Kakoulidis Panos, Theotoki Eleni I, Pantazopoulou Vasiliki I, Vlachos Ioannis S, Emiris Ioannis Z, Stravopodis Dimitrios J, Anastasiadou Ema
Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 16122, Athens, Greece.
Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, 11527, Athens, Greece.
Sci Rep. 2025 Mar 19;15(1):9432. doi: 10.1038/s41598-025-91849-5.
The four human Argonaute (AGO) proteins, critical in RNA interference and gene regulation, exhibit high sequence and structural similarity but differ functionally. We investigated the underexplored structural relationships of these paralogs through microsecond-scale molecular dynamics simulations. Our findings reveal that AGO proteins adopt similar, yet unsynchronized, open-close states. We observed similar and unique local conformations, interdomain distances and intramolecular interactions. Conformational differences at GW182/ZSWIM8 interaction sites and in catalytic/pseudo-catalytic tetrads were minimal. Tetrads display conserved movements, interacting with distant miRNA binding residues. We pinpointed long common protein subsequences with consistent molecular movement but varying solvent accessibility per AGO. We observed diverse conformational patterns at the post-transcriptional sites of the AGOs, except for AGO4. By combining simulation data with large datasets of experimental structures and AlphaFold's predictions, we identified proteins with genomic and proteomic similarities. Some of the identified proteins operate in the mitosis pathway, sharing mitosis-related interactors and miRNA targets. Additionally, we suggest that AGOs interact with a mitosis initiator, zinc ion, by predicting potential binding sites and detecting structurally similar proteins with the same function. These findings further advance our understanding for the human AGO protein family and their role in central cellular processes.
四种人类AGO（Argonaute）蛋白在RNA干扰和基因调控中起关键作用，它们在序列和结构上具有高度相似性，但功能不同。我们通过微秒级分子动力学模拟研究了这些旁系同源物尚未充分探索的结构关系。我们的研究结果表明，AGO蛋白采用相似但不同步的开闭状态。我们观察到了相似和独特的局部构象、结构域间距离和分子内相互作用。GW182/ZSWIM8相互作用位点以及催化/假催化四联体的构象差异最小。四联体表现出保守的运动，与远处的miRNA结合残基相互作用。我们确定了长的共同蛋白质子序列，其分子运动一致，但每个AGO的溶剂可及性不同。除了AGO4外，我们在AGO的转录后位点观察到了不同的构象模式。通过将模拟数据与大量实验结构数据集和AlphaFold的预测结果相结合，我们确定了具有基因组和蛋白质组相似性的蛋白质。一些确定的蛋白质在有丝分裂途径中起作用，共享与有丝分裂相关的相互作用分子和miRNA靶点。此外，我们通过预测潜在的结合位点并检测具有相同功能的结构相似蛋白质，表明AGO与有丝分裂启动子锌离子相互作用。这些发现进一步加深了我们对人类AGO蛋白家族及其在细胞核心过程中作用的理解。
