Document Details
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Document Type |
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Article In Journal |
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Document Title |
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Screening for clusters of charge in human virus proteomes Screening for clusters of charge in human virus proteomes |
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Document Language |
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English |
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Abstract |
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Background: The identification of charge clusters (runs of charged residues) in proteins and their mapping within
the protein structure sequence is an important step toward a comprehensive analysis of how these particular
motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation,
docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these
charge clusters have been designed and described in the literature. In this study, 197 distinctive human viral
proteomes were screened for the occurrence of charge clusters (CC) using a new computational approach.
Results: Three hundred and seventy three CC have been identified within the 2549 viral protein sequences
screened. The number of protein sequences that are CC-free is 2176 (85.3 %) while 150 and 180 proteins contained
positive charge (PCC) and negative charge clusters (NCC), respectively. The NCCs (211 detected) were more
prevalent than PCC (162). PCC-containing proteins are significantly longer than those having NCCs (p = 2.10-16). The
most prevalent virus families having PCC and NCC were Herpesviridae followed by Papillomaviridae. However, the
single-strand RNA group has in average three times more NCC than PCC. According to the functional domain
classification, a significant difference in distribution was observed between PCC and NCC (p = 2. 10−8) with the
occurrence of NCCs being more frequent in C-terminal region while PCC more often fall within functional domains.
Only 29 proteins sequences contained both NCC and PCC. Moreover, 101 NCC were conserved in 84 proteins while
only 62 PCC were conserved in 60 protein sequences. To understand the mechanism by which the membrane
translocation functionalities are embedded in viral proteins, we screened our PCC for sequences corresponding to
cell-penetrating peptides (CPPs) using two online databases: CellPPd and CPPpred. We found that all our PCCs,
having length varying from 7 to 30 amino-acids were predicted as CPPs. Experimental validation is required to
improve our understanding of the role of these PCCs in viral infection process.
Conclusions: Screening distinctive cluster charges in viral proteomes suggested a functional role of these protein
regions and might provide potential clues to improve the current understanding of viral diseases in order to tailor
better preventive and therapeutic approaches. |
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ISSN |
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1471-2164 |
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Journal Name |
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BMC genomics |
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Volume |
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17 |
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Issue Number |
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9 |
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Publishing Year |
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1437 AH
2016 AD |
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Article Type |
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Article |
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Added Date |
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Thursday, July 20, 2017 |
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Researchers
| Najla Kharrat | Kharrat, Najla | Researcher | Doctorate | |
| Sabrine Belmabrouk | Belmabrouk, Sabrine | Researcher | Doctorate | |
| Rania Abdelhedi | Abdelhedi, Rania | Researcher | Doctorate | |
| Riadh Benmarzoug | Benmarzoug, Riadh | Researcher | Doctorate | |
| Mourad Assidi | Assidi, Mourad | Researcher | Doctorate | |
| Mohammed H. Al Qahtani | Al Qahtani, Mohammed H. | Researcher | Doctorate | |
| Ahmed Rebai | Rebai, Ahmed | Researcher | Doctorate | |
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