Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation.
Identifieur interne : 001C37 ( Main/Exploration ); précédent : 001C36; suivant : 001C38Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation.
Auteurs : Manika Awasthi [Inde] ; Nivedita Jaiswal ; Swati Singh ; Veda P. Pandey ; Upendra N. DwivediSource :
- Journal of biomolecular structure & dynamics [ 1538-0254 ] ; 2015.
Descripteurs français
- KwdFr :
- Catalyse (MeSH), Champignons (enzymologie), Conformation des protéines (MeSH), Domaine catalytique (MeSH), Laccase (composition chimique), Lignine (biosynthèse), Lignine (composition chimique), Lignine (métabolisme), Oxydoréduction (MeSH), Plantes (enzymologie), Simulation de docking moléculaire (MeSH), Simulation de dynamique moléculaire (MeSH), Simulation numérique (MeSH).
- MESH :
- biosynthèse : Lignine.
- composition chimique : Laccase, Lignine.
- enzymologie : Champignons, Plantes.
- métabolisme : Lignine.
- Catalyse, Conformation des protéines, Domaine catalytique, Oxydoréduction, Simulation de docking moléculaire, Simulation de dynamique moléculaire, Simulation numérique.
English descriptors
- KwdEn :
- Catalysis (MeSH), Catalytic Domain (MeSH), Computer Simulation (MeSH), Fungi (enzymology), Laccase (chemistry), Lignin (biosynthesis), Lignin (chemistry), Lignin (metabolism), Molecular Docking Simulation (MeSH), Molecular Dynamics Simulation (MeSH), Oxidation-Reduction (MeSH), Plants (enzymology), Protein Conformation (MeSH).
- MESH :
- chemical , biosynthesis : Lignin.
- chemical , chemistry : Laccase, Lignin.
- enzymology : Fungi, Plants.
- chemical , metabolism : Lignin.
- Catalysis, Catalytic Domain, Computer Simulation, Molecular Docking Simulation, Molecular Dynamics Simulation, Oxidation-Reduction, Protein Conformation.
Abstract
Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using in-silico molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, Populus trichocarpa and Trametes versicolor, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase.
DOI: 10.1080/07391102.2014.975282
PubMed: 25301391
Affiliations:
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Pandey</name></author><author><name sortKey="Dwivedi, Upendra N" sort="Dwivedi, Upendra N" uniqKey="Dwivedi U" first="Upendra N" last="Dwivedi">Upendra N. 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Pandey</name></author><author><name sortKey="Dwivedi, Upendra N" sort="Dwivedi, Upendra N" uniqKey="Dwivedi U" first="Upendra N" last="Dwivedi">Upendra N. Dwivedi</name></author></analytic><series><title level="j">Journal of biomolecular structure & dynamics</title><idno type="eISSN">1538-0254</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Catalysis (MeSH)</term><term>Catalytic Domain (MeSH)</term><term>Computer Simulation (MeSH)</term><term>Fungi (enzymology)</term><term>Laccase (chemistry)</term><term>Lignin (biosynthesis)</term><term>Lignin (chemistry)</term><term>Lignin (metabolism)</term><term>Molecular Docking Simulation (MeSH)</term><term>Molecular Dynamics Simulation (MeSH)</term><term>Oxidation-Reduction (MeSH)</term><term>Plants (enzymology)</term><term>Protein Conformation (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Catalyse (MeSH)</term><term>Champignons (enzymologie)</term><term>Conformation des protéines (MeSH)</term><term>Domaine catalytique (MeSH)</term><term>Laccase (composition chimique)</term><term>Lignine (biosynthèse)</term><term>Lignine (composition chimique)</term><term>Lignine (métabolisme)</term><term>Oxydoréduction (MeSH)</term><term>Plantes (enzymologie)</term><term>Simulation de docking moléculaire (MeSH)</term><term>Simulation de dynamique moléculaire (MeSH)</term><term>Simulation numérique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Laccase</term><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Laccase</term><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Champignons</term><term>Plantes</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Fungi</term><term>Plants</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Catalysis</term><term>Catalytic Domain</term><term>Computer Simulation</term><term>Molecular Docking Simulation</term><term>Molecular Dynamics Simulation</term><term>Oxidation-Reduction</term><term>Protein Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Catalyse</term><term>Conformation des protéines</term><term>Domaine catalytique</term><term>Oxydoréduction</term><term>Simulation de docking moléculaire</term><term>Simulation de dynamique moléculaire</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using in-silico molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, Populus trichocarpa and Trametes versicolor, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25301391</PMID><DateCompleted><Year>2016</Year><Month>04</Month><Day>19</Day></DateCompleted><DateRevised><Year>2015</Year><Month>07</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1538-0254</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>9</Issue><PubDate><Year>2015</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J Biomol Struct Dyn</ISOAbbreviation></Journal><ArticleTitle>Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation.</ArticleTitle><Pagination><MedlinePgn>1835-49</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/07391102.2014.975282</ELocationID><Abstract><AbstractText>Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using in-silico molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, Populus trichocarpa and Trametes versicolor, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Awasthi</LastName><ForeName>Manika</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>a Bioinformatics Infrastructure Facility, Center of Excellence in Bioinformatics, Department of Biochemistry , University of Lucknow , Lucknow 226007 , India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jaiswal</LastName><ForeName>Nivedita</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Swati</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Pandey</LastName><ForeName>Veda P</ForeName><Initials>VP</Initials></Author><Author ValidYN="Y"><LastName>Dwivedi</LastName><ForeName>Upendra N</ForeName><Initials>UN</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>11</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Biomol Struct Dyn</MedlineTA><NlmUniqueID>8404176</NlmUniqueID><ISSNLinking>0739-1102</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.10.3.2</RegistryNumber><NameOfSubstance UI="D042845">Laccase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002384" MajorTopicYN="N">Catalysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D042845" MajorTopicYN="N">Laccase</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D062105" MajorTopicYN="N">Molecular Docking Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056004" MajorTopicYN="N">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010084" MajorTopicYN="N">Oxidation-Reduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">homology modeling</Keyword><Keyword MajorTopicYN="N">laccase</Keyword><Keyword MajorTopicYN="N">lignin biosynthesis and degradation</Keyword><Keyword MajorTopicYN="N">molecular docking</Keyword><Keyword MajorTopicYN="N">molecular dynamics simulation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>10</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>10</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25301391</ArticleId><ArticleId IdType="doi">10.1080/07391102.2014.975282</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li></country></list><tree><noCountry><name sortKey="Dwivedi, Upendra N" sort="Dwivedi, Upendra N" uniqKey="Dwivedi U" first="Upendra N" last="Dwivedi">Upendra N. Dwivedi</name><name sortKey="Jaiswal, Nivedita" sort="Jaiswal, Nivedita" uniqKey="Jaiswal N" first="Nivedita" last="Jaiswal">Nivedita Jaiswal</name><name sortKey="Pandey, Veda P" sort="Pandey, Veda P" uniqKey="Pandey V" first="Veda P" last="Pandey">Veda P. Pandey</name><name sortKey="Singh, Swati" sort="Singh, Swati" uniqKey="Singh S" first="Swati" last="Singh">Swati Singh</name></noCountry><country name="Inde"><noRegion><name sortKey="Awasthi, Manika" sort="Awasthi, Manika" uniqKey="Awasthi M" first="Manika" last="Awasthi">Manika Awasthi</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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