Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites
Both direct and indirect readouts are utilized when the trp repressor binds to its operators. Here, we use gel-electrophoretic methods to examine the role played by direct and indirect readouts in the interaction of the repressor with a non-canonical binding site, similar to the mtr operator, and na...
Gespeichert in:
Veröffentlicht in: | Journal of molecular biology 1998-04, Vol.277 (5), p.1071-1080 |
---|---|
Hauptverfasser: | , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 1080 |
---|---|
container_issue | 5 |
container_start_page | 1071 |
container_title | Journal of molecular biology |
container_volume | 277 |
creator | Bareket-Samish, Avital Cohen, Ilana Haran, Tali E |
description | Both direct and indirect readouts are utilized when the
trp repressor binds to its operators. Here, we use gel-electrophoretic methods to examine the role played by direct and indirect readouts in the interaction of the repressor with a non-canonical binding site, similar to the
mtr operator, and named trpGG. The stability and affinity of the 1:1 complexes of the
trp repressor with this non-canonical site are lower than those of the 1:1 complexes formed with either the natural consensus sequence or a consensus sequence found in a selection experiment. We attribute this to the inability of the trpGG target to make the same number of water-mediated hydrogen bonds as canonical
trp binding sites. On the other hand, the 2:1 complex of the repressor with trpGG has high stability and affinity, similar to that of the 2:1 complex with a consensus sequence found by a selection experiment. The bend angle induced on the trpGG target by the binding of one repressor molecule is 27°, which is similar to that measured in other 1:1 complexes with the repressor. The angle for the 2:1 complex is significantly larger (43°
versus 30° in other 2:1 complexes). We present evidence suggesting that the deleterious effect of the sequence substitution in trpGG is compensated by the increased bend angle in the 2:1 complex. These observations demonstrate that indirect readout may complement for direct readout in determining the nature of the interaction between
trp repressor and its binding sites. |
doi_str_mv | 10.1006/jmbi.1998.1638 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_79839988</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0022283698916382</els_id><sourcerecordid>16476011</sourcerecordid><originalsourceid>FETCH-LOGICAL-c370t-4909ae649b3f25ff6f025526e9ab6553821d54981e57eb48f603887c2175cf1c3</originalsourceid><addsrcrecordid>eNqFkb1v2zAQxYmgges4WbMV0NRNDj9EihwLN19AgCzJTFDUMaFhiy5Jpch_HyoyshVd7o53P77hPYQuCV4TjMXVdt_5NVFKrolg8gQtCZaqlmX-hpYYU1pTycR3dJbSFmPMWSMXaKF4SzBlS_Ty20ewuXqDmMZU-aGf3xFMH8ZcFlV-hdIyRGOzD0MV3Ocqx0OhDhFSCrH66_NrNYShtqZUb82u6iax4aVKPkM6R6fO7BJcHPsKPd9cP23u6ofH2_vNr4fashbnulFYGRCN6pij3DnhMOWcClCmE5wzSUnPGyUJ8Ba6RjqBmZStpaTl1hHLVujnrHuI4c8IKeu9TxZ2OzNAGJNulWTFLPlfkIimFZiQAq5n0MaQUgSnD9HvTXzXBOspAj1FoKcI9BRB-fDjqDx2e-i_8KPn5S7nOxQf3jxEnayHwcJsve6D_5f0Byjilfc</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>16476011</pqid></control><display><type>article</type><title>Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites</title><source>MEDLINE</source><source>Elsevier ScienceDirect Journals Complete</source><creator>Bareket-Samish, Avital ; Cohen, Ilana ; Haran, Tali E</creator><creatorcontrib>Bareket-Samish, Avital ; Cohen, Ilana ; Haran, Tali E</creatorcontrib><description>Both direct and indirect readouts are utilized when the
trp repressor binds to its operators. Here, we use gel-electrophoretic methods to examine the role played by direct and indirect readouts in the interaction of the repressor with a non-canonical binding site, similar to the
mtr operator, and named trpGG. The stability and affinity of the 1:1 complexes of the
trp repressor with this non-canonical site are lower than those of the 1:1 complexes formed with either the natural consensus sequence or a consensus sequence found in a selection experiment. We attribute this to the inability of the trpGG target to make the same number of water-mediated hydrogen bonds as canonical
trp binding sites. On the other hand, the 2:1 complex of the repressor with trpGG has high stability and affinity, similar to that of the 2:1 complex with a consensus sequence found by a selection experiment. The bend angle induced on the trpGG target by the binding of one repressor molecule is 27°, which is similar to that measured in other 1:1 complexes with the repressor. The angle for the 2:1 complex is significantly larger (43°
