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

doi:10.1016/j.xpro.2022.101648

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

STAR Protoc. 2022 Aug 3;3(3):101648. doi: 10.1016/j.xpro.2022.101648. eCollection 2022 Sep 16.

Authors

David D Holcomb¹, Katarzyna I Jankowska², Nancy Hernandez², Kyle Laurie², Jacob Kames², Nobuko Hamasaki-Katagiri², Anton A Komar³, Michael DiCuccio⁴, Chava Kimchi-Sarfaty⁵

Affiliations

¹ 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. Electronic address: holcombddf@gmail.com.
² 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.
³ Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.
⁴ National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
⁵ 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. Electronic address: chava.kimchi-sarfaty@fda.hhs.gov.

Abstract

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).

Keywords: Bioinformatics; Computer sciences; Genetics; Health sciences; Molecular biology.

Publication types

Research Support, U.S. Gov't, P.H.S.

MeSH terms

Binding Sites
COVID-19* / genetics
Host Microbial Interactions
Humans
SARS-CoV-2* / genetics
Viral Proteins / genetics

Substances

Viral Proteins

Grants and funding

R01 HL151392/HL/NHLBI NIH HHS/United States