Protein-protein interaction networks as miners of biological discovery.

Steven Wang, Runxin Wu, Jiaqi Lu, Yijia Jiang, Tao Huang, Yu-Dong Cai

Journal: Proteomics 2022;22(15-16):e2100190

PMID: 35567424

Abstract

Protein-protein interactions (PPIs) form the basis of a myriad of biological pathways and mechanism, such as the formation of protein complexes or the components of signaling cascades. Here, we reviewed experimental methods for identifying PPI pairs, including yeast two-hybrid (Y2H), mass spectrometry (MS), co-localization, and co-immunoprecipitation. Furthermore, a range of computational methods leveraging biochemical properties, evolution history, protein structures and more have enabled identification of additional PPIs. Given the wealth of known PPIs, we reviewed important network methods to construct and analyze networks of PPIs. These methods aid biological discovery through identifying hub genes and dynamic changes in the network, and have been thoroughly applied in various fields of biological research. Lastly, we discussed the challenges and future direction of research utilizing the power of PPI networks.

Address: Department of Biological Sciences, Columbia University, New York, New York, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.; Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.; Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.; School of Life Sciences, Shanghai University, Shanghai, China.

DOI: 10.1002/pmic.202100190

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https://doi.org/10.1002/pmic.202100190

MeSH Terms: Protein Interaction Mapping, Protein Interaction Maps, Proteins, Saccharomyces cerevisiae