Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity
Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were...
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| Veröffentlicht in: | PloS one 2021-02, Vol.16 (2), p.e0247236-e0247236 |
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| creator | Li, Ying Wei, Jinqing Yang, Huizhen Dai, Jing Ge, Xizhen |
| description | Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici. |
| doi_str_mv | 10.1371/journal.pone.0247236 |
| format | Article |
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However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0247236</identifier><identifier>PMID: 33606796</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Antifungal agents ; Berberine ; Biodegradation ; Biology and Life Sciences ; Biomass ; Chemical properties ; Control ; Cutinase ; Engineering ; Enzymatic activity ; Enzyme activity ; Enzymes ; Ethylene glycol ; Experiments ; Fungi ; Fungi, Phytopathogenic ; Histidine ; Hydrophobicity ; Laboratories ; Medicine and Health Sciences ; Molecular dynamics ; Pathogenicity ; Pathogens ; Physical Sciences ; Plant cuticle ; Plant diseases ; Simulation ; Sodium dodecyl sulfate ; Sodium lauryl sulfate ; Substrates ; Water chemistry</subject><ispartof>PloS one, 2021-02, Vol.16 (2), p.e0247236-e0247236</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Li et al 2021 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-bcf9fdab5285686a478a894aaf8a86080f3116db3dd2ae3fa841eda9d0a5fbe33</citedby><cites>FETCH-LOGICAL-c692t-bcf9fdab5285686a478a894aaf8a86080f3116db3dd2ae3fa841eda9d0a5fbe33</cites><orcidid>0000-0001-6495-0361</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894860/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894860/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53770,53772,79347,79348</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33606796$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ansari, Mahmood ur Rahman</contributor><creatorcontrib>Li, Ying</creatorcontrib><creatorcontrib>Wei, Jinqing</creatorcontrib><creatorcontrib>Yang, Huizhen</creatorcontrib><creatorcontrib>Dai, Jing</creatorcontrib><creatorcontrib>Ge, Xizhen</creatorcontrib><title>Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.</description><subject>Antifungal agents</subject><subject>Berberine</subject><subject>Biodegradation</subject><subject>Biology and Life Sciences</subject><subject>Biomass</subject><subject>Chemical properties</subject><subject>Control</subject><subject>Cutinase</subject><subject>Engineering</subject><subject>Enzymatic activity</subject><subject>Enzyme activity</subject><subject>Enzymes</subject><subject>Ethylene glycol</subject><subject>Experiments</subject><subject>Fungi</subject><subject>Fungi, Phytopathogenic</subject><subject>Histidine</subject><subject>Hydrophobicity</subject><subject>Laboratories</subject><subject>Medicine and Health Sciences</subject><subject>Molecular dynamics</subject><subject>Pathogenicity</subject><subject>Pathogens</subject><subject>Physical Sciences</subject><subject>Plant cuticle</subject><subject>Plant diseases</subject><subject>Simulation</subject><subject>Sodium dodecyl sulfate</subject><subject>Sodium lauryl sulfate</subject><subject>Substrates</subject><subject>Water 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dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity</title><author>Li, Ying ; Wei, Jinqing ; Yang, Huizhen ; Dai, Jing ; Ge, Xizhen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-bcf9fdab5285686a478a894aaf8a86080f3116db3dd2ae3fa841eda9d0a5fbe33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Antifungal agents</topic><topic>Berberine</topic><topic>Biodegradation</topic><topic>Biology and Life Sciences</topic><topic>Biomass</topic><topic>Chemical properties</topic><topic>Control</topic><topic>Cutinase</topic><topic>Engineering</topic><topic>Enzymatic activity</topic><topic>Enzyme activity</topic><topic>Enzymes</topic><topic>Ethylene glycol</topic><topic>Experiments</topic><topic>Fungi</topic><topic>Fungi, 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Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Ying</au><au>Wei, Jinqing</au><au>Yang, Huizhen</au><au>Dai, Jing</au><au>Ge, Xizhen</au><au>Ansari, Mahmood ur Rahman</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-02-19</date><risdate>2021</risdate><volume>16</volume><issue>2</issue><spage>e0247236</spage><epage>e0247236</epage><pages>e0247236-e0247236</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33606796</pmid><doi>10.1371/journal.pone.0247236</doi><tpages>e0247236</tpages><orcidid>https://orcid.org/0000-0001-6495-0361</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Antifungal agents Berberine Biodegradation Biology and Life Sciences Biomass Chemical properties Control Cutinase Engineering Enzymatic activity Enzyme activity Enzymes Ethylene glycol Experiments Fungi Fungi, Phytopathogenic Histidine Hydrophobicity Laboratories Medicine and Health Sciences Molecular dynamics Pathogenicity Pathogens Physical Sciences Plant cuticle Plant diseases Simulation Sodium dodecyl sulfate Sodium lauryl sulfate Substrates Water chemistry |
| title | Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity |
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