versus 30° in other 2:1 complexes). We present evidence suggesting that the deleterious effect of the sequence substitution in trpGG is compensated by the increased bend angle in the 2:1 complex. These observations demonstrate that indirect readout may complement for direct readout in determining the nature of the interaction between
trp repressor and its binding sites.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1006/jmbi.1998.1638</identifier><identifier>PMID: 9571023</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Bacterial Proteins ; Binding Sites - genetics ; Consensus Sequence - genetics ; direct readout ; DNA bendability ; DNA-Binding Proteins - metabolism ; Hydrogen Bonding ; indirect readout ; Molecular Conformation ; Molecular Structure ; Operator Regions, Genetic - genetics ; Repressor Proteins - metabolism ; trp operators ; trp repressor</subject><ispartof>Journal of molecular biology, 1998-04, Vol.277 (5), p.1071-1080</ispartof><rights>1998 Academic Press</rights><rights>Copyright 1998 Academic Press Limited.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c370t-4909ae649b3f25ff6f025526e9ab6553821d54981e57eb48f603887c2175cf1c3</citedby><cites>FETCH-LOGICAL-c370t-4909ae649b3f25ff6f025526e9ab6553821d54981e57eb48f603887c2175cf1c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1006/jmbi.1998.1638$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9571023$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bareket-Samish, Avital</creatorcontrib><creatorcontrib>Cohen, Ilana</creatorcontrib><creatorcontrib>Haran, Tali E</creatorcontrib><title>Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Both direct and indirect readouts are utilized when the
trp repressor binds to its operators. Here, we use gel-electrophoretic methods to examine the role played by direct and indirect readouts in the interaction of the repressor with a non-canonical binding site, similar to the
mtr operator, and named trpGG. The stability and affinity of the 1:1 complexes of the
trp repressor with this non-canonical site are lower than those of the 1:1 complexes formed with either the natural consensus sequence or a consensus sequence found in a selection experiment. We attribute this to the inability of the trpGG target to make the same number of water-mediated hydrogen bonds as canonical
trp binding sites. On the other hand, the 2:1 complex of the repressor with trpGG has high stability and affinity, similar to that of the 2:1 complex with a consensus sequence found by a selection experiment. The bend angle induced on the trpGG target by the binding of one repressor molecule is 27°, which is similar to that measured in other 1:1 complexes with the repressor. The angle for the 2:1 complex is significantly larger (43°
versus 30° in other 2:1 complexes). We present evidence suggesting that the deleterious effect of the sequence substitution in trpGG is compensated by the increased bend angle in the 2:1 complex. These observations demonstrate that indirect readout may complement for direct readout in determining the nature of the interaction between
trp repressor and its binding sites.</description><subject>Bacterial Proteins</subject><subject>Binding Sites - genetics</subject><subject>Consensus Sequence - genetics</subject><subject>direct readout</subject><subject>DNA bendability</subject><subject>DNA-Binding Proteins - metabolism</subject><subject>Hydrogen Bonding</subject><subject>indirect readout</subject><subject>Molecular Conformation</subject><subject>Molecular Structure</subject><subject>Operator Regions, Genetic - genetics</subject><subject>Repressor Proteins - metabolism</subject><subject>trp operators</subject><subject>trp repressor</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkb1v2zAQxYmgges4WbMV0NRNDj9EihwLN19AgCzJTFDUMaFhiy5Jpch_HyoyshVd7o53P77hPYQuCV4TjMXVdt_5NVFKrolg8gQtCZaqlmX-hpYYU1pTycR3dJbSFmPMWSMXaKF4SzBlS_Ty20ewuXqDmMZU-aGf3xFMH8ZcFlV-hdIyRGOzD0MV3Ocqx0OhDhFSCrH66_NrNYShtqZUb82u6iax4aVKPkM6R6fO7BJcHPsKPd9cP23u6ofH2_vNr4fashbnulFYGRCN6pij3DnhMOWcClCmE5wzSUnPGyUJ8Ba6RjqBmZStpaTl1hHLVujnrHuI4c8IKeu9TxZ2OzNAGJNulWTFLPlfkIimFZiQAq5n0MaQUgSnD9HvTXzXBOspAj1FoKcI9BRB-fDjqDx2e-i_8KPn5S7nOxQf3jxEnayHwcJsve6D_5f0Byjilfc</recordid><startdate>19980417</startdate><enddate>19980417</enddate><creator>Bareket-Samish, Avital</creator><creator>Cohen, Ilana</creator><creator>Haran, Tali