In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
Open accessPreprint — published as 10.7554/elife.101967.3 · Paper page
Abstract
Protein–protein interactions are fundamental to understanding the molecular functions and regulation of proteins. Despite the availability of extensive databases, many interactions remain uncharacterized due to the labor-intensive nature of experimental validation. In this study, we utilized the AlphaFold2 program to predict interactions among proteins localized in the nuage, a germline-specific non-membrane organelle essential for piRNA biogenesis in Drosophila . We screened 20 nuage proteins for 1:1 interactions and predicted dimer structures. Among these, five represented novel interaction candidates. Three pairs, including Spn-E_Squ, were verified by co-immunoprecipitation. Disruption of the salt bridges at the Spn-E_Squ interface confirmed their functional importance, underscoring the predictive model’s accuracy. We extended our analysis to include interactions between three representative nuage components—Vas, Squ, and Tej—and approximately 430 oogenesis-related proteins. Co-immunoprecipitation verified interactions for three pairs: Mei-W68_Squ, CSN3_Squ, and Pka-C1_Tej. Furthermore, we screened the majority of Drosophila proteins (~12,000) for potential interaction with the Piwi protein, a central player in the piRNA pathway, identifying 164 pairs as potential binding partners. This in silico approach not only efficiently identifies potential interaction partners but also significantly bridges the gap by facilitating the integration of bioinformatics and experimental biology.
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- Authors
- Kawaguchi, S., Xu, X., Soga, T., Yamaguchi, K., Kawasaki, R., Shimouchi, R., Date, S., & Kai, T.
- Affiliations
- The University of Osaka (JP)
- Graduate School of Frontier Biosciences, Osaka University
- D3 Center, Osaka University
- NEC Solution Innovators, Ltd.
- Graduate School of Information Science and Technology, Osaka University
- Corresponding author
- Kawaguchi, Shinichi
- Kai, Toshie
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2025-04-22
- Volume
- 13
- Pages
- RP101967
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC12014135
- OpenAlex
- W4401158629
- Cited by
- 10
- References
- 57
- Citations by year
- 2026: 7 · 2025: 3
- Type
- posted content
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- OUKA (Osaka University Knowledge Archive) (Osaka University) (submittedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by)
- Funders
- Takeda Science Foundation (J191503009)
- Ministry of Education, Culture, Sports, Science and Technology (21H05275)
- Osaka University (Na22990007)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- nuage, protein-protein interaction, piRNA biogenesis, piRNA pathway, Piwi, Drosophila oogenesis, salt bridges, protein dimerization
- MeSH terms
- Piwi-Interacting RNA, Animals, Computer Simulation, Drosophila melanogaster, Protein Binding, Computational Biology, Protein Interaction Mapping, Drosophila Proteins, RNA, Small Interfering
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