In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata
Identifieur interne : 003B87 ( Pmc/Corpus ); précédent : 003B86; suivant : 003B88In 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
Links to Exploration step
PMC:4166771Le document en format XML
<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></author><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></author><author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25258487</idno><idno type="pmc">4166771</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166771</idno><idno type="RBID">PMC:4166771</idno><idno type="doi">10.6026/97320630010512</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">003B87</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">003B87</idno></publicationStmt><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></author><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></author><author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name></author></analytic><series><title level="j">Bioinformation</title><idno type="ISSN">0973-8894</idno><idno type="eISSN">0973-2063</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Sharma, Op" uniqKey="Sharma O">OP Sharma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwab, Ae" uniqKey="Schwab A">AE Schwab</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Perez Ca Adillas, Jm" uniqKey="Perez Ca Adillas J">JM Pérez Cañadillas</name></author><author><name sortKey="Varani, G" uniqKey="Varani G">G Varani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Clery, A" uniqKey="Clery A">A Cléry</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformation</journal-id><journal-id journal-id-type="iso-abbrev">Bioinformation</journal-id><journal-id journal-id-type="publisher-id">Bioinformation</journal-id><journal-title-group><journal-title>Bioinformation</journal-title></journal-title-group><issn pub-type="ppub">0973-8894</issn><issn pub-type="epub">0973-2063</issn><publisher><publisher-name>Biomedical Informatics</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25258487</article-id><article-id pub-id-type="pmc">4166771</article-id><article-id pub-id-type="publisher-id">97320630010512</article-id><article-id pub-id-type="doi">10.6026/97320630010512</article-id><article-categories><subj-group subj-group-type="heading"><subject>Hypothesis</subject></subj-group></article-categories><title-group><article-title><italic>In silico</italic> characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Nagaratnam</surname><given-names>Nirupa</given-names></name></contrib><contrib contrib-type="author"><name><surname>Karunanayake</surname><given-names>Eric Hamilton</given-names></name><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Tennekoon</surname><given-names>Kamani Hemamala</given-names></name></contrib><contrib contrib-type="author"><name><surname>Samarakoon</surname><given-names>Sameera Ranganath</given-names></name></contrib><contrib contrib-type="author"><name><surname>Mayan</surname><given-names>Karthika</given-names></name></contrib><aff>Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>Eric Hamilton Karunanayake: <email>erick@ibmbb.cmb.ac.lk</email></corresp></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>30</day><month>8</month><year>2014</year></pub-date><volume>10</volume><issue>8</issue><fpage>512</fpage><lpage>517</lpage><history><date date-type="received"><day>08</day><month>7</month><year>2014</year></date><date date-type="accepted"><day>11</day><month>7</month><year>2014</year></date></history><permissions><copyright-statement>© 2014 Biomedical Informatics</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access"><license-p>This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited.</license-p></license></permissions><abstract><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></abstract><kwd-group><kwd>Cleavage stimulation factor</kwd><kwd>RRM domain</kwd><kwd>superimposition</kwd><kwd>Ramachandran plot</kwd><kwd>pre-mRNA polyadenylation</kwd><kwd>GU-rich downstream sequence element</kwd><kwd>Molecular docking</kwd></kwd-group></article-meta></front><body><sec id="s1"><title>Background</title><p>Human Lymphatic Filariasis (HLF) is a neglected tropical
disease caused by three types of thread like round worms;
<italic>Wuchereria bancrofti</italic>, Brugia malayi, and Brugia timori. Adult
nematodes live for 6-8 years and produce millions of small
larvae. The circulating microfilariae are transmitted by bloodsucking
arthropods (e.g. Culex mosquito). More than 120
million people are currently infected, with about 40 million
disfigured and debilitated by the disease. HLF results in an
altered lymphatic system and chronic lymphoedema, causing
pain and severe disability. Disease transmission is prevented
by annual mass drug administration of single doses of two
medicines given together – albendazole plus either ivermectin
in areas where onchocerciasis is also endemic or
diethylcarbamazine citrate (DEC) in areas where
onchocerciasis is not endemic [<xref rid="R01" ref-type="bibr">1</xref>]. These drugs eliminate
microfilariae from the bloodstream, but cannot clear adult
nematodes that lodge in the lymphatic system. In addition,
studies have reported that many helminth parasites are
developing resistance against albendazole and ivermectin
[<xref rid="R02" ref-type="bibr">2</xref>].</p><p>Therefore, potential research strategies are needed to develop
or design other effective pharmacological therapeutics to
eradicate HLF globally. Due to difficulties in procuring human
filarial parasite material, cattle filarial parasite <italic>Setaria digitata</italic>was studied as a model organism to identify novel drug targets
against HLF. <italic>S. digitata</italic> closely resembles <italic>W. bancrofti</italic> in many
aspects such as morphology, histology, response to drugs and
antigenicity. <italic>S. digitata</italic> cDNA library was constructed and
several cDNA clones had been sequenced and characterized to
identify novel filarial proteins [<xref rid="R03" ref-type="bibr">3</xref>]. The present work is
primarily focused on a selected cDNA sequence which has
nucleotide similarity to human filarial parasite gene sequence.
