Design Strategy of Multi‐electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes
Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and...
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| Veröffentlicht in: | Molecular informatics 2018-08, Vol.37 (8), p.e1700139-n/a |
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| creator | Ooka, Hideshi Hashimoto, Kazuhito Nakamura, Ryuhei |
| description | Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. The different bioenergetics observed between PS II and COX suggest that in addition to the catalytic activity rationalized by the Sabatier principle, stability factors have also provided a major influence on the design strategy of biological multi‐electron transfer enzymes. |
| doi_str_mv | 10.1002/minf.201700139 |
| format | Article |
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Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. The different bioenergetics observed between PS II and COX suggest that in addition to the catalytic activity rationalized by the Sabatier principle, stability factors have also provided a major influence on the design strategy of biological multi‐electron transfer enzymes.</description><identifier>ISSN: 1868-1743</identifier><identifier>EISSN: 1868-1751</identifier><identifier>DOI: 10.1002/minf.201700139</identifier><identifier>PMID: 29756682</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Bacterial Proteins - chemistry ; Bacterial Proteins - metabolism ; Biocatalysis ; Bioenergetics ; Bioinformatics ; Catalysis ; Catalysts ; Catalytic activity ; Chemical evolution ; Chemical reduction ; Communication ; Communications ; Computational Biology - methods ; Cyanobacteria ; Cyanobacteria - enzymology ; Cytochrome ; Cytochrome-c oxidase ; Cytochromes ; Design ; Electron transfer ; Electron Transport Complex IV - chemistry ; Electron Transport Complex IV - metabolism ; Enzymes ; Evolution ; Life-cycle assessment ; Oxidation-Reduction ; Oxygen ; Oxygen evolution ; Photosynthesis ; Photosystem II ; Photosystem II Protein Complex - chemistry ; Photosystem II Protein Complex - metabolism ; Phylogeny ; Protein Engineering - methods ; Respiratory enzymes ; Stability ; Strategy</subject><ispartof>Molecular informatics, 2018-08, Vol.37 (8), p.e1700139-n/a</ispartof><rights>2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.</rights><rights>2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.</rights><rights>2018 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5719-c9ec5dc82c7e05b20220210659080f9d418c28670bd50f9ddfb8e2738b1bd8cc3</citedby><cites>FETCH-LOGICAL-c5719-c9ec5dc82c7e05b20220210659080f9d418c28670bd50f9ddfb8e2738b1bd8cc3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fminf.201700139$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fminf.201700139$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29756682$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ooka, Hideshi</creatorcontrib><creatorcontrib>Hashimoto, Kazuhito</creatorcontrib><creatorcontrib>Nakamura, Ryuhei</creatorcontrib><title>Design Strategy of Multi‐electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes</title><title>Molecular informatics</title><addtitle>Mol Inform</addtitle><description>Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. The different bioenergetics observed between PS II and COX suggest that in addition to the catalytic activity rationalized by the Sabatier principle, stability factors have also provided a major influence on the design strategy of biological multi‐electron transfer enzymes.</description><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biocatalysis</subject><subject>Bioenergetics</subject><subject>Bioinformatics</subject><subject>Catalysis</subject><subject>Catalysts</subject><subject>Catalytic activity</subject><subject>Chemical evolution</subject><subject>Chemical reduction</subject><subject>Communication</subject><subject>Communications</subject><subject>Computational Biology - methods</subject><subject>Cyanobacteria</subject><subject>Cyanobacteria - enzymology</subject><subject>Cytochrome</subject><subject>Cytochrome-c oxidase</subject><subject>Cytochromes</subject><subject>Design</subject><subject>Electron transfer</subject><subject>Electron Transport Complex IV - chemistry</subject><subject>Electron Transport Complex IV - metabolism</subject><subject>Enzymes</subject><subject>Evolution</subject><subject>Life-cycle assessment</subject><subject>Oxidation-Reduction</subject><subject>Oxygen</subject><subject>Oxygen