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  • Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks #MMPMID33103435
  • Nadeau R; Shahryari Fard S; Scheer A; Hashimoto-Roth E; Nygard D; Abramchuk I; Chung YE; Bennett SAL; Lavallee-Adam M
  • J Proteome Res 2020[Nov]; 19 (11): 4553-4566 PMID33103435show ga
  • While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK 293 cells published by Gordon et al. (Nature 2020, 583, 459-468) to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on PPI networks generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in PPI networks. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in PPI networks. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
  • |*Betacoronavirus/chemistry/metabolism/pathogenicity[MESH]
  • |*Coronavirus Infections/metabolism/virology[MESH]
  • |*Pandemics[MESH]
  • |*Pneumonia, Viral/metabolism/virology[MESH]
  • |*Protein Interaction Maps/genetics/physiology[MESH]
  • |Algorithms[MESH]
  • |Amino Acid Motifs[MESH]
  • |COVID-19[MESH]
  • |Cluster Analysis[MESH]
  • |Gene Ontology[MESH]
  • |HEK293 Cells[MESH]
  • |Host-Pathogen Interactions/*genetics[MESH]
  • |Humans[MESH]
  • |Molecular Sequence Annotation[MESH]
  • |Protein Binding[MESH]
  • |Proteins/chemistry/classification/genetics/metabolism[MESH]
  • |SARS-CoV-2[MESH]
  • |Viral Proteins/chemistry/genetics/metabolism[MESH]

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  • suck abstract from ncbi

    4553 11.19 2020