In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata
Identifieur interne : 002E78 ( Main/Merge ); précédent : 002E77; suivant : 002E79In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata
Auteurs : Nirupa Nagaratnam ; Eric Hamilton Karunanayake ; Kamani Hemamala Tennekoon ; Sameera Ranganath Samarakoon ; Karthika MayanSource :
- Bioinformation [ 0973-8894 ] ; 2014.
Abstract
Human lymphatic filariasis (HLF) is a neglected tropical disease which threatens nearly 1.4 billion people in 73 countries
worldwide.
Url:
DOI: 10.6026/97320630010512
PubMed: 25258487
PubMed Central: 4166771
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>In silico</italic>
characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic>
</title>
<author><name sortKey="Nagaratnam, Nirupa" sort="Nagaratnam, Nirupa" uniqKey="Nagaratnam N" first="Nirupa" last="Nagaratnam">Nirupa Nagaratnam</name>
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<author><name sortKey="Karunanayake, Eric Hamilton" sort="Karunanayake, Eric Hamilton" uniqKey="Karunanayake E" first="Eric Hamilton" last="Karunanayake">Eric Hamilton Karunanayake</name>
</author>
<author><name sortKey="Tennekoon, Kamani Hemamala" sort="Tennekoon, Kamani Hemamala" uniqKey="Tennekoon K" first="Kamani Hemamala" last="Tennekoon">Kamani Hemamala Tennekoon</name>
</author>
<author><name sortKey="Samarakoon, Sameera Ranganath" sort="Samarakoon, Sameera Ranganath" uniqKey="Samarakoon S" first="Sameera Ranganath" last="Samarakoon">Sameera Ranganath Samarakoon</name>
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<author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic>
characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic>
</title>
<author><name sortKey="Nagaratnam, Nirupa" sort="Nagaratnam, Nirupa" uniqKey="Nagaratnam N" first="Nirupa" last="Nagaratnam">Nirupa Nagaratnam</name>
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<author><name sortKey="Karunanayake, Eric Hamilton" sort="Karunanayake, Eric Hamilton" uniqKey="Karunanayake E" first="Eric Hamilton" last="Karunanayake">Eric Hamilton Karunanayake</name>
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<author><name sortKey="Tennekoon, Kamani Hemamala" sort="Tennekoon, Kamani Hemamala" uniqKey="Tennekoon K" first="Kamani Hemamala" last="Tennekoon">Kamani Hemamala Tennekoon</name>
</author>
<author><name sortKey="Samarakoon, Sameera Ranganath" sort="Samarakoon, Sameera Ranganath" uniqKey="Samarakoon S" first="Sameera Ranganath" last="Samarakoon">Sameera Ranganath Samarakoon</name>
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<author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name>
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<series><title level="j">Bioinformation</title>
<idno type="ISSN">0973-8894</idno>
<idno type="eISSN">0973-2063</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>Human lymphatic filariasis (HLF) is a neglected tropical disease which threatens nearly 1.4 billion people in 73 countries
worldwide. <italic>Wuchereria bancrofti</italic>
is the major causative agent of HLF and it closely resembles cattle filarial parasite <italic>Setaria digitata</italic>
.
Due to difficulties in procuring <italic>W. bancrofti</italic>
parasite material, <italic>S. digitata</italic>
cDNA library has been constructed to identify novel drug
targets against HLF and many of the cDNA sequences are yet to be assigned structure and function. In this study, a 549 bp long
cDNA (<italic>sdrbp</italic>
) has been sequenced and characterized <italic>in silico</italic>
. The shortest ORF of 249 bp from the isolated cDNA encodes a
polypeptide of 82 amino acids and shows an amino acid identity of 54% with the RRM domain of human cleavage stimulation
factor-64 kDa subunit (CstF-64). Structure of the protein (sdRBP) obtained by homology modelling using RRM of CstF-64 as
template adopts classical RRM topology (β1α1β2β3α2β4). sdRBP model built was validated by superimposition tools and
Ramachandran plot analysis. CstF-64 plays an important role in pre-mRNA polyadenylation by interacting with specific GU-rich
downstream sequence element. Molecular docking studies of sdRBP with different RNA molecules revealed that sdRBP has greater
binding affinity to GU-rich RNA and comparable results were obtained upon similar docking of RRM of CstF-64 with the same
RNA molecules. Therefore, sdRBP is likely to perform homologous function in <italic>S. digitata</italic>
. This study brings new dimensions to the
functional analysis of RNA binding proteins of <italic>S. digitata</italic>
and their evaluation as new drug targets against HLF.</p>
</div>
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