The simplicity of completion time distributions for common complex biochemical processes
The simplicity of completion time distributions for common complex biochemical processes
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DOI：
10.1088/1478-3975/7/1/016003
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发表时间：
2010-03-01
期刊：
影响因子：
2
通讯作者：
Nemenman, Ilya
中科院分区：
文献类型：
--
作者：
Bel, Golan;Munsky, Brian;Nemenman, Ilya
生化过程通常涉及大量单独的可逆步骤，每个步骤都有自己的动态速率常数。例如，动力学校对过程依赖于大量的顺序反应，以确保特定大分子的精确结构。在这项工作中，我们研究了这类系统的暂态性质，并充分刻画了它们的首次通过(完成)时间分布。特别是，我们给出了动力学校对过程的完成时间的均值和方差的显式表达式，并对更复杂的生化系统进行了计算分析。我们发现，对于很大范围的参数，随着系统规模的增大，完成时间行为被简化：它要么是确定性的，要么是指数分布的，在两个区域之间有一个非常窄的过渡。在这两种情况下，整个系统的动力学复杂性与其明显的结构复杂性相比微不足道。类似的简单性很可能出现在许多复杂的多步骤生化过程的动力学中。特别是，这些发现不仅表明，人们可能无法从宏观观察中理解个别的元素反应，而且这种理解可能是不必要的。
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the precise construction of specific macromolecules. In this work, we study the transient properties of such systems and fully characterize their first passage (completion) time distributions. In particular, we provide explicit expressions for the mean and the variance of the completion time for a kinetic proofreading process and computational analyses for more complicated biochemical systems. We find that, for a wide range of parameters, as the system size grows, the completion time behavior simplifies: it becomes either deterministic or exponentially distributed, with a very narrow transition between the two regimes. In both regimes, the dynamical complexity of the full system is trivial compared to its apparent structural complexity. Similar simplicity is likely to arise in the dynamics of many complex multistep biochemical processes. In particular, these findings suggest not only that one may not be able to understand individual elementary reactions from macroscopic observations, but also that such an understanding may be unnecessary.