Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2.
COVID-19
/ virology
Coronavirus
/ metabolism
Coronavirus Infections
/ virology
Host Microbial Interactions
/ physiology
Humans
Models, Theoretical
Pandemics
Pneumonia, Viral
/ virology
Programming, Linear
Protein Binding
/ physiology
Protein Interaction Maps
/ physiology
Proteins
/ metabolism
SARS-CoV-2
/ metabolism
Spike Glycoprotein, Coronavirus
/ metabolism
Virus Replication
/ physiology
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
02
07
2020
accepted:
24
11
2020
entrez:
7
12
2020
pubmed:
8
12
2020
medline:
20
1
2021
Statut:
epublish
Résumé
Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks, and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.
Identifiants
pubmed: 33284827
doi: 10.1371/journal.pone.0236304
pii: PONE-D-20-20450
pmc: PMC7721128
doi:
Substances chimiques
Proteins
0
Spike Glycoprotein, Coronavirus
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0236304Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Sci Rep. 2018 Oct 10;8(1):15107
pubmed: 30305653
Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63
pubmed: 24234451
Bioinformatics. 2014 Sep 1;30(17):i438-44
pubmed: 25161231
Cell. 2011 Mar 18;144(6):986-98
pubmed: 21414488
BMC Bioinformatics. 2020 Nov 18;21(Suppl 6):265
pubmed: 33203353
Bioinformatics. 2012 May 1;28(9):1239-45
pubmed: 22419782
Nat Microbiol. 2020 Apr;5(4):536-544
pubmed: 32123347
Bioinformatics. 2015 Jul 1;31(13):2182-9
pubmed: 25725498
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8
pubmed: 15215356
Nucleic Acids Res. 2015 Jan;43(Database issue):D583-7
pubmed: 25392406
Brief Bioinform. 2016 May;17(3):517-26
pubmed: 26261187
BMC Bioinformatics. 2020 Nov 18;21(Suppl 6):434
pubmed: 33203352
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
J Mol Biol. 1970 Mar;48(3):443-53
pubmed: 5420325
BMC Bioinformatics. 2018 Dec 7;19(1):470
pubmed: 30526489
Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5527-30
pubmed: 17945906
Nature. 2020 Jul;583(7816):459-468
pubmed: 32353859
Science. 2003 May 30;300(5624):1399-404
pubmed: 12730501