E</creator><general>Elsevier Ltd</general><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>7QL</scope><scope>7TM</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>19980417</creationdate><title>Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites</title><author>Bareket-Samish, Avital ; Cohen, Ilana ; Haran, Tali E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c370t-4909ae649b3f25ff6f025526e9ab6553821d54981e57eb48f603887c2175cf1c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Bacterial Proteins</topic><topic>Binding Sites - genetics</topic><topic>Consensus Sequence - genetics</topic><topic>direct readout</topic><topic>DNA bendability</topic><topic>DNA-Binding Proteins - metabolism</topic><topic>Hydrogen Bonding</topic><topic>indirect readout</topic><topic>Molecular Conformation</topic><topic>Molecular Structure</topic><topic>Operator Regions, Genetic - genetics</topic><topic>Repressor Proteins - metabolism</topic><topic>trp operators</topic><topic>trp repressor</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bareket-Samish, Avital</creatorcontrib><creatorcontrib>Cohen, Ilana</creatorcontrib><creatorcontrib>Haran, Tali E</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Nucleic Acids Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bareket-Samish, Avital</au><au>Cohen, Ilana</au><au>Haran, Tali E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>1998-04-17</date><risdate>1998</risdate><volume>277</volume><issue>5</issue><spage>1071</spage><epage>1080</epage><pages>1071-1080</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Both direct and indirect readouts are utilized when the
trp repressor binds to its operators. Here, we use gel-electrophoretic methods to examine the role played by direct and indirect readouts in the interaction of the repressor with a non-canonical binding site, similar to the
mtr operator, and named trpGG. The stability and affinity of the 1:1 complexes of the
trp repressor with this non-canonical site are lower than those of the 1:1 complexes formed with either the natural consensus sequence or a consensus sequence found in a selection experiment. We attribute this to the inability of the trpGG target to make the same number of water-mediated hydrogen bonds as canonical
trp binding sites. On the other hand, the 2:1 complex of the repressor with trpGG has high stability and affinity, similar to that of the 2:1 complex with a consensus sequence found by a selection experiment. The bend angle induced on the trpGG target by the binding of one repressor molecule is 27°, which is similar to that measured in other 1:1 complexes with the repressor. The angle for the 2:1 complex is significantly larger (43°
versus 30° in other 2:1 complexes). We present evidence suggesting that the deleterious effect of the sequence substitution in trpGG is compensated by the increased bend angle in the 2:1 complex. These observations demonstrate that indirect readout may complement for direct readout in determining the nature of the interaction between
trp repressor and its binding sites.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>9571023</pmid><doi>10.1006/jmbi.1998.1638</doi><tpages>10</tpages></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0022-2836 |
ispartof | Journal of molecular biology, 1998-04, Vol.277 (5), p.1071-1080 |
issn | 0022-2836 1089-8638 |
language | eng |
recordid | cdi_proquest_miscellaneous_79839988 |
source | MEDLINE; Elsevier ScienceDirect Journals Complete |
subjects | Bacterial Proteins Binding Sites - genetics Consensus Sequence - genetics direct readout DNA bendability DNA-Binding Proteins - metabolism Hydrogen Bonding indirect readout Molecular Conformation Molecular Structure Operator Regions, Genetic - genetics Repressor Proteins - metabolism trp operators trp repressor |
title | Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T09%3A34%3A50IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Direct%20versus%20indirect%20readout%20in%20the%20interaction%20of%20the%20trp%20repressor%20with%20non-canonical%20binding%20sites&rft.jtitle=Journal%20of%20molecular%20biology&rft.au=Bareket-Samish,%20Avital&rft.date=1998-04-17&rft.volume=277&rft.issue=5&rft.spage=1071&rft.epage=1080&rft.pages=1071-1080&rft.issn=0022-2836&rft.eissn=1089-8638&rft_id=info:doi/10.1006/jmbi.1998.1638&rft_dat=%3Cproquest_cross%3E16476011%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=16476011&rft_id=info:pmid/9571023&rft_els_id=S0022283698916382&rfr_iscdi=true |