Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags
To readily analyze the binding mode of protein-ligand interactions, we developed ligand-bound-type and ligand-dissociation-type probes having 6-amidopyrene (apy) as a detecting group. Matrix- and label-assisted laser desorption/ionization mass spectrometry (MALDI and LA-LDI MS) analyses and a covale...
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| Veröffentlicht in: | Organic & biomolecular chemistry 2018-10, Vol.16 (42), p.7883-7890 |
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| container_issue | 42 |
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| container_title | Organic & biomolecular chemistry |
| container_volume | 16 |
| creator | Watanabe, Rei Hu, Yaping Iio, Keita Yoneda, Kozo Hattori, Atsunori Arai, Atsushi Kigoshi, Hideo Kita, Masaki |
| description | To readily analyze the binding mode of protein-ligand interactions, we developed ligand-bound-type and ligand-dissociation-type probes having 6-amidopyrene (apy) as a detecting group. Matrix- and label-assisted laser desorption/ionization mass spectrometry (MALDI and LA-LDI MS) analyses and a covalent docking simulation using these probes precisely determined the binding position of the ligand biotin on the target protein avidin (RMSD = 0.786 and 0.332 Å). Our apy-probe-labeling method may be useful for determining the unknown ligand-binding sites of various target proteins. |
| doi_str_mv | 10.1039/c8ob02222d |
| format | Article |
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Matrix- and label-assisted laser desorption/ionization mass spectrometry (MALDI and LA-LDI MS) analyses and a covalent docking simulation using these probes precisely determined the binding position of the ligand biotin on the target protein avidin (RMSD = 0.786 and 0.332 Å). Our apy-probe-labeling method may be useful for determining the unknown ligand-binding sites of various target proteins.</description><identifier>ISSN: 1477-0520</identifier><identifier>EISSN: 1477-0539</identifier><identifier>DOI: 10.1039/c8ob02222d</identifier><identifier>PMID: 30306182</identifier><language>eng</language><publisher>England: Royal Society of Chemistry</publisher><subject>Avidin ; Binding sites ; Biotin ; Docking ; Ionization ; Labeling ; Ligands ; Mass spectrometry ; Mass spectroscopy ; Probes ; Proteins</subject><ispartof>Organic & biomolecular chemistry, 2018-10, Vol.16 (42), p.7883-7890</ispartof><rights>Copyright Royal Society of Chemistry 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c315t-eb6d75fafd4aa05b16112465abb2674c773bee28da5567e09d76eca303821fb93</citedby><cites>FETCH-LOGICAL-c315t-eb6d75fafd4aa05b16112465abb2674c773bee28da5567e09d76eca303821fb93</cites><orcidid>0000-0001-6685-4461 ; 0000-0003-1554-5129</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30306182$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Watanabe, Rei</creatorcontrib><creatorcontrib>Hu, Yaping</creatorcontrib><creatorcontrib>Iio, Keita</creatorcontrib><creatorcontrib>Yoneda, Kozo</creatorcontrib><creatorcontrib>Hattori, Atsunori</creatorcontrib><creatorcontrib>Arai, Atsushi</creatorcontrib><creatorcontrib>Kigoshi, Hideo</creatorcontrib><creatorcontrib>Kita, Masaki</creatorcontrib><title>Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags</title><title>Organic & biomolecular chemistry</title><addtitle>Org Biomol Chem</addtitle><description>To readily analyze the binding mode of protein-ligand interactions, we developed ligand-bound-type and ligand-dissociation-type probes having 6-amidopyrene (apy) as a detecting group. Matrix- and label-assisted laser desorption/ionization mass spectrometry (MALDI and LA-LDI MS) analyses and a covalent docking simulation using these probes precisely determined the binding position of the ligand biotin on the target protein avidin (RMSD = 0.786 and 0.332 Å). Our apy-probe-labeling method may be useful for determining the unknown ligand-binding sites of various target proteins.