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Optimizing computational prediction of shrimp-WSSV protein interactions through integration of homology- and topology-based predictions

文献类型：期刊论文

作者Yang, Zhanyuan1,3; Yuan, Jianbo1,2,3; Li, Shihao1,2,3; Zhang, Xiaojun1,2,3; Li, Fuhua1,2,3
刊名MOLECULAR GENETICS AND GENOMICS
出版日期2026-01-21
卷号301期号:1页码:10
关键词Protein-protein interactions Penaeid shrimp STRING interaction AlphaFold3 modeling Molecular dynamics simulations
ISSN号1617-4615
DOI10.1007/s00438-025-02347-2
通讯作者Yuan, Jianbo(yuanjb@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
英文摘要Understanding and predicting protein-protein interactions (PPIs) between Penaeus vannamei and white spot syndrome virus (WSSV) is essential for elucidating viral infection mechanisms and developing antiviral strategies in shrimp aquaculture. Traditional experimental methods and classical homology-based computational approaches such as STRING have been used to identify shrimp-WSSV PPIs, but both face inherent limitations in accuracy and scalability. Recently, the breakthrough of AlphaFold3 has enabled PPI prediction from the perspective of complex structures, although its performance requires systematic evaluation. To address these gaps, this study establishes an integrated computational framework that combines homology-based network inference and structure-based (topology-based) complex modeling for predicting shrimp-WSSV PPIs. Homology-based interaction networks and 3D structural models of putative PPIs between three WSSV proteins and host proteins were constructed, including 2580 PPIs of wsv067, 389 PPIs of wsv172, and 2310 PPIs of wsv188. Notably, we found substantial discrepancies between STRING- and AlphaFold3-derived predictions, indicating that reliance on a single method may yield an numerous false positives. Nevertheless, interactions with high STRING scores showed a greater likelihood of forming structurally stable complexes in AlphaFold3. By applying dual thresholds (STRING score > 700 and composite AlphaFold3 score > 0.7) and validating representative complexes using molecular dynamics simulations, we identified a small but reliable set of high-confidence PPIs. These host proteins were primarily enriched in DNA replication, highlighting potential targets that may facilitate WSSV replication after invasion. Together, this work establishes a practical framework for prioritizing virus-host PPIs and reveals mechanistically plausible interactions between WSSV and shrimp, offering promising perspectives for antiviral target discovery and health management in aquaculture.
资助项目Strategic Priority Research Program of the Chinese Academy of Sciences[XDB0730201] ; China Agriculture Research system-48[CARS-48] ; Natural Science Foundation of China[42176105] ; Natural Science Foundation of Shandong Province[ZR2024YQ030] ; Science & Technology Innovation Project of Laoshan Laboratory[LSKJ202203001] ; Taishan Scholars Program[Taishan Scholars Program] ; National Key Research & Development Program of China[2022YFD2400203]
WOS研究方向Biochemistry & Molecular Biology ; Genetics & Heredity
语种英语
WOS记录号WOS:001666686000003
出版者SPRINGER HEIDELBERG
源URL[http://ir.qdio.ac.cn/handle/337002/204595]  
专题海洋研究所_实验海洋生物学重点实验室
通讯作者Yuan, Jianbo; Li, Fuhua
作者单位1.Chinese Acad Sci, Inst Oceanol, State Key Lab Breeding Biotechnol & Sustainable Aq, Qingdao, Peoples R China
2.Chinese Acad Sci, Inst Oceanol, Lab Expt Marine Biol, Qingdao, Peoples R China
3.Qingdao Marine Sci & Technol Ctr, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
推荐引用方式
GB/T 7714		 Yang, Zhanyuan,Yuan, Jianbo,Li, Shihao,et al. Optimizing computational prediction of shrimp-WSSV protein interactions through integration of homology- and topology-based predictions[J]. MOLECULAR GENETICS AND GENOMICS,2026,301(1):10.
APA Yang, Zhanyuan,Yuan, Jianbo,Li, Shihao,Zhang, Xiaojun,&Li, Fuhua.(2026).Optimizing computational prediction of shrimp-WSSV protein interactions through integration of homology- and topology-based predictions.MOLECULAR GENETICS AND GENOMICS,301(1),10.
MLA Yang, Zhanyuan,et al."Optimizing computational prediction of shrimp-WSSV protein interactions through integration of homology- and topology-based predictions".MOLECULAR GENETICS AND GENOMICS 301.1(2026):10.

入库方式： OAI收割

来源：海洋研究所

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