Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
Biophys J. 2018 Oct 16;115(8):1589-1602. doi: 10.1016/j.bpj.2018.08.034. Epub 2018 Sep 1.
Actin filaments continually assemble and disassemble within a cell. Assembled filaments "age" as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate P, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and P release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and P release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and P release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.
肌动蛋白丝在细胞内不断组装和解聚。组装好的纤维随着每个肌动蛋白亚基内结合的核苷酸 ATP 的快速水解而“老化”，随后磷酸盐 P 缓慢释放，留下结合的 ADP。肌动蛋白亚基核苷酸状态的这种细微变化会影响纤维的刚性及其与结合伴侣的相互作用。我们在这里提出了一种系统的多尺度超粗粒化方法，该方法提供了一种计算效率高的方法，可以模拟一个长肌动蛋白丝进行 ATP 水解和磷酸盐释放反应，同时系统地考虑到可用的原子细节。较慢的构象变化及其对化学反应的依赖性通过超粗粒化模型来模拟，该模型通过为粗粒化位点分配内部状态来实现。每个状态都由局部非均匀弹性网络的独特势能面表示。内部状态经历随机跃迁，与基础分子系统的构象耦合。该模型再现了纤维的力学性能，并允许我们研究肌动蛋白亚基中的构象波动是否会产生协同纤维老化。我们发现，相邻亚基的核苷酸状态调节反应动力学，这意味着 ATP 水解和 P 释放的协同性。我们进一步将系统系统地粗粒化为一个马尔可夫状态模型，该模型包含组装和解组装，便于与之前发表的模型进行直接比较。我们发现，ATP 水解和 P 释放的协同作用仅在接近临界 G-肌动蛋白浓度时才会显著影响纤维生长动力学，而在远离该浓度时，协同和随机机制都显示出相似的生长动力学。相比之下，在研究的所有单体浓度下，结合核苷酸分布的纤维组成都有很大的变化。这些结果为我们所知，提供了对 ATP 水解和 P 释放协同性及其对肌动蛋白纤维性质的影响的新见解，为未来的实验研究提供了新的预测。
