun
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin, USA.
Biophys J. 2009 Feb 18;96(4):1333-40. doi: 10.1016/j.bpj.2008.11.030.
The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, p(rxn). A value of p(rxn) < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents--in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately.
利用理论和计算机模拟研究了大分子拥挤对缔合反应速率的影响。反应物和拥挤剂均为硬球，当两个反应物碰撞时，它们以反应概率p(rxn)形成产物。p(rxn) < 1的值粗略地模拟了蛋白质必须正确取向才能发生缔合反应这一事实。模拟结果表明，反应速率对拥挤剂体积分数的依赖性随反应概率而变化。对于反应概率接近1的情况，即反应物之间的大多数碰撞都会导致反应，由于反应物扩散系数降低，反应速率总是随着拥挤剂体积分数的增加而降低。另一方面，对于反应概率非常小的情况，即在大多数碰撞中反应不会发生，反应速率随拥挤剂体积分数增加——在这种情况下，是由于再碰撞概率增加。用辐射边界条件和接触时的径向分布函数改进的斯莫卢霍夫斯基理论与反应速率常数的模拟结果在定量上一致，并允许分别对这两种效应进行定量分析。
