Characterization of Flavonol Inhibition of DnaB Helicase : Real-Time Monitoring, Structural Modeling, and Proposed Mechanism
DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB hel...
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| description | DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity of KpDnaB. The ssDNA-stimulated ATPase activity of KpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity of KpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring of KpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity of KpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding to KpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that target K. pneumoniae and other bacterial DnaB helicases. |
| doi_str_mv | 10.1155/2012/735368 |
| format | Article |
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L.</contributor><creatorcontrib>Lin, Hsin-Hsien ; Huang, Cheng-Yang ; Mowbray, S. L.</creatorcontrib><description>DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity of KpDnaB. The ssDNA-stimulated ATPase activity of KpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity of KpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring of KpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity of KpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding to KpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that target K. pneumoniae and other bacterial DnaB helicases.</description><identifier>ISSN: 1110-7243</identifier><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 1110-7251</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2012/735368</identifier><identifier>PMID: 23091356</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Puplishing Corporation</publisher><subject>Adenosinetriphosphatase ; Antibiotics ; Bacterial pneumonia ; Binding Sites ; Bioflavonoids ; Chemical properties ; Computer Simulation ; Computer Systems ; Deoxyribonucleic acid ; DNA ; DNA replication ; DnaB Helicases - chemistry ; DnaB Helicases - ultrastructure ; Enzyme Activation ; Enzyme Inhibitors - chemistry ; Enzyme Stability ; Enzymes ; Flavones ; Flavonoids ; Flavonols - chemistry ; Infections ; Klebsiella pneumoniae ; Life sciences ; Models, Chemical ; Models, Molecular ; Myosin ; Pneumonia ; Protein Binding ; Protein Conformation ; Proteins</subject><ispartof>BioMed research international, 2012-01, Vol.2012 (2012), p.1-11</ispartof><rights>Copyright © 2012 Hsin-Hsien Lin and Cheng-Yang Huang.</rights><rights>COPYRIGHT 2012 John Wiley & Sons, Inc.</rights><rights>Copyright © 2012 Hsin-Hsien Lin and Cheng-Yang Huang. Hsin-Hsien Lin et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2012 H.-H. Lin and C.-Y. Huang. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c637t-7795e8e27b90e1aecd0e9f3f54ffc3f7ed617bbaafe9e2da0ceaa9193b2d4923</citedby><cites>FETCH-LOGICAL-c637t-7795e8e27b90e1aecd0e9f3f54ffc3f7ed617bbaafe9e2da0ceaa9193b2d4923</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468084/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468084/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23091356$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Mowbray, S. L.</contributor><creatorcontrib>Lin, Hsin-Hsien</creatorcontrib><creatorcontrib>Huang, Cheng-Yang</creatorcontrib><title>Characterization of Flavonol Inhibition of DnaB Helicase : Real-Time Monitoring, Structural Modeling, and Proposed Mechanism</title><title>BioMed research international</title><addtitle>J Biomed Biotechnol</addtitle><description>DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity of KpDnaB. The ssDNA-stimulated ATPase activity of KpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity of KpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring of KpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity of KpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding to KpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that target K. pneumoniae and other bacterial DnaB helicases.</description><subject>Adenosinetriphosphatase</subject><subject>Antibiotics</subject><subject>Bacterial pneumonia</subject><subject>Binding Sites</subject><subject>Bioflavonoids</subject><subject>Chemical properties</subject><subject>Computer Simulation</subject><subject>Computer Systems</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA replication</subject><subject>DnaB Helicases - chemistry</subject><subject>DnaB Helicases - ultrastructure</subject><subject>Enzyme Activation</subject><subject>Enzyme Inhibitors - chemistry</subject><subject>Enzyme Stability</subject><subject>Enzymes</subject><subject>Flavones</subject><subject>Flavonoids</subject><subject>Flavonols - chemistry</subject><subject>Infections</subject><subject>Klebsiella pneumoniae</subject><subject>Life