Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins

• Published in: STAR protocols Vol. 3; no. 3; p. 101648
• Main Authors: Holcomb, David D., Jankowska, Katarzyna I., Hernandez, Nancy, Laurie, Kyle, Kames, Jacob, Hamasaki-Katagiri, Nobuko, Komar, Anton A., DiCuccio, Michael, Kimchi-Sarfaty, Chava
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16.09.2022; Elsevier
• Subjects: Binding Sites; Bioinformatics; Computer sciences; COVID-19 - genetics; Genetics; Health sciences; Host Microbial Interactions; Humans; Molecular biology; Protocol; SARS-CoV-2 - genetics; Viral Proteins - genetics; Health sciences; Genetics; Computer sciences; Molecular biology; Bioinformatics
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2022.101648

Here, we describe a bioinformatics pipeline that evaluates the interactions between coagulation-related proteins and genetic variants with SARS-CoV-2 proteins. This pipeline searches for host proteins that may bind to viral protein and identifies and scores the protein genetic variants to predict the disease pathogenesis in specific subpopulations. Additionally, it is able to find structurally similar motifs and identify potential binding sites within the host-viral protein complexes to unveil viral impact on regulated biological processes and/or host-protein impact on viral invasion or reproduction. For complete details on the use and execution of this protocol, please refer to Holcomb et al. (2021). [Display omitted] •Pipeline identifies coagulation-related proteins that interact with SARS-CoV-2 proteins•The pipeline searches databases such as COVID-19 HGI for host protein genetic variants•Score selected host-protein genetic variants based on numerous in silico tools•Finds similar motifs and regions of protein-protein interaction in viral-host system Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we describe a bioinformatics pipeline that evaluates the interactions between coagulation-related proteins and genetic variants with SARS-CoV-2 proteins. This pipeline searches for host proteins that may bind to viral protein and identifies and scores the protein genetic variants to predict the disease pathogenesis in specific subpopulations. Additionally, it is able to find structurally similar motifs and identify potential binding sites within the host-viral protein complexes to unveil viral impact on regulated biological processes and/or host-protein impact on viral invasion or reproduction.