The structure-function relationship of the hypothetical protein
of <italic>S. digitata</italic> is predicted using similarity search, homology
modelling, superimposition tools, Ramachandran plot analysis
and molecular docking studies <italic>in silico</italic>.</p></sec><sec sec-type="methods" id="s2"><title>Methodology</title><sec id="s2a"><title><italic>cDNA Sequencing</italic>:</title><p>Twenty recombinant clones from <italic>S. digitata</italic> cDNA library were
randomly selected and amplified. Plasmid DNA was isolated
by alkaline lysis method and digested by EcoR1 and Xho1
restriction enzymes. Clones having inserts of more than 500 bp
in length were chosen for DNA sequencing. Sequencing
reactions were performed using BigDye Terminator v3.1 Cycle
Sequencing Kit (Applied Biosystems) with pBK-CMV vector
specific primers T3 and T7. Products of sequencing reactions
were resolved by the genetic analyser; Applied Biosystems®
3500 Dx and data were viewed by BioEdit Sequence Alignment
Editor.</p></sec><sec id="s2b"><title><italic>Nucleotide analysis</italic>:</title><p>Segments of vector origin were removed from insert sequences
by VecScreen program [<xref rid="R04" ref-type="bibr">4</xref>]. Obtained cDNA sequences were
used as query for searching homologous sequences using
BLASTn [<xref rid="R05" ref-type="bibr">5</xref>]. cDNA which contains uncharacterized filarial
parasite protein and shows only partial similarity to human
proteins was selected for further bioinformatics
characterization.</p></sec><sec id="s2c"><title><italic>Amino acid sequence analysis</italic>:</title><p>All possible open reading frames (ORFs) for the selected cDNA
were identified by ORF finder [<xref rid="R06" ref-type="bibr">6</xref>]. Amino acid sequences
derived by conceptual translation of each of the ORFs were
used as query for searching homologous sequences using
BLASTp [<xref rid="R05" ref-type="bibr">5</xref>]. Amino acid sequence which contained putative
conserved domain and shows sequence similarity to human
filarial parasite protein was selected for structural modelling.</p></sec><sec id="s2d"><title><italic>Homology modelling and structural analysis</italic>:</title><p>Three dimensional (3D) structure of <italic>S. digitata</italic> hypothetical
protein was built by SWISS-MODEL Workspace of ExPASy
Proteomics Server [<xref rid="R07" ref-type="bibr">7</xref>] using RRM (RNA recognition motif) of
cleavage stimulation factor 64 kda subunit (CstF-64) (PDB ID:
1P1T_A) as template and viewed by UCSF Chimera tool [<xref rid="R08" ref-type="bibr">8</xref>].
Amino acid sequences of both <italic>S. digitata</italic> and the homologous
protein were aligned using MultAlignViewer function of UCSF
Chimera and active site residues, organization of protein
secondary structures and amino acid sequence of functional
domains were analysed.</p></sec><sec id="s2e"><title><italic>Structure validation and structural comparison</italic>:</title><p>Quality of sdRBP model built was validated by
Ramachandran׳s map using PROCHECK [<xref rid="R09" ref-type="bibr">9</xref>]. 3D structure of
CstF-64 (PDB ID: 1P1T) was downloaded from RCSB-PDB
[<xref rid="R10" ref-type="bibr">10</xref>]
and RRM domain of CstF-64 was separated using UCSF
Chimera. For comparative analysis, RRM of CstF-64 was also
submitted to PROCHECK program and plot statistics were
compared. sdRBP and RRM of CstF-64 were superimposed for
structural similarity using Matchmaker function of UCSF
Chimera and RMSD (root mean square deviation) value was
obtained.</p></sec><sec id="s2f"><title><italic>Automated Molecular Docking</italic>:</title><p>3D structures of two octameric RNAs (PDB ID: 1SA9 and
472D) were retrieved from RCSB-PDB. RNA duplexes were
separated into single strand RNAs (1SA9: 5'-
R(*GP*GP*CP*GP*AP*GP*CP*C)-3', 472D_A: 5'-
R(*GP*UP*GP*UP*UP*UP*AP*C)-3', and 472D_B: 5'-
R(*GP*UP*AP*GP*GP*CP*AP*C)-3') by UCSF Chimera and
docked with sdRBP by Hex 8.0.0 Cuda software
[<xref rid="R11" ref-type="bibr">11</xref>]. Docking
results were viewed by UCSF Chimera. Default parameters
were used for docking process and Energy (E) values of each
docking event were obtained. For comparative analysis RRM
of CstF-64 was docked with the same RNA molecules and E
values were compared.</p></sec><sec id="s2g"><title><italic>Validation of various physiological parameters</italic>:</title><p>Structure-function relationship of sdRBP was further validated
