Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study.
Identifieur interne : 000088 ( Main/Exploration ); précédent : 000087; suivant : 000089Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study.
Auteurs : Jefferson O. Romero [Chili] ; Elena Fernández-Fueyo [Espagne, Pays-Bas] ; Fabián Avila-Salas [Chili] ; Rodrigo Recabarren [Chili] ; Jans Alzate-Morales [Chili] ; Angel T. Martínez [Espagne]Source :
- Computational and structural biotechnology journal [ 2001-0370 ] ; 2019.
Abstract
Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of Phanerochaete chrysosporium LiP (isoenzyme H8) with VA and its radical cation (VA•+, resulting from substrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA•+ enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264, and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental results were further rationalized through new calculations of interaction energies between VA/VA•+ and LiP with each of the single mutations. Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.
DOI: 10.1016/j.csbj.2019.07.002
PubMed: 31452859
PubMed Central: PMC6700493
Affiliations:
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Romero</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca</wicri:regionArea><wicri:noRegion>Talca</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Doctorado en Ciencias Mencion Investigacion y Desarrollo de Productos Bioactivos, Instituto de Química de Recursos Naturales, Universidad de Talca, 2 Norte 685, Casilla 747, Talca, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Doctorado en Ciencias Mencion Investigacion y Desarrollo de Productos Bioactivos, Instituto de Química de Recursos Naturales, Universidad de Talca, 2 Norte 685, Casilla 747, Talca</wicri:regionArea><wicri:noRegion>Talca</wicri:noRegion></affiliation></author><author><name sortKey="Fernandez Fueyo, Elena" sort="Fernandez Fueyo, Elena" uniqKey="Fernandez Fueyo E" first="Elena" last="Fernández-Fueyo">Elena Fernández-Fueyo</name><affiliation wicri:level="2"><nlm:affiliation>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid</wicri:regionArea><placeName><region nuts="2" type="communauté">Communauté de Madrid</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft</wicri:regionArea><wicri:noRegion>Delft</wicri:noRegion></affiliation></author><author><name sortKey="Avila Salas, Fabian" sort="Avila Salas, Fabian" uniqKey="Avila Salas F" first="Fabián" last="Avila-Salas">Fabián Avila-Salas</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba</wicri:regionArea><wicri:noRegion>Huechuraba</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Escuela de Agronomía, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Escuela de Agronomía, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba</wicri:regionArea><wicri:noRegion>Huechuraba</wicri:noRegion></affiliation></author><author><name sortKey="Recabarren, Rodrigo" sort="Recabarren, Rodrigo" uniqKey="Recabarren R" first="Rodrigo" last="Recabarren">Rodrigo Recabarren</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca</wicri:regionArea><wicri:noRegion>Talca</wicri:noRegion></affiliation></author><author><name sortKey="Alzate Morales, Jans" sort="Alzate Morales, Jans" uniqKey="Alzate Morales J" first="Jans" last="Alzate-Morales">Jans Alzate-Morales</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca</wicri:regionArea><wicri:noRegion>Talca</wicri:noRegion></affiliation></author><author><name sortKey="Martinez, Angel T" sort="Martinez, Angel T" uniqKey="Martinez A" first="Angel T" last="Martínez">Angel T. Martínez</name><affiliation wicri:level="2"><nlm:affiliation>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid</wicri:regionArea><placeName><region nuts="2" type="communauté">Communauté de Madrid</region></placeName></affiliation></author></analytic><series><title level="j">Computational and structural biotechnology journal</title><idno type="ISSN">2001-0370</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of <i>Phanerochaete chrysosporium</i> LiP (isoenzyme H8) with VA and its radical cation (VA<sup>•+</sup>, resulting from substrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA<sup>•+</sup> enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264, and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental results were further rationalized through new calculations of interaction energies between VA/VA<sup>•+</sup> and LiP with each of the single mutations. Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31452859</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2001-0370</ISSN><JournalIssue CitedMedium="Print"><Volume>17</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Computational and structural biotechnology journal</Title><ISOAbbreviation>Comput Struct Biotechnol J</ISOAbbreviation></Journal><ArticleTitle>Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study.</ArticleTitle><Pagination><MedlinePgn>1066-1074</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.csbj.2019.07.002</ELocationID><Abstract><AbstractText>Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of <i>Phanerochaete chrysosporium</i> LiP (isoenzyme H8) with VA and its radical cation (VA<sup>•+</sup>, resulting from substrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA<sup>•+</sup> enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264, and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental results were further rationalized through new calculations of interaction energies between VA/VA<sup>•+</sup> and LiP with each of the single mutations. Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Romero</LastName><ForeName>Jefferson O</ForeName><Initials>JO</Initials><AffiliationInfo><Affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Doctorado en Ciencias Mencion Investigacion y Desarrollo de Productos Bioactivos, Instituto de Química de Recursos Naturales, Universidad de Talca, 2 Norte 685, Casilla 747, Talca, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fernández-Fueyo</LastName><ForeName>Elena</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Avila-Salas</LastName><ForeName>Fabián</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Escuela de Agronomía, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Recabarren</LastName><ForeName>Rodrigo</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alzate-Morales</LastName><ForeName>Jans</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martínez</LastName><ForeName>Angel T</ForeName><Initials>AT</Initials><AffiliationInfo><Affiliation>Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>07</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Comput Struct Biotechnol J</MedlineTA><NlmUniqueID>101585369</NlmUniqueID><ISSNLinking>2001-0370</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Interaction energy</Keyword><Keyword MajorTopicYN="N">Lignin peroxidase</Keyword><Keyword MajorTopicYN="N">Phanerochaete chrysosporium</Keyword><Keyword MajorTopicYN="N">QM/MM</Keyword><Keyword MajorTopicYN="N">SQM</Keyword><Keyword MajorTopicYN="N">Sited-directed mutagenesis</Keyword><Keyword MajorTopicYN="N">Veratryl alcohol</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>05</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>07</Month><Day>03</Day></PubMedPubDate><PubMedPubDate 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Romero</name></noRegion><name sortKey="Alzate Morales, Jans" sort="Alzate Morales, Jans" uniqKey="Alzate Morales J" first="Jans" last="Alzate-Morales">Jans Alzate-Morales</name><name sortKey="Avila Salas, Fabian" sort="Avila Salas, Fabian" uniqKey="Avila Salas F" first="Fabián" last="Avila-Salas">Fabián Avila-Salas</name><name sortKey="Avila Salas, Fabian" sort="Avila Salas, Fabian" uniqKey="Avila Salas F" first="Fabián" last="Avila-Salas">Fabián Avila-Salas</name><name sortKey="Recabarren, Rodrigo" sort="Recabarren, Rodrigo" uniqKey="Recabarren R" first="Rodrigo" last="Recabarren">Rodrigo Recabarren</name><name sortKey="Romero, Jefferson O" sort="Romero, Jefferson O" uniqKey="Romero J" first="Jefferson O" last="Romero">Jefferson O. 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