In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
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 Alp...
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eLife Sciences Publications Ltd
2025-04-01
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| Online Access: | https://elifesciences.org/articles/101967 |
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| author | Shinichi Kawaguchi Xin Xu Takashi Soga Kenta Yamaguchi Ryuuya Kawasaki Ryota Shimouchi Susumu Date Toshie Kai |
| author_facet | Shinichi Kawaguchi Xin Xu Takashi Soga Kenta Yamaguchi Ryuuya Kawasaki Ryota Shimouchi Susumu Date Toshie Kai |
| author_sort | Shinichi Kawaguchi |
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| description | 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. |
| format | Article |
| id | doaj-art-9486b216dccf4015acf80294c426346e |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | eLife Sciences Publications Ltd |
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| spelling | doaj-art-9486b216dccf4015acf80294c426346e2025-08-20T02:24:56ZengeLife Sciences Publications LtdeLife2050-084X2025-04-011310.7554/eLife.101967In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteinsShinichi Kawaguchi0https://orcid.org/0000-0002-7832-1918Xin Xu1Takashi Soga2Kenta Yamaguchi3Ryuuya Kawasaki4Ryota Shimouchi5Susumu Date6Toshie Kai7https://orcid.org/0000-0001-8675-8469Graduate School of Frontier Biosciences, Osaka University, Osaka, JapanGraduate School of Frontier Biosciences, Osaka University, Osaka, JapanD3 Center, Osaka University, Osaka, JapanNEC Solution Innovators, Ltd., Tokyo, JapanNEC Solution Innovators, Ltd., Tokyo, JapanGraduate School of Information Science and Technology, Osaka University, Osaka, JapanD3 Center, Osaka University, Osaka, Japan; Graduate School of Information Science and Technology, Osaka University, Osaka, JapanGraduate School of Frontier Biosciences, Osaka University, Osaka, JapanProtein–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.https://elifesciences.org/articles/101967AlphaFold2protein–protein interactionin silico screeningpiRNAnuage |
| spellingShingle | Shinichi Kawaguchi Xin Xu Takashi Soga Kenta Yamaguchi Ryuuya Kawasaki Ryota Shimouchi Susumu Date Toshie Kai In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins eLife AlphaFold2 protein–protein interaction in silico screening piRNA nuage |
| title | In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins |
| title_full | In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins |
| title_fullStr | In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins |
| title_full_unstemmed | In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins |
| title_short | In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins |
| title_sort | in silico screening by alphafold2 program revealed the potential binding partners of nuage localizing proteins and pirna related proteins |
| topic | AlphaFold2 protein–protein interaction in silico screening piRNA nuage |
| url | https://elifesciences.org/articles/101967 |
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