Brooks F J, Carlsson A E
Department of Physics, Washington University, St. Louis, Missouri 63130, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Mar;79(3 Pt 1):031914. doi: 10.1103/PhysRevE.79.031914. Epub 2009 Mar 24.
Actin polymerization time courses can exhibit rich nonequilibrium dynamics that have not yet been accurately described by simplified rate equations. Sophisticated stochastic simulations and elaborate recursion schemes have been used to model the nonequilibrium dynamics resulting from the hydrolysis and subsequent exchange of the nucleotide bound within the actin molecules. In this work, we use a truncation approach to derive a set of readily accessible deterministic rate equations which are significantly simpler than previous attempts at such modeling. These equations may be incorporated into whole-cell motility models which otherwise quickly become computationally inaccessible if polymerization of individual actin filaments is stochastically simulated within a virtual cell. Our equations accurately predict the relative concentrations of both monomeric and polymerized actin in differing nucleotide hydrolysis states throughout entire polymerization time courses nucleated via seed filaments. We extend our model to include the effects of capping protein. We also detail how our rate-equation method may be used to extract key parameters from experimental data.
肌动蛋白聚合时间进程可以展现出丰富的非平衡动力学，而简化的速率方程尚未准确描述这些动力学。复杂的随机模拟和精细的递归方案已被用于对肌动蛋白分子内结合的核苷酸水解及随后的交换所产生的非平衡动力学进行建模。在这项工作中，我们采用一种截断方法来推导一组易于理解的确定性速率方程，这些方程比以往此类建模尝试要简单得多。这些方程可纳入全细胞运动模型中，否则，如果在虚拟细胞内对单个肌动蛋白丝的聚合进行随机模拟，全细胞运动模型很快就会在计算上变得难以处理。我们的方程准确预测了在通过种子丝成核的整个聚合时间进程中，处于不同核苷酸水解状态的单体肌动蛋白和聚合肌动蛋白的相对浓度。我们将模型扩展到包括封端蛋白的影响。我们还详细说明了如何使用我们的速率方程方法从实验数据中提取关键参数。
