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. 2018 Jun 25;19(1):238.
doi: 10.1186/s12859-018-2237-8.

Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus

Carlos A García-Pérez  1 , Xianwu Guo  1 , Juan García Navarro  2 , Diego Alonso Gómez Aguilar  1 , Edgar E Lara-Ramírez  3
Affiliations

Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus

Carlos A García-Pérez et al. BMC Bioinformatics. .

Abstract

Background: The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen.

Results: In this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (PPI) from VirusMentha,Virus MINT, IntAct, and Pfam databases, to mine motif-domain interactions (MDIs) stored as Regular Expressions (RegExp) in 3DID database. A total of 107 RegExp related to human MDIs were searched on 51,242 protein fragments from H1N1, H1N2, H2N2, H3N2 and H5N1 strains obtained from Virus Variation database. A total 46 MDIs were frequently mapped on the IAV proteins and shared between the different strains. IAV kept host-like MDIs that were associated with the virus survival, which could be related to essential biological process such as microtubule-based processes, regulation of cell cycle check point, regulation of replication and transcription of DNA, etc. in human cells. The amino acid motifs were searched for matches in the immune epitope database and it was found that some motifs are part of experimentally determined epitopes on IAV, implying that such interactions exist.

Conclusion: The directed data-mining method employed could be used to identify functional motifs in other viruses for envisioning new therapies.

Keywords: Data-mining; Influenza; Motif-domain interactions; Protein-protein interactions.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Flow diagram of the data mining methodology employed
Fig. 2
Fig. 2
Circular layout network representation for MDIs mapped across the five strains and proteins. a) Strain-MDIs network b) Protein-MDI network. The red diamond represents strains a) and proteins b) respectively, the black ellipse represents the MDIs. The edges highlighted are the motifs mentioned in the text. Both figures can be reproduced in Cytoscape with the first four column information presented in the Additional file 2: Table S3
Fig. 3
Fig. 3
The structural localization for the Pkinase_Tyr_LIG_1–1 MDIs on the HA and the amino acid motifs for the H1N1 strain. a) The Haemagglutinin (HA, PDBID: 3Al4), with the Pkinase_Tyr_LIG_1–1 MDI marked in red. b) The RegExp, c, d) Seqlogo showing the frequently amino acid motifs found in the H1NI strain
Fig. 4
Fig. 4
Biological processes related to the MDIs and GO clusters of the IAV-Human mined Network. a) REVIGO summary for the MDIs related GO terms b, c, d, e, f) Identified GO clusters in the IAV-human Network related to the MDIs with the MCODE app for cytoscape
See this image and copyright information in PMC

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