In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins

Kawaguchi, Shinichi; Xu, Xin; Soga, Takashi; Yamaguchi, Kenta; Kawasaki, Ryuuya; Shimouchi, Ryota; Date, Susumu; Kai, Toshie

doi:https://doi.org/10.7554/eLife.101967.3

In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins

Kawaguchi, Shinichi; Xu, Xin; Soga, Takashi et al.

eLife, 2025, 13, RP101967

アクセス数:474件（2025-08-15 07:41 集計）

固定URL: https://hdl.handle.net/11094/101355

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タイトル	In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
著者	NRID 1000040321749 1000040321749 researchmap permalink 1234567890abc 1234567890abc Scopus Author ID 36762092600 36762092600 著者名 Kawaguchi, Shinichi
	著者名 Xu, Xin
	著者名 Soga, Takashi
	著者名 Yamaguchi, Kenta
	著者名 Kawasaki, Ryuuya
	著者名 Shimouchi, Ryota
	NRID 1000020346175 1000020346175 ORCID 0000-0001-7159-289X 0000-0001-7159-289X researchmap permalink read0068638 read0068638 Scopus Author ID 7103003722 7103003722 著者名 Date, Susumu
	NRID 1000040579786 1000040579786 ORCID 0000-0001-8675-8469 0000-0001-8675-8469 researchmap permalink toshie_kai toshie_kai Scopus Author ID 7102037941 7102037941 著者名 Kai, Toshie
内容	Kawaguchi Shinichi, Xu Xin, Soga Takashi, et al. In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins. eLife 13, RP101967 (2025); https://doi.org/10.7554/eLife.101967.3.
抄録	Protein–protein interactions are fundamental to understanding the molecular functions and regulation of proteins. Despite the availability of extensive databases, many interactionsremain 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.
出版者	eLife Sciences Publications, Ltd
収録物名	eLife
巻(号)	13
ページ	RP101967
刊行年月	2025-04-22
言語	英語
ハンドルURL	https://hdl.handle.net/11094/101355
eISSN	2050084X
関連情報 (isIdenticalTo)	DOI (出版社版) https://doi.org/10.7554/eLife.101967.3
アクセス権	open access
権利情報	This article is licensed under a Creative Commons Attribution 4.0 International License.
出版タイプ	Version of Record
カテゴリ	学術雑誌論文 Journal Article

資源タイプ	学術雑誌論文
ローカル資源タイプ	学術雑誌論文
DCMI資源タイプ	text
DCTERMS.bibliographicCitation	eLife. 2025, 13, p. RP101967
DC.title	In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
DC.creator	Kawaguchi, Shinichi
	Xu, Xin
	Soga, Takashi
	Yamaguchi, Kenta
	Kawasaki, Ryuuya
	Shimouchi, Ryota
	Date, Susumu
	Kai, Toshie
DC.publisher	eLife Sciences Publications, Ltd
DC.language' scheme='DCTERMS.RFC1766	英語
DC.type' scheme='DCTERMS.DCMIType	text
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2025-04-22
DC.identifier	https://doi.org/10.7554/eLife.101967.3
DC.description	Kawaguchi Shinichi, Xu Xin, Soga Takashi, et al. In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins. eLife 13, RP101967 (2025); https://doi.org/10.7554/eLife.101967.3.
DCTERMS.abstract	Protein–protein interactions are fundamental to understanding the molecular functions and regulation of proteins. Despite the availability of extensive databases, many interactionsremain 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.
DC.rights	This article is licensed under a Creative Commons Attribution 4.0 International License.
DC.format	101355
citation_title	In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
citation_author	Kawaguchi, Shinichi
	Xu, Xin
	Soga, Takashi
	Yamaguchi, Kenta
	Kawasaki, Ryuuya
	Shimouchi, Ryota
	Date, Susumu
	Kai, Toshie
citation_publisher	eLife Sciences Publications, Ltd
citation_language	英語
citation_date	2025-04-22
citation_journal_title	eLife
citation_volume	13
citation_firstpage	RP101967
citation_doi	https://doi.org/10.7554/eLife.101967.3
citation_public_url	https://hdl.handle.net/11094/101355

In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins

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