using ProtParam tool of ExPASy Proteomics Server [<xref rid="R12" ref-type="bibr">12</xref>] for
various parameters such as theoretical pI, estimated half-life,
instability index, aliphatic index and grand average of
hydropathicity (GRAVY).</p></sec></sec><sec id="s3"><title>Results & Discussion</title><sec id="s3a"><title><italic>cDNA sequencing</italic>:</title><p>Upon plasmid isolation and restriction enzyme digestion of the
twenty recombinant clones from <italic>S. digitata</italic> cDNA library,
eighteen clones had inserts of more than 500 bp in length and
their nucleotide sequences were obtained.</p></sec><sec id="s3b"><title><italic>Nucleotide sequence analysis</italic>:</title><p>In nucleotide database searches, a 549 bp long cDNA showed
82% nucleotide identity to complete coding sequences of <italic>B.
malayi</italic> putative RNA binding protein (bm-rbp-1) and <italic>W.
bancrofti</italic> putative RNA binding protein. The full-length cDNA
containing a poly A tail and a hypothetical polyadenylation
signal sequence (AATAAA) was named sdrbp for <italic>S. digitata</italic>RNA binding protein. The entire sdrbp sequence contains four
ORFs and sequence analysis of the shortest ORF (249 bp)
reveals an initiation codon (ATG) located within the Kozak
sequence context, GAAAACATGT).</p></sec><sec id="s3c"><title><italic>Amino acid sequence analysis</italic>:</title><p>The shortest ORF encodes an 82 amino acid polypeptide which
contains a RRM domain. In protein database searches, the
polypeptide shows 100% identity to RNA binding protein -
identical [<italic>B. malayi</italic>] and hypothetical protein - partial [<italic>W.
bancrofti</italic>] and 54% identity to the RRM of human CstF-64.</p></sec><sec id="s3d"><title><italic>Homology Modelling and structural analysis</italic>:</title><p>Homology modelling of the hypothetical protein, sdRBP by
SWISS-MODEL Workspace resulted in three PDB files, out of
which the best quality model (<xref ref-type="fig" rid="F1">Figure 1a</xref>) built using RRM
domain (<xref ref-type="fig" rid="F1">Figure 1b</xref>) of
human CstF-64 (<xref ref-type="fig" rid="F1">Figure 1c</xref>) as template
was chosen based on QMEAN scoring function and sequence
identity. sdRBP adopts classical β1α1β2β3α2β4 RRM-topology
forming four stranded β‑sheet packed against two α‑helices.</p></sec><sec id="s3e"><title><italic>Structure validation and structural comparison of sdRBP</italic>:</title><p>sdRBP model built was validated using PROCHECK server
which produced Ramachandran plot calculations and plot
statistics for Φ and ψ distributions for non-glycine non-proline
residues. Similar results were obtained for RRM of CstF-64
template (1P1T_A) suggesting sdRBP model built is reliable.
For structural comparison, sdRBP was superimposed with
RRM of CstF-64 (<xref ref-type="fig" rid="F1">Figure 1d</xref>) and an RMSD of 0.084 A0 was
obtained. Reasonably, a low RMSD value indicates proper
structural and functional similarities between the two proteins;
so it is considered as the best model.</p></sec><sec id="s3f"><title><italic>Assessment of structure-function relationship</italic>:</title><p>The template protein, cleavage stimulation factor (CstF) is a
heterotrimeric protein complex which plays a key role in
polyadenylation of mRNA precursors. In vertebrates,
polyadenylation site comprises two elements: AAUAAA
hexamer and a more diffuse GU-rich sequence. GU-rich
sequence is recognized by the 64 kDa subunit of CstF (CstF-
64). CstF-64 is a multi-domain protein and the RRM is a 104
amino acid long domain located at the N-terminus of the
protein. Studies have revealed that CstF-64 forms more stable
complexes with GU-rich sequences containing at least two
consecutive Us [<xref rid="R13" ref-type="bibr">13</xref>].</p><p>Classical RRM domain is identified at the primary sequence
level as a 90 amino acids long polypeptide containing two
conserved sequences of eight and six amino acids called RNP1
([R/K]-G-[F/Y]-[G/A]-[F/Y]-[I/L/V]-X-[F/Y]) and RNP2
([I/L/V]-[F/Y]-[I/L/V]-X-N-L) located in the two central
β‑strands, β3 and β1 of the motif respectively exposing three
conserved aromatic residues [<xref rid="R14" ref-type="bibr">14</xref>]. In the proposed RNP1
(RGFGFCEF) and RNP2 (VFVGNL) sequences of sdRBP, all
amino acids except for one residue are conserved and expected
to form the primary RNA binding surface (<xref ref-type="fig" rid="F1">Figure 1e & 2a</xref>).
