S.N. Bose National Centre For Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098, India.
J Chem Phys. 2012 Apr 21;136(15):154502. doi: 10.1063/1.3703505.
Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production shows the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the non-equilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient of some relevant experimental result and gives a microscopic insight on the mechanism of cooperative binding of substrate on a single oligomeric enzyme which is usually estimated from the macroscopic reaction rate.
在这里，我们在化学静态条件下系统地研究了单体酶活性部位上底物分子的协同结合。通过对分类为空间和时间的协同结合的随机主方程进行公式化，可以研究结合的底物的平均数量和酶催化反应的净速度。我们使用动力学蒙特卡罗技术基于单个轨迹分析估计了协同结合方案的熵产生。结果发现，总熵产生和介质熵产生都显示出相同的通用诊断特征，用于检测通常以反应的净速度来描述的协同作用。该特征也被发现对于非平衡稳态下的总熵产生率有效。我们引入了一个协同性指数 C，该指数是根据完全结合状态的协同和非协同情况的惊讶或等效的随机系统熵的比值来定义的。协同性的标准是根据一些相关实验结果的 Hill 系数来比较的，并从宏观反应速率通常估计的角度，对单体酶上的底物协同结合的机制进行了微观分析。
