Structure-based prediction of protein-protein interaction network in rice

Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark s...

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Bibliographic Details
Published in:Genetics and molecular biology 2024-01, Vol.47 (1), p.e20230068-e20230068
Main Authors: Sun, Fangnan, Deng, Yaxin, Ma, Xiaosong, Liu, Yuan, Zhao, Lingxia, Yu, Shunwu, Zhang, Lida
Format: Article
Language:English
Subjects:
BIOCHEMISTRY & MOLECULAR BIOLOGY
Docking
Functional morphology
GENETICS & HEREDITY
Genomics and Bioinformatics
interactome
Nucleotides
protein docking
Protein interaction
Protein structure
protein-protein interaction
Proteins
Proteomes
Rice
Single-nucleotide polymorphism
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Summary:Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.
ISSN:1415-4757
1678-4685
1678-4685
DOI:10.1590/1678-4685-GMB-2023-0068