Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins.

Ema Anastasiadou, Ioannis S Vlachos, Ioannis Z Emiris, Panos Kakoulidis, Eleni I Theotoki, Vasiliki I Pantazopoulou, Dimitrios J Stravopodis

Journal: Scientific reports 2025;15(1):9432

PMID: 40108192

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Abstract

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.

Address: Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 16122, Athens, Greece. [email protected].; Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, 11527, Athens, Greece. [email protected].; Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, 11527, Athens, Greece.; Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701, Athens, Greece.; Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece.; Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA.; Cancer Research Institute, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA.; Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.; Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Dana BuildingBoston, MA, 02215, USA.; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 16122, Athens, Greece.; ATHENA Research Center, Aigialias & Chalepa, 15125, Marousi, Greece.; Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15701, Athens, Greece.; Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St, 11527, Athens, Greece.; Department of Health Science, Higher Colleges of Technology (HCT), Academic City Campus, 17155, Dubai, United Arab Emirates.

DOI: 10.1038/s41598-025-91849-5

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MeSH Terms: Humans, Argonaute Proteins, Molecular Dynamics Simulation, Protein Conformation, MicroRNAs, Protein Binding, Binding Sites