Four key amino acids of the RRM of human CstF-64 reported
to be essential for RNA binding activity are conserved in
sdRBP in similar positions (<xref ref-type="fig" rid="F2">Figure 2b</xref>).</p></sec><sec id="s3g"><title><italic>Automated molecular docking</italic>:</title><p>Consistent with structure-function similarities, automated
molecular docking studies have demonstrated that sdRBP has
a greater binding affinity to GU-rich RNA (<xref ref-type="fig" rid="F3">Figure 3a</xref>). Upon
docking of sdRBP with the three types of RNA octamers, larger
energy values <xref ref-type="supplementary-material" rid="SD1">Table 1</xref> (see supplementary material) were
obtained for GU-rich RNA which comprises of consecutive Us
and similar results were obtained for docking of RRM of CstF-
64 with same RNA octamers (<xref ref-type="fig" rid="F3">Figure 3b</xref>). Since RRM of CstF-64
and sdRBP share 54% sequence identity and their docking
energy values are similar, this is an evidence to believe that
sdRBP has similar biological function as that for CstF-64.</p></sec><sec id="s3h"><title><italic>Validation of various physiological parameters</italic>:</title><p>The functional similarity was further validated by Protparam
which reveals sdRBP to have a theoretical pI of 5.75 and
estimated half-life to be >20 hours (yeast, <italic>in vivo</italic>). The
instability index (II) is computed to be 30.60 and this classifies
the protein as stable. Grand average of hydropathicity
(GRAVY) is -0.293 and aliphatic index of sdRBP is 65.37. As
mentioned in the Protparam tool, aliphatic index is regarded as
a positive factor for the increase of thermo stability of globular
proteins.</p></sec></sec><sec id="s4"><title>Conclusion</title><p><italic>In silico</italic> structural modelling and automated molecular
docking of <italic>S. digitata</italic> predicted protein using different
bioinformatics tools, suggest that it has similar structural and
functional features as human CstF-64 and therefore, predicted
to be involved in pre-mRNA polyadenylation process.
Therefore, 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></sec><sec sec-type="supplementary-material"><title>Supplementary material</title><supplementary-material content-type="local-data" id="SD1"><caption><title>Data 1</title></caption><media mimetype="application" mime-subtype="pdf" xlink:href="97320630010512S1.pdf" xlink:type="simple" id="d35e423" position="anchor"></media></supplementary-material></sec></body><back><ack><p>Financial support from International Programme in Chemical
Sciences, University of Uppsala, Sweden and sida Secretariat
for Research Cooperation with Developing countries (formerly
SAREC) are gratefully acknowledged. We would like to thank
Kanchana Senanayake for providing computational assistance
and Anoma jayasoma for supporting in DNA sequencing.</p></ack><fn-group><fn id="FN1" fn-type="other"><p><bold>Citation:</bold>Nagaratnam <italic>et al</italic>, Bioinformation 10(8): 512-517 (2014)</p></fn></fn-group><ref-list><title>References</title><ref id="R01"><label>1</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sharma</surname><given-names>OP</given-names></name><etal></etal></person-group><source>J Vector Borne Dis</source><year>2013</year><volume>50</volume><fpage>155</fpage><pub-id pub-id-type="pmid">24220073</pub-id></element-citation></ref><ref id="R02"><label>2</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schwab</surname><given-names>AE</given-names></name><etal></etal></person-group><source>Am J Trop Med Hyg</source><year>2005</year><volume>73</volume><fpage>234</fpage><pub-id pub-id-type="pmid">16103581</pub-id></element-citation></ref><ref id="R03"><label>3</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://repo.jfn.ac.lk/med/handle/701/925">http://repo.jfn.ac.lk/med/handle/701/925</ext-link></comment></element-citation></ref><ref id="R04"><label>4</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/tools/vecscreen/">http://www.ncbi.nlm.nih.gov/tools/vecscreen/</ext-link></comment></element-citation></ref><ref id="R05"><label>5</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?/PROGRAM=/blastn&/PAGE_/TYPE=/BlastSearch&/LINK_/LOC=/blasthome">https://blast.ncbi.nlm.nih.gov/Blast.cgi?/PROGRAM=/blas
