Monomeric G-actin polymerizes into F-actin to perform various cellular functions. Actin depolymerization drugs, such as latrunculin-A (Lat-A), inhibit filament formation and disrupt the cytoskeleton. Interestingly, the green algae Chlamydomonas alternatively produces a non-conventional actin, NAP1, that responds to inhibition by latrunculin. However, the molecular mechanism underlying latrunculin resistance of NAP1 remains unclear because of the difficulty due to its low in vitro polymerizability. Instead of biochemical experiments, we performed molecular dynamics (MD) simulations to investigate whether NAP1 has a lower affinity for Lat-A than the conventional actins. Our phylogenetic comparison of the binding free energies shows that Lat-A is evolutionarily optimized for skeletal muscles. By decomposing the binding free energy into each amino acid residue, we found that some residues in NAP1 play an important role in latrunculin resistance, suggesting that the primary mechanism of latrunculin resistance is the loss of affinity for Lat-A due to substitutions. In conclusion, our binding-free-energy calculations using MD simulations provide the critical insight that loss of affinity is the direct mechanism of latrunculin resistance.

中文翻译：

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分子动力学模拟揭示非传统肌动蛋白NAP1的Latrunculin抗性机制

单体 G-肌动蛋白聚合成 F-肌动蛋白以执行各种细胞功能。肌动蛋白解聚药物，例如 latrunculin-A (Lat-A)，可抑制丝形成并破坏细胞骨架。有趣的是，绿藻衣藻交替产生一种非常规肌动蛋白 NAP1，它对 latrunculin 的抑制作出反应。然而，由于其体外聚合性较低，导致 NAP1 耐 latrunculin 的分子机制仍不清楚。我们没有进行生化实验，而是进行了分子动力学 (MD) 模拟，以研究 NAP1 对 Lat-A 的亲和力是否比传统肌动蛋白更低。我们对结合自由能的系统发育比较表明，Lat-A 针对骨骼肌进行了进化优化。通过将结合自由能分解为每个氨基酸残基，我们发现NAP1中的一些残基在latrunculin抗性中发挥重要作用，这表明latrunculin抗性的主要机制是由于取代而丧失对Lat-A的亲和力。总之，我们使用 MD 模拟进行的结合自由能计算提供了重要的见解，即亲和力丧失是拉特库林耐药的直接机制。