Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.
Identifieur interne : 000074 ( Main/Exploration ); précédent : 000073; suivant : 000075Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.
Auteurs : Bhimanagoud Kumbar ; Shivananda Kandagalla [Russie] ; Bharath B R ; Sharath B S ; Riaz MahmoodSource :
- Combinatorial chemistry & high throughput screening [ 1875-5402 ] ; 2020.
Abstract
AIM AND OBJECTIVES
Phytophthora infestans (Mont.) de Bary, fungal pathogen it causes late blight, which results in devastating economic loss among the Solanaceae. The bacillus lipopeptides shows the antagonistic activity against the many plant pathogens, among bacillus lipopeptides Iturin A reported as the antifungal gene. Hence, to understand the in silico antifungal activity, we have selected gene iturin A (AXN89987) produced by Bacillus spp to check the molecular dynamics study with the effector proteins of the P. infestanse. In this concern known effectors proteins of P. infestans were subjected to the protein-protein interaction and followed by simulation.
MATERIAL AND METHOD
Iturin A gene was amplified using the soil bacterium Bacillus subtilis with gene specific primers. Cloned into pTZ 57R/T vector and confirmed by sequencing. To get better insight the protein model was developed for Iturin A using Modeller 9.17, also for the effector proteins by using PDB structure of ID 4MRT (Phosphopantetheine Transferase Sfp) and 1QR0 (4'-phosphopantetheinyl moiety of coenzyme A) as template it shares the identity 72% and expected P-value: 3e-121 respectively. The model quality was assessed using ProSA and PROCHECK programs.
RESULTS
The potency of modelled protein against effector proteins of P. infestans were evaluated in silico using the HADDOCK server and the results showed the high affinity of Iturin A toward the effector protein Host ATG8 (PDB-5L83). Finally, the simulation was performed to the docked conformation of Iturin A with Host ATG8 to further understand the stability of the complex using Desmond program.
CONCLUSION
Altogether the protein-protein interaction and simulation study propose a new methodology and intern it also attempted to uncover possible antifungal activity of iturin A against effector proteins of P. infestans.
DOI: 10.2174/1386207323666200720012054
PubMed: 32691704
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.</title><author><name sortKey="Kumbar, Bhimanagoud" sort="Kumbar, Bhimanagoud" uniqKey="Kumbar B" first="Bhimanagoud" last="Kumbar">Bhimanagoud Kumbar</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author><author><name sortKey="Kandagalla, Shivananda" sort="Kandagalla, Shivananda" uniqKey="Kandagalla S" first="Shivananda" last="Kandagalla">Shivananda Kandagalla</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, 4540008. Russian Federation.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Russie</country><wicri:regionArea>Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk</wicri:regionArea><wicri:noRegion>Chelyabinsk</wicri:noRegion></affiliation></author><author><name sortKey="Bharath B R" sort="Bharath B R" uniqKey="Bharath B R" last="Bharath B R">Bharath B R</name><affiliation><nlm:affiliation>Department of Biotechnology, NMAM, Institute of Technology, NITTE, Karnataka. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka</wicri:noCountry></affiliation></author><author><name sortKey="Sharath B S" sort="Sharath B S" uniqKey="Sharath B S" last="Sharath B S">Sharath B S</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author><author><name sortKey="Mahmood, Riaz" sort="Mahmood, Riaz" uniqKey="Mahmood R" first="Riaz" last="Mahmood">Riaz Mahmood</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32691704</idno><idno type="pmid">32691704</idno><idno type="doi">10.2174/1386207323666200720012054</idno><idno type="wicri:Area/Main/Corpus">000179</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000179</idno><idno type="wicri:Area/Main/Curation">000179</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000179</idno><idno type="wicri:Area/Main/Exploration">000179</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.</title><author><name sortKey="Kumbar, Bhimanagoud" sort="Kumbar, Bhimanagoud" uniqKey="Kumbar B" first="Bhimanagoud" last="Kumbar">Bhimanagoud Kumbar</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author><author><name sortKey="Kandagalla, Shivananda" sort="Kandagalla, Shivananda" uniqKey="Kandagalla S" first="Shivananda" last="Kandagalla">Shivananda Kandagalla</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, 4540008. Russian Federation.