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

Number of Access:474（2025-08-15 10:01 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/101355

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Title
In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
Creator
NRID
1000040321749 1000040321749
researchmap permalink
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Scopus Author ID
36762092600 36762092600
CreatorName
Kawaguchi, Shinichi
CreatorName
Xu, Xin
CreatorName
Soga, Takashi
CreatorName
Yamaguchi, Kenta
CreatorName
Kawasaki, Ryuuya
CreatorName
Shimouchi, Ryota
NRID
1000020346175 1000020346175
ORCID
0000-0001-7159-289X 0000-0001-7159-289X
researchmap permalink
read0068638 read0068638
Scopus Author ID
7103003722 7103003722
CreatorName
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
CreatorName
Kai, Toshie
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.
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.
Publisher
eLife Sciences Publications, Ltd
Source Title
eLife
Volume (Issue)
13
Page
RP101967
Date of Issued
2025-04-22
Language
English
Handle URL
https://hdl.handle.net/11094/101355
eISSN
2050084X
Relation.isIdenticalTo
DOI (Publisher Version)
https://doi.org/10.7554/eLife.101967.3
Access Rights
open access
CopyRight
This article is licensed under a Creative Commons Attribution 4.0 International License.
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Version of Record
Category
学術雑誌論文 Journal Article