tn&/PAGE_/TYPE=/BlastSearch&/LINK_/LOC=/blasthome</ext-link></comment></element-citation></ref><ref id="R06"><label>6</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/gorf/gorf.html">https://www.ncbi.nlm.nih.gov/gorf/gorf.html</ext-link></comment></element-citation></ref><ref id="R07"><label>7</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://swissmodel.expasy.org/workspace/">http://swissmodel.expasy.org/workspace/</ext-link></comment></element-citation></ref><ref id="R08"><label>8</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="www.cgl.ucsf.edu/chimera/">www.cgl.ucsf.edu/chimera/</ext-link></comment></element-citation></ref><ref id="R09"><label>9</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="www.ebi.ac.uk/thornton-srv/software/PROCHECK/">www.ebi.ac.uk/thornton-srv/software/PROCHECK/</ext-link></comment></element-citation></ref><ref id="R10"><label>10</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://www.rcsb.org/pdb/home/home.do">http://www.rcsb.org/pdb/home/home.do</ext-link></comment></element-citation></ref><ref id="R11"><label>11</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://hex.loria.fr/">http://hex.loria.fr/</ext-link></comment></element-citation></ref><ref id="R12"><label>12</label><element-citation publication-type="webpage"><comment><ext-link ext-link-type="uri" xlink:href="http://web.expasy.org/protparam/">http://web.expasy.org/protparam/</ext-link></comment></element-citation></ref><ref id="R13"><label>13</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pérez Cañadillas</surname><given-names>JM</given-names></name><name><surname>Varani</surname><given-names>G</given-names></name></person-group><source>EMBO J</source><year>2003</year><volume>22</volume><fpage>2821</fpage><pub-id pub-id-type="pmid">12773396</pub-id></element-citation></ref><ref id="R14"><label>14</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cléry</surname><given-names>A</given-names></name><etal></etal></person-group><source>Curr Opin Struc Biol</source><year>2008</year><volume>18</volume><fpage>290</fpage><pub-id pub-id-type="pmid">18515081</pub-id></element-citation></ref></ref-list></back><floats-group><fig id="F1" position="float"><label>Figure 1</label><caption><p>(a) Homology model of the hypothetical protein,
sdRBP built by SWISS-MODEL Workspace. (b) NMR structure
of the N-terminal RRM domain of human CstF-64 (PDB ID:
1P1T_A). (c) NMR structure of human CstF-64 (PDB ID: 1P1T)
retrieved from RCSB-PDB (d) Superposition of sdRBP (blue)
with the RRM of CstF-64 (pink) showing how similar these
proteins are even in the orientation of the loops, with one
significant exception at two N- and C-terminal helices of the
RRM of CstF-64 which are not found in sdRBP. (e) Proposed
RNP1 (RGFGFCEF) and RNP2 (VFVGNL) sequences of sdRBP
are located in the two central β‑strands, β3 and β1 respectively</p></caption><graphic xlink:href="97320630010512F1"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p>(a) 82 amino acid polypeptide (sdRBP) derived by the conceptual translation of the shortest ORF (249 bp) showing the
locations and sequences of four β strands (green) and two α helices (yellow). (b) Multiple alignment of sdRBP with CstF-64 using
UCSF chimera results in 54% amino acid identity and the four key amino acids of the RRM of CstF-64 (S10, F12, R39, and F54)
reported to be essential for RNA binding activity are conserved in sdRBP (conserved positions are indicated in the alignment by
red spots).</p></caption><graphic xlink:href="97320630010512F2"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p>(a) Automated molecular docking of sdRBP with three types of RNA octamers shown in pink (1: 5'GUGUUUAC-3'
[472D_A], 2: 5'GUAGGCAC-3' [472D_B], 3: 5'- GGCGAGCC)-3' [1SA9]) using Hex 8.0.0 Cuda software (viewed by UCSF Chimera)
showing sdRBP has greater binding affinity to GU-rich RNA which comprises of consecutive Us (a.1). (b) Automated molecular
docking of RRM of CstF-64 with the same three types of RNA octamers results in comparable results as obtained for sdRBP
revealing the fact that sdRBP has significant functional similarity with human CstF-64.</p></caption><graphic xlink:href="97320630010512F3"></graphic></fig></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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