Alisaraie Laleh, Stueker Oliver, Tati Sayi'Mone
School of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr, St. John's A1B3V6, Canada.
ACENET, Memorial University of Newfoundland, 230 Elizabeth Ave, St. John's A1C5S7, Canada.
Comput Struct Biotechnol J. 2025 May 20;27:2359-2374. doi: 10.1016/j.csbj.2025.05.024. eCollection 2025.
Cytoskeletal motor protein dynein belongs to the AAA+ superfamily of enzymes, functioning as a mechanochemical ATPase that converts chemical energy into force to drive its retrograde movements along microtubules. Dynein is responsible for cellular cargo transportation; however, viral particles can also recruit dynein. Dynein's mutation is also critical in neurodegenerative and neurodevelopmental diseases. SHE1 is a yeast-specific MT-associated protein that promotes polarizing dynein-mediated spindle movements. Unlike dynein's adaptor proteins, SHE1 is the only protein known to inhibit dynein motility, act independently from dynactin, and alter dynein activity. Despite SHE1's unique mode of action, its structure has not yet been solved experimentally. This work presents the SHE1 structure obtained using Temperature Replica Exchange Molecular Dynamics simulations. The resulting structure was used to explore the conformations of the complex formed by SHE1 binding to dynein and/or microtubule. The conformations of the complex obtained from the computational protein-protein binding study were clustered using the unsupervised machine learning K-means algorithm. The results helped identify the potential SHE1-dynein interaction sites and the participating amino acids, as well as explaining the structural details underlying SHE1's potential inhibitory mechanisms. In one of the two main recognized binding sites of SHE1 in the SHE1-dynein complexes, its inhibitory mechanism can be due to its interference with the long-range allosteric communications of dynein's domains, namely strut-stalk-MTBD. In that binding mode, SHE1 can restrain the AAA1/AAA4 modules of the motor ring, affecting its "open-closed" conformational changes. That suggests SHE1 could directly interfere with the ATP-hydrolyzing modules necessary for dynein motility. In the second observed binding site, SHE1 interacts with MTBD, α-tubulin, and the C-terminal tail of β-tubulin (E-hook) thereby inhibiting the high binding affinity mode of MTBD to microtubules preventing its motility, which aligns with recent experimental data. Characterizing the SHE1 structure and its complex with SHE1-dynein can aid in the design and development of therapeutic peptide inhibitors of dynein or its mutants for treating dynein-involved diseases.
细胞骨架运动蛋白动力蛋白属于AAA+酶超家族，作为一种机械化学ATP酶发挥作用，将化学能转化为驱动力，沿微管进行逆行运动。动力蛋白负责细胞货物运输；然而，病毒颗粒也可以招募动力蛋白。动力蛋白的突变在神经退行性疾病和神经发育疾病中也至关重要。SHE1是一种酵母特异性微管相关蛋白，可促进极化动力蛋白介导的纺锤体运动。与动力蛋白的衔接蛋白不同，SHE1是已知的唯一一种抑制动力蛋白运动、独立于动力肌动蛋白发挥作用并改变动力蛋白活性的蛋白质。尽管SHE1具有独特的作用方式，但其结构尚未通过实验解析。这项工作展示了使用温度复制交换分子动力学模拟获得的SHE1结构。所得结构用于探索SHE1与动力蛋白和/或微管结合形成的复合物的构象。从计算蛋白质-蛋白质结合研究中获得的复合物构象使用无监督机器学习K均值算法进行聚类。这些结果有助于确定潜在的SHE1-动力蛋白相互作用位点和参与的氨基酸，以及解释SHE1潜在抑制机制的结构细节。在SHE1-动力蛋白复合物中SHE1两个主要公认结合位点之一，其抑制机制可能是由于它干扰了动力蛋白结构域的远程变构通讯，即支柱-柄-微管结合结构域。在那种结合模式下，SHE1可以抑制运动环中的AAA1/AAA4模块，影响其“开放-关闭”构象变化。这表明SHE1可能直接干扰动力蛋白运动所需的ATP水解模块。在第二个观察到的结合位点，SHE1与微管结合结构域、α-微管蛋白和β-微管蛋白的C末端尾巴（E钩）相互作用，从而抑制微管结合结构域与微管的高结合亲和力模式，阻止其运动，这与最近的实验数据一致。表征SHE1结构及其与SHE1-动力蛋白的复合物有助于设计和开发动力蛋白或其突变体的治疗性肽抑制剂，用于治疗与动力蛋白相关的疾病。
