Thermodynamics of sequence-specific protein-DNA interactions
Identifieur interne : 002F41 ( Istex/Corpus