evolution</subject><subject>Photosynthesis</subject><subject>Photosystem II</subject><subject>Photosystem II Protein Complex - chemistry</subject><subject>Photosystem II Protein Complex - metabolism</subject><subject>Phylogeny</subject><subject>Protein Engineering - methods</subject><subject>Respiratory enzymes</subject><subject>Stability</subject><subject>Strategy</subject><issn>1868-1743</issn><issn>1868-1751</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>EIF</sourceid><recordid>eNqFkc9u1DAQxi0EolXplSOyxIXLLrYTJ_YFqd1uoVJLJShny7Eni6vELnZSCCfEE_CMPAkOW5Y_F6yR7NH8_GlmPoQeU7KkhLDnvfPtkhFaE0ILeQ_tU1GJBa05vb97l8UeOkzpmuRTsKoW8iHaY7LmVSXYPvp6AsltPH47RD3AZsKhxRdjN7jvX75BB2aIweOrqH1qIeKVHnQ3pSHhY53A4lzT-NiF3EeIvR6cwUd-JlyahS4_TRvweH0bunFwM-wtfgN2ND-ztf889ZAeoQet7hIc3t0H6N3p-mr1anF--fJsdXS-MLymcmEkGG6NYKYGwhtGWA5KKi6JIK20JRWGiaomjeVzbttGAKsL0dDGCmOKA_Riq3szNj1YAz7P3Kmb6HodJxW0U39XvHuvNuFWVUwwzqos8OxOIIYPI6RB9S4Z6DrtIYxJMVKImoiyLDP69B_0Oowxr2amRCkEY5JnarmlTAwpRWh3zVCiZofV7LDaOZw_PPlzhB3-y88MyC3w0XUw_UdOXZy9Pv0t_gNidLXt</recordid><startdate>201808</startdate><enddate>201808</enddate><creator>Ooka, Hideshi</creator><creator>Hashimoto, Kazuhito</creator><creator>Nakamura, Ryuhei</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201808</creationdate><title>Design Strategy of Multi‐electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes</title><author>Ooka, Hideshi ; Hashimoto, Kazuhito ; Nakamura, Ryuhei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5719-c9ec5dc82c7e05b20220210659080f9d418c28670bd50f9ddfb8e2738b1bd8cc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biocatalysis</topic><topic>Bioenergetics</topic><topic>Bioinformatics</topic><topic>Catalysis</topic><topic>Catalysts</topic><topic>Catalytic activity</topic><topic>Chemical evolution</topic><topic>Chemical reduction</topic><topic>Communication</topic><topic>Communications</topic><topic>Computational Biology - methods</topic><topic>Cyanobacteria</topic><topic>Cyanobacteria - enzymology</topic><topic>Cytochrome</topic><topic>Cytochrome-c oxidase</topic><topic>Cytochromes</topic><topic>Design</topic><topic>Electron transfer</topic><topic>Electron Transport Complex IV - chemistry</topic><topic>Electron Transport Complex IV - metabolism</topic><topic>Enzymes</topic><topic>Evolution</topic><topic>Life-cycle assessment</topic><topic>Oxidation-Reduction</topic><topic>Oxygen</topic><topic>Oxygen evolution</topic><topic>Photosynthesis</topic><topic>Photosystem II</topic><topic>Photosystem II Protein Complex - chemistry</topic><topic>Photosystem II Protein Complex - metabolism</topic><topic>Phylogeny</topic><topic>Protein Engineering - methods</topic><topic>Respiratory enzymes</topic><topic>Stability</topic><topic>Strategy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ooka, Hideshi</creatorcontrib><creatorcontrib>Hashimoto, Kazuhito</creatorcontrib><creatorcontrib>Nakamura, Ryuhei</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular informatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ooka, Hideshi</au><au>Hashimoto, Kazuhito</au><au>Nakamura, Ryuhei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Design Strategy of Multi‐electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes</atitle><jtitle>Molecular informatics</jtitle><addtitle>Mol Inform</addtitle><date>2018-08</date><risdate>2018</risdate><volume>37</volume><issue>8</issue><spage>e1700139</spage><epage>n/a</epage><pages>e1700139-n/a</pages><issn>1868-1743</issn><eissn>1868-1751</eissn><abstract>Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. 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| subjects | Bacterial Proteins - chemistry Bacterial Proteins - metabolism Biocatalysis Bioenergetics Bioinformatics Catalysis Catalysts Catalytic activity Chemical evolution Chemical reduction Communication Communications Computational Biology - methods Cyanobacteria Cyanobacteria - enzymology Cytochrome Cytochrome-c oxidase Cytochromes Design Electron transfer Electron Transport Complex IV - chemistry Electron Transport Complex IV - metabolism Enzymes Evolution Life-cycle assessment Oxidation-Reduction Oxygen Oxygen evolution Photosynthesis Photosystem II Photosystem II Protein Complex - chemistry Photosystem II Protein Complex - metabolism Phylogeny Protein Engineering - methods Respiratory enzymes Stability Strategy |
| title | Design Strategy of Multi‐electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes |
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