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Russie</country><wicri:regionArea>Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk</wicri:regionArea><wicri:noRegion>Chelyabinsk</wicri:noRegion></affiliation></author><author><name sortKey="Bharath B R" sort="Bharath B R" uniqKey="Bharath B R" last="Bharath B R">Bharath B R</name><affiliation><nlm:affiliation>Department of Biotechnology, NMAM, Institute of Technology, NITTE, Karnataka. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka</wicri:noCountry></affiliation></author><author><name sortKey="Sharath B S" sort="Sharath B S" uniqKey="Sharath B S" last="Sharath B S">Sharath B S</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author><author><name sortKey="Mahmood, Riaz" sort="Mahmood, Riaz" uniqKey="Mahmood R" first="Riaz" last="Mahmood">Riaz Mahmood</name><affiliation><nlm:affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</nlm:affiliation><wicri:noCountry code="subField">Karnataka 577451</wicri:noCountry></affiliation></author></analytic><series><title level="j">Combinatorial chemistry & high throughput screening</title><idno type="eISSN">1875-5402</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>AIM AND OBJECTIVES</b></p><p>Phytophthora infestans (Mont.) de Bary, fungal pathogen it causes late blight, which results in devastating economic loss among the Solanaceae. The bacillus lipopeptides shows the antagonistic activity against the many plant pathogens, among bacillus lipopeptides Iturin A reported as the antifungal gene. Hence, to understand the in silico antifungal activity, we have selected gene iturin A (AXN89987) produced by Bacillus spp to check the molecular dynamics study with the effector proteins of the P. infestanse. In this concern known effectors proteins of P. infestans were subjected to the protein-protein interaction and followed by simulation.</p></div><div type="abstract" xml:lang="en"><p><b>MATERIAL AND METHOD</b></p><p>Iturin A gene was amplified using the soil bacterium Bacillus subtilis with gene specific primers. Cloned into pTZ 57R/T vector and confirmed by sequencing. To get better insight the protein model was developed for Iturin A using Modeller 9.17, also for the effector proteins by using PDB structure of ID 4MRT (Phosphopantetheine Transferase Sfp) and 1QR0 (4'-phosphopantetheinyl moiety of coenzyme A) as template it shares the identity 72% and expected P-value: 3e-121 respectively. The model quality was assessed using ProSA and PROCHECK programs.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The potency of modelled protein against effector proteins of P. infestans were evaluated in silico using the HADDOCK server and the results showed the high affinity of Iturin A toward the effector protein Host ATG8 (PDB-5L83). Finally, the simulation was performed to the docked conformation of Iturin A with Host ATG8 to further understand the stability of the complex using Desmond program.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Altogether the protein-protein interaction and simulation study propose a new methodology and intern it also attempted to uncover possible antifungal activity of iturin A against effector proteins of P. infestans.</p></div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32691704</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1875-5402</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Jul</Month><Day>19</Day></PubDate></JournalIssue><Title>Combinatorial chemistry & high throughput screening</Title><ISOAbbreviation>Comb Chem High Throughput Screen</ISOAbbreviation></Journal><ArticleTitle>Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.2174/1386207323666200720012054</ELocationID><Abstract><AbstractText Label="AIM AND OBJECTIVES" NlmCategory="OBJECTIVE">Phytophthora infestans (Mont.) de Bary, fungal pathogen it causes late blight, which results in devastating economic loss among the Solanaceae. The bacillus lipopeptides shows the antagonistic activity against the many plant pathogens, among bacillus lipopeptides Iturin A reported as the antifungal gene. Hence, to understand the in silico antifungal activity, we have selected gene iturin A (AXN89987) produced by Bacillus spp to check the molecular dynamics study with the effector proteins of the P. infestanse. In this concern known effectors proteins of P. infestans were subjected to the protein-protein interaction and followed by simulation.