TY - JOUR
T1 - Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus
AU - García-Pérez, Carlos A.
AU - Guo, Xianwu
AU - Navarro, Juan García
AU - Aguilar, Diego Alonso Gómez
AU - Lara-Ramírez, Edgar E.
N1 - Publisher Copyright:
© 2018 The Author(s).
PY - 2018/6/25
Y1 - 2018/6/25
N2 - 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.
AB - 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.
KW - Data-mining
KW - Influenza
KW - Motif-domain interactions
KW - Protein-protein interactions
UR - http://www.scopus.com/inward/record.url?scp=85049058421&partnerID=8YFLogxK
U2 - 10.1186/s12859-018-2237-8
DO - 10.1186/s12859-018-2237-8
M3 - Artículo
SN - 1471-2105
VL - 19
JO - BMC Bioinformatics
JF - BMC Bioinformatics
IS - 1
M1 - 238
ER -