Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments.
Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments.
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DOI：
10.1186/1752-0509-3-101
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发表时间：
2009-10-08
影响因子：
--
通讯作者：
Grima R
中科院分区：
文献类型：
--
作者：
Grima R
酶动力学的经典描述忽略了细胞内环境的物理性质。这些方法背后的主要隐含假设是反应发生在足够大的隔室体积中，使得分子离散性可以忽略，并且分子运输通过扩散发生。虽然这些条件经常在实验室条件下得到满足，但它们不是细胞内环境的特征，细胞内环境在微米和亚微米尺度上被划分，并且活性运输手段在其中发挥重要作用。从酶反应动力学的主方程描述和假设代谢稳态条件开始，我们推导出新的介观速率方程，该方程考虑到（i）由于细胞内室中分子的低拷贝数而引起的固有分子噪声（ii）底物运输过程的物理性质，即扩散或囊泡介导的运输。这些方程取代了传统的宏观和确定性的细胞内动力学方程。后者在无限隔室体积的限制下回收。我们发现，偏离经典动力学的预测是明显的（百分之几百的反应速度的估计）酶反应发生在车厢是小于约200 nm的情况下，基板运输到车厢主要介导的囊泡或颗粒运输和竞争性酶抑制剂的存在下。导出的介观速率方程描述亚细胞酶反应动力学，考虑到，第一次，同时影响的固有噪声和运输方式。他们清楚地显示了传统的确定性方程模型的适用范围，即细胞内的条件与扩散运输和简单的酶机制在几百纳米大小的隔间兼容。一个积极的运输机制，再加上大的内在噪声酶浓度的确定性模型的预测，导致巨大的偏差。这对使用常微分方程建模大型细胞内反应网络的常用方法以及计算竞争性抑制剂药物的有效剂量具有影响。
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular discreteness can be ignored and that molecular transport occurs via diffusion. Though these conditions are frequently met in laboratory conditions, they are not characteristic of the intracellular environment, which is compartmentalized at the micron and submicron scales and in which active means of transport play a significant role. Starting from a master equation description of enzyme reaction kinetics and assuming metabolic steady-state conditions, we derive novel mesoscopic rate equations which take into account (i) the intrinsic molecular noise due to the low copy number of molecules in intracellular compartments (ii) the physical nature of the substrate transport process, i.e. diffusion or vesicle-mediated transport. These equations replace the conventional macroscopic and deterministic equations in the context of intracellular kinetics. The latter are recovered in the limit of infinite compartment volumes. We find that deviations from the predictions of classical kinetics are pronounced (hundreds of percent in the estimate for the reaction velocity) for enzyme reactions occurring in compartments which are smaller than approximately 200 nm, for the case of substrate transport to the compartment being mediated principally by vesicle or granule transport and in the presence of competitive enzyme inhibitors. The derived mesoscopic rate equations describe subcellular enzyme reaction kinetics, taking into account, for the first time, the simultaneous influence of both intrinsic noise and the mode of transport. They clearly show the range of applicability of the conventional deterministic equation models, namely intracellular conditions compatible with diffusive transport and simple enzyme mechanisms in several hundred nanometre-sized compartments. An active transport mechanism coupled with large intrinsic noise in enzyme concentrations is shown to lead to huge deviations from the predictions of deterministic models. This has implications for the common approach of modeling large intracellular reaction networks using ordinary differential equations and also for the calculation of the effective dosage of competitive inhibitor drugs.
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影响因子：
8.6
作者：
Grima, R.
通讯作者：
Grima, R.
影响因子：
3.8
作者：
Qian, H;Elson, EL
通讯作者：
Elson, EL
DOI：
10.1016/j.pbiomolbio.2004.01.012
发表时间：
2004-06-01
影响因子：
3.8
作者：
Schnell, S;Turner, TE
通讯作者：
Turner, TE
影响因子：
4
作者：
Minton, Allen P.
通讯作者：
Minton, Allen P.
影响因子：
56.9
作者：
Medalia, O;Weber, I;Baumeister, W
通讯作者：
Baumeister, W