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

David D. Holcomb; Katarzyna I. Jankowska; Nancy Hernandez; Kyle Laurie; Jacob Kames; Nobuko Hamasaki-Katagiri; Anton A. Komar; Michael DiCuccio; Chava Kimchi-Sarfaty

STAR Protocols (Sep 2022)

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

David D. Holcomb,
Katarzyna I. Jankowska,
Nancy Hernandez,
Kyle Laurie,
Jacob Kames,
Nobuko Hamasaki-Katagiri,
Anton A. Komar,
Michael DiCuccio,
Chava Kimchi-Sarfaty

Affiliations

David D. Holcomb: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA; Corresponding author
Katarzyna I. Jankowska: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
Nancy Hernandez: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
Kyle Laurie: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
Jacob Kames: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
Nobuko Hamasaki-Katagiri: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
Anton A. Komar: Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
Michael DiCuccio: National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
Chava Kimchi-Sarfaty: Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA; Corresponding author

Journal volume & issue: Vol. 3, no. 3
p. 101648

Abstract

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Summary: 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). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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Abstract

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