sciences</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Myosin</subject><subject>Pneumonia</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Proteins</subject><issn>1110-7243</issn><issn>2314-6133</issn><issn>1110-7251</issn><issn>2314-6141</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>RHX</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqN0k1v1DAQBuAIUdFSOHEGReoFAWn9EScxB6SytLRSKxDs3Zo4411Xib04SRGIH49XaReKVirKIdH48euPTJI8o-SQUiGOGKHsqOSCF9WDZI9SSrKSCfpw853z3eRx318RQsuqkI-SXcaJpFwUe8mv2RIC6AGD_QmD9S71Jj1t4do736bnbmlre1v-4OB9eoat1dBj-jb9gtBmc9theumdHXywbvEm_TqEUQ9jgDaWm6jXRXBN-jn4le-xSS9RL8HZvnuS7Bhoe3x6895P5qcn89lZdvHp4_ns-CLTBS-HrCylwApZWUuCFFA3BKXhRuTGaG5KbApa1jWAQYmsAaIRQFLJa9bkkvH95N0UuxrrDhuNboi7U6tgOwg_lAer7o44u1QLf614XlSkymPAy5uA4L-N2A-qs73GtgWHfuwVZZUgMkLxH1SUpWAVLe6nlOZSEJaTSA_-oVd-DC7e2XptxrhkTPxRC2hRWWd8PI1eh6pjziUhZFLZFrVAh_Ho3qGxsXzHH27x8Wmws3rrhNfTBB183wc0m5umRK07Vq07Vk0dG_WLv3_Oxt62aASvJrC0roHv9p605xPGSNDABucyzyXhvwE0J_ta</recordid><startdate>20120101</startdate><enddate>20120101</enddate><creator>Lin, Hsin-Hsien</creator><creator>Huang, Cheng-Yang</creator><general>Hindawi Puplishing Corporation</general><general>Hindawi Publishing Corporation</general><general>John Wiley & Sons, Inc</general><general>Hindawi Limited</general><scope>ADJCN</scope><scope>AHFXO</scope><scope>RHU</scope><scope>RHW</scope><scope>RHX</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>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TK</scope><scope>7U7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>CWDGH</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>7TM</scope><scope>5PM</scope></search><sort><creationdate>20120101</creationdate><title>Characterization of Flavonol Inhibition of DnaB Helicase : Real-Time Monitoring, Structural Modeling, and Proposed Mechanism</title><author>Lin, Hsin-Hsien ; Huang, Cheng-Yang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c637t-7795e8e27b90e1aecd0e9f3f54ffc3f7ed617bbaafe9e2da0ceaa9193b2d4923</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Adenosinetriphosphatase</topic><topic>Antibiotics</topic><topic>Bacterial pneumonia</topic><topic>Binding Sites</topic><topic>Bioflavonoids</topic><topic>Chemical properties</topic><topic>Computer Simulation</topic><topic>Computer Systems</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA replication</topic><topic>DnaB Helicases - chemistry</topic><topic>DnaB Helicases - ultrastructure</topic><topic>Enzyme Activation</topic><topic>Enzyme Inhibitors - chemistry</topic><topic>Enzyme Stability</topic><topic>Enzymes</topic><topic>Flavones</topic><topic>Flavonoids</topic><topic>Flavonols - chemistry</topic><topic>Infections</topic><topic>Klebsiella pneumoniae</topic><topic>Life sciences</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Myosin</topic><topic>Pneumonia</topic><topic>Protein Binding</topic><topic>Protein Conformation</topic><topic>Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Hsin-Hsien</creatorcontrib><creatorcontrib>Huang, Cheng-Yang</creatorcontrib><collection>الدوريات العلمية والإحصائية - e-Marefa Academic and Statistical Periodicals</collection><collection>معرفة - المحتوى العربي الأكاديمي المتكامل - e-Marefa Academic Complete</collection><collection>Hindawi Publishing Complete</collection><collection>Hindawi Publishing Subscription Journals</collection><collection>Hindawi Publishing Open Access Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>Middle East & Africa Database</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - 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L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of Flavonol Inhibition of DnaB Helicase : Real-Time Monitoring, Structural Modeling, and Proposed Mechanism</atitle><jtitle>BioMed research international</jtitle><addtitle>J Biomed Biotechnol</addtitle><date>2012-01-01</date><risdate>2012</risdate><volume>2012</volume><issue>2012</issue><spage>1</spage><epage>11</epage><pages>1-11</pages><issn>1110-7243</issn><issn>2314-6133</issn><eissn>1110-7251</eissn><eissn>2314-6141</eissn><abstract>DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity of KpDnaB. The ssDNA-stimulated ATPase activity of KpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity of KpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring of KpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity of KpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding to KpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that target K. pneumoniae and other bacterial DnaB helicases.</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Puplishing Corporation</pub><pmid>23091356</pmid><doi>10.1155/2012/735368</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adenosinetriphosphatase Antibiotics Bacterial pneumonia Binding Sites Bioflavonoids Chemical properties Computer Simulation Computer Systems Deoxyribonucleic acid DNA DNA replication DnaB Helicases - chemistry DnaB Helicases - ultrastructure Enzyme Activation Enzyme Inhibitors - chemistry Enzyme Stability Enzymes Flavones Flavonoids Flavonols - chemistry Infections Klebsiella pneumoniae Life sciences Models, Chemical Models, Molecular Myosin Pneumonia Protein Binding Protein Conformation Proteins |
| title | Characterization of Flavonol Inhibition of DnaB Helicase : Real-Time Monitoring, Structural Modeling, and Proposed Mechanism |
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