</AbstractText><AbstractText Label="MATERIAL AND METHOD" NlmCategory="METHODS">Iturin A gene was amplified using the soil bacterium Bacillus subtilis with gene specific primers. Cloned into pTZ 57R/T vector and confirmed by sequencing. To get better insight the protein model was developed for Iturin A using Modeller 9.17, also for the effector proteins by using PDB structure of ID 4MRT (Phosphopantetheine Transferase Sfp) and 1QR0 (4'-phosphopantetheinyl moiety of coenzyme A) as template it shares the identity 72% and expected P-value: 3e-121 respectively. The model quality was assessed using ProSA and PROCHECK programs.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The potency of modelled protein against effector proteins of P. infestans were evaluated in silico using the HADDOCK server and the results showed the high affinity of Iturin A toward the effector protein Host ATG8 (PDB-5L83). Finally, the simulation was performed to the docked conformation of Iturin A with Host ATG8 to further understand the stability of the complex using Desmond program.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Altogether the protein-protein interaction and simulation study propose a new methodology and intern it also attempted to uncover possible antifungal activity of iturin A against effector proteins of P. infestans.</AbstractText><CopyrightInformation>Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kumbar</LastName><ForeName>Bhimanagoud</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kandagalla</LastName><ForeName>Shivananda</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, 4540008. Russian Federation.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bharath B R</LastName><AffiliationInfo><Affiliation>Department of Biotechnology, NMAM, Institute of Technology, NITTE, Karnataka. India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sharath B S</LastName><AffiliationInfo><Affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mahmood</LastName><ForeName>Riaz</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka 577451. India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>United Arab Emirates</Country><MedlineTA>Comb Chem High Throughput Screen</MedlineTA><NlmUniqueID>9810948</NlmUniqueID><ISSNLinking>1386-2073</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bacillus</Keyword><Keyword MajorTopicYN="N">HADDOCK</Keyword><Keyword MajorTopicYN="N">Modeller v9.17.</Keyword><Keyword MajorTopicYN="N">Phytophthora infestans</Keyword><Keyword MajorTopicYN="N">Protein interaction</Keyword><Keyword MajorTopicYN="N">iturin A</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>05</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32691704</ArticleId><ArticleId IdType="pii">CCHTS-EPUB-108304</ArticleId><ArticleId IdType="doi">10.2174/1386207323666200720012054</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Russie</li></country></list><tree><noCountry><name sortKey="Bharath B R" sort="Bharath B R" uniqKey="Bharath B R" last="Bharath B R">Bharath B R</name><name sortKey="Kumbar, Bhimanagoud" sort="Kumbar, Bhimanagoud" uniqKey="Kumbar B" first="Bhimanagoud" last="Kumbar">Bhimanagoud Kumbar</name><name sortKey="Mahmood, Riaz" sort="Mahmood, Riaz" uniqKey="Mahmood R" first="Riaz" last="Mahmood">Riaz Mahmood</name><name sortKey="Sharath B S" sort="Sharath B S" uniqKey="Sharath B S" last="Sharath B S">Sharath B S</name></noCountry><country name="Russie"><noRegion><name sortKey="Kandagalla, Shivananda" sort="Kandagalla, Shivananda" uniqKey="Kandagalla S" first="Shivananda" last="Kandagalla">Shivananda Kandagalla</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PlantPathoEffV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000074 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000074 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PlantPathoEffV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32691704
|texte= Protein-protein interaction and molecular dynamics of Iturin A gene on effector proteins Phytophthora infestans.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32691704" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PlantPathoEffV1
| This area was generated with Dilib version V0.6.38. |  |