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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments.
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An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments.

机译：集成模拟模型，将肌动蛋白聚合的主要生化反应与肌动蛋白丝的结构特性联系起来。

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摘要

We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branching, fragmentation and annealing or the effects of regulatory proteins. Importantly, these reactions are linked to information on the nucleotide state of actin subunits in filaments (ATP hydrolysis) and the distribution of actin filament lengths. The developed stochastic simulation modelling schemes were validated on: i) synthetic theoretical data generated by a deterministic model and ii) sets of our and published experimental data obtained from fluorescence pyrene-actin experiments. Build on an open-architecture principle, the designed model can be extended for predictive evaluation of the activities of other actin-interacting proteins and can be applied for the analysis of experimental pyrene actin-based or fluorescence microscopy data. We provide a user-friendly, free software package ActinSimChem that integrates the implemented simulation algorithms and that is made available to the scientific community for modelling in silico any specific actin-polymerization system.
机译：我们报告了肌动蛋白聚合过程的高级通用蒙特卡罗模拟模型，提供了广泛的应用范围。该模型整合了与肌动蛋白相关的主要反应，例如肌动蛋白核的组装，单体与长丝末端的缔合/解离，通过ADP-Pi形成和ADP-ATP交换的ATP水解，长丝分支，断裂和退火或调节作用蛋白质。重要的是，这些反应与丝中肌动蛋白亚基的核苷酸状态（ATP水解）和肌动蛋白丝长度分布有关的信息有关。所开发的随机模拟建模方案在以下方面得到了验证：i）由确定性模型生成的合成理论数据，以及ii）从荧光pyr-肌动蛋白实验获得的本组和已发表实验数据集。建立在开放式结构原理的基础上，可以扩展设计的模型，以便对其他肌动蛋白相互作用蛋白的活性进行预测性评估，并且可以用于分析基于act的肌动蛋白或荧光显微镜数据。我们提供了一个用户友好的免费软件包ActinSimChem，该软件包集成了已实现的仿真算法，可供科学界在计算机上对任何特定的肌动蛋白聚合系统进行建模。

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