Department of Chemistry, University College London, London, UK.
School of Physics and Astronomy, University of Leeds, Leeds, UK.
Q Rev Biophys. 2020 Aug 10;53:e9. doi: 10.1017/S0033583520000062.
Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject to explicit thermal noise, we have quantified the constraints on the range of molecular conformations that can be explored by dynein-c within the crowded architecture of the axoneme. We subsequently assess the influence of crowding on the 3D exploration of microtubule-binding sites, and specifically on the axial step length. Our calculations combine experimental information on the shape, flexibility and environment of dynein-c from three distinct sources; negative stain electron microscopy, cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET). Our FFEA simulations show that the super-macromolecular organisation of multiple protein complexes into higher-order structures can have a significant influence on the effective flexibility of the individual molecular components, and may, therefore, play an important role in the physical mechanisms underlying their biological function.
鞭毛动力蛋白是产生纤毛和鞭毛传播弯曲运动的分子马达。它们位于一个密集排列且高度组织化的超大分子细胞骨架结构中，称为轴丝。我们使用介观模拟技术 Fluctuating Finite Element Analysis (FFEA)，将蛋白质表示为受显式热噪声影响的粘弹性连续体物体，从而量化了在轴丝拥挤的结构内，动力蛋白-c 可以探索的分子构象范围的限制。我们随后评估了拥挤对微管结合位点的 3D 探索的影响，特别是对轴向步长的影响。我们的计算结合了来自三个不同来源的关于动力蛋白-c 的形状、灵活性和环境的实验信息：负染色电子显微镜、冷冻电子显微镜 (cryo-EM) 和冷冻电子断层扫描 (cryo-ET)。我们的 FFEA 模拟表明，多个蛋白质复合物的超大分子组织成更高阶结构会对单个分子成分的有效灵活性产生重大影响，因此可能在其生物学功能的物理机制中发挥重要作用。