</description><subject>Avidin</subject><subject>Binding sites</subject><subject>Biotin</subject><subject>Docking</subject><subject>Ionization</subject><subject>Labeling</subject><subject>Ligands</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Probes</subject><subject>Proteins</subject><issn>1477-0520</issn><issn>1477-0539</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNpdkMtOwzAQRS0EoqWw4QOQJTYIKeBHEidLaHlUKuqisI7seFJcJXGIE6H-PQ4tXTCbGc0cXc29CF1SckcJT-_zxCrCfOkjNKahEAGJeHp8mBkZoTPnNoTQVMThKRpxwklMEzZGsGogN4XJcdPaDkwdlFJBaeo1lrXGpVn7FihT62HVWGc6Y2t_k-XWGYe_TfeJZWW0bbYt1DDIKHBYOryYzfHbCndy7c7RSSFLBxf7PkEfz0_v09dgsXyZTx8WQc5p1AWgYi2iQhY6lJJEisaUsjCOpFIsFmEuBFcALNEyimIBJNUihlx6NwmjhUr5BN3sdP0XXz24LquMy6EsZQ22dxmjNOHUp8A8ev0P3di-9bYGiokwZEnIPXW7o_LWOtdCkTWtqWS7zSjJhvCzabJ8_A1_5uGrvWSvKtAH9C9t_gPwUX73</recordid><startdate>20181031</startdate><enddate>20181031</enddate><creator>Watanabe, Rei</creator><creator>Hu, Yaping</creator><creator>Iio, Keita</creator><creator>Yoneda, Kozo</creator><creator>Hattori, Atsunori</creator><creator>Arai, Atsushi</creator><creator>Kigoshi, Hideo</creator><creator>Kita, Masaki</creator><general>Royal Society of Chemistry</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7T7</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-6685-4461</orcidid><orcidid>https://orcid.org/0000-0003-1554-5129</orcidid></search><sort><creationdate>20181031</creationdate><title>Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags</title><author>Watanabe, Rei ; Hu, Yaping ; Iio, Keita ; Yoneda, Kozo ; Hattori, Atsunori ; Arai, Atsushi ; Kigoshi, Hideo ; Kita, Masaki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c315t-eb6d75fafd4aa05b16112465abb2674c773bee28da5567e09d76eca303821fb93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Avidin</topic><topic>Binding sites</topic><topic>Biotin</topic><topic>Docking</topic><topic>Ionization</topic><topic>Labeling</topic><topic>Ligands</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>Probes</topic><topic>Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Watanabe, Rei</creatorcontrib><creatorcontrib>Hu, Yaping</creatorcontrib><creatorcontrib>Iio, Keita</creatorcontrib><creatorcontrib>Yoneda, Kozo</creatorcontrib><creatorcontrib>Hattori, Atsunori</creatorcontrib><creatorcontrib>Arai, Atsushi</creatorcontrib><creatorcontrib>Kigoshi, Hideo</creatorcontrib><creatorcontrib>Kita, Masaki</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Organic & biomolecular chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Watanabe, Rei</au><au>Hu, Yaping</au><au>Iio, Keita</au><au>Yoneda, Kozo</au><au>Hattori, Atsunori</au><au>Arai, Atsushi</au><au>Kigoshi, Hideo</au><au>Kita, Masaki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags</atitle><jtitle>Organic & biomolecular chemistry</jtitle><addtitle>Org Biomol Chem</addtitle><date>2018-10-31</date><risdate>2018</risdate><volume>16</volume><issue>42</issue><spage>7883</spage><epage>7890</epage><pages>7883-7890</pages><issn>1477-0520</issn><eissn>1477-0539</eissn><abstract>To readily analyze the binding mode of protein-ligand interactions, we developed ligand-bound-type and ligand-dissociation-type probes having 6-amidopyrene (apy) as a detecting group. 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| ispartof | Organic & biomolecular chemistry, 2018-10, Vol.16 (42), p.7883-7890 |
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| language | eng |
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| source | Royal Society Of Chemistry Journals; Alma/SFX Local Collection |
| subjects | Avidin Binding sites Biotin Docking Ionization Labeling Ligands Mass spectrometry Mass spectroscopy Probes Proteins |
| title | Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags |
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