In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin.
Identifieur interne : 000413 ( Main/Exploration ); précédent : 000412; suivant : 000414In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin.
Auteurs : Le Thanh Mai Pham [Corée du Sud] ; Hogyun Seo [Corée du Sud] ; Kyung-Jin Kim [Corée du Sud] ; Yong Hwan Kim [Corée du Sud]Source :
- Biotechnology for biofuels [ 1754-6834 ] ; 2018.
Abstract
Background
The lignin peroxidase isozyme H8 from the white-rot fungus
Results
The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from
Conclusion
Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.
DOI: 10.1186/s13068-018-1324-4
PubMed: 30555531
PubMed Central: PMC6287364
Affiliations:
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Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu</wicri:regionArea><wicri:noRegion>Daegu</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Kyung Jin" sort="Kim, Kyung Jin" uniqKey="Kim K" first="Kyung-Jin" last="Kim">Kyung-Jin Kim</name><affiliation wicri:level="1"><nlm:affiliation>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu</wicri:regionArea><wicri:noRegion>Daegu</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Yong Hwan" sort="Kim, Yong Hwan" uniqKey="Kim Y" first="Yong Hwan" last="Kim">Yong Hwan Kim</name><affiliation wicri:level="1"><nlm:affiliation>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan</wicri:regionArea><wicri:noRegion>Ulsan</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30555531</idno><idno type="pmid">30555531</idno><idno type="doi">10.1186/s13068-018-1324-4</idno><idno type="pmc">PMC6287364</idno><idno type="wicri:Area/Main/Corpus">000316</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" 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sortKey="Seo, Hogyun" sort="Seo, Hogyun" uniqKey="Seo H" first="Hogyun" last="Seo">Hogyun Seo</name><affiliation wicri:level="1"><nlm:affiliation>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu</wicri:regionArea><wicri:noRegion>Daegu</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Kyung Jin" sort="Kim, Kyung Jin" uniqKey="Kim K" first="Kyung-Jin" last="Kim">Kyung-Jin Kim</name><affiliation wicri:level="1"><nlm:affiliation>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu</wicri:regionArea><wicri:noRegion>Daegu</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Yong Hwan" sort="Kim, Yong Hwan" uniqKey="Kim Y" first="Yong Hwan" last="Kim">Yong Hwan Kim</name><affiliation wicri:level="1"><nlm:affiliation>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan</wicri:regionArea><wicri:noRegion>Ulsan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Biotechnology for biofuels</title><idno type="ISSN">1754-6834</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>Background</b></p><p>The lignin peroxidase isozyme H8 from the white-rot fungus </p></div><div type="abstract" xml:lang="en"><p><b>Results</b></p><p>The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from </p></div><div type="abstract" xml:lang="en"><p><b>Conclusion</b></p><p>Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30555531</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1754-6834</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>Biotechnology for biofuels</Title><ISOAbbreviation>Biotechnol Biofuels</ISOAbbreviation></Journal><ArticleTitle>In silico-designed lignin peroxidase from <i>Phanerochaete chrysosporium</i> shows enhanced acid stability for depolymerization of lignin.</ArticleTitle><Pagination><MedlinePgn>325</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13068-018-1324-4</ELocationID><Abstract><AbstractText Label="Background" NlmCategory="UNASSIGNED">The lignin peroxidase isozyme H8 from the white-rot fungus <i>Phanerochaete chrysosporium</i> (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin.</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from <i>Phanerochaete chrysosporium</i> and acid-stable manganese peroxidase isozyme 6 (MnP6) from <i>Ceriporiopsis subvermispora.</i> Effective salt bridges were probed by molecular dynamics simulation and changes to Gibbs free energy following mutagenesis were predicted, suggesting promising variants with higher stability under extremely acidic conditions. The rationally designed variant, A55R/N156E-H239E, demonstrated a 12.5-fold increased half-life under extremely acidic conditions, 9.9-fold increased catalytic efficiency toward veratryl alcohol, and a 7.8-fold enhanced lignin model dimer conversion efficiency compared to those of native LiPH8. Furthermore, the two constructed salt bridges in the variant A55R/N156E-H239E were experimentally confirmed to be identical to the intentionally designed LiPH8 variant using X-ray crystallography (PDB ID: 6A6Q).</AbstractText><AbstractText Label="Conclusion" NlmCategory="UNASSIGNED">Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pham</LastName><ForeName>Le Thanh Mai</ForeName><Initials>LTM</Initials><AffiliationInfo><Affiliation>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea.</Affiliation><Identifier Source="ISNI">0000 0004 0381 814X</Identifier><Identifier Source="GRID">grid.42687.3f</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seo</LastName><ForeName>Hogyun</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</Affiliation><Identifier Source="ISNI">0000 0001 0661 1556</Identifier><Identifier Source="GRID">grid.258803.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Kyung-Jin</ForeName><Initials>KJ</Initials><AffiliationInfo><Affiliation>2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.</Affiliation><Identifier Source="ISNI">0000 0001 0661 1556</Identifier><Identifier Source="GRID">grid.258803.4</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Yong Hwan</ForeName><Initials>YH</Initials><AffiliationInfo><Affiliation>1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea.</Affiliation><Identifier Source="ISNI">0000 0004 0381 814X</Identifier><Identifier Source="GRID">grid.42687.3f</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>12</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biotechnol Biofuels</MedlineTA><NlmUniqueID>101316935</NlmUniqueID><ISSNLinking>1754-6834</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Acid stability</Keyword><Keyword MajorTopicYN="N">In silico design</Keyword><Keyword MajorTopicYN="N">Lignin degradation</Keyword><Keyword MajorTopicYN="N">Lignin peroxidase</Keyword><Keyword MajorTopicYN="N">Phanerochaete chrysosporium</Keyword><Keyword MajorTopicYN="N">Salt bridges</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>09</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>11</Month><Day>29</Day></PubMedPubDate><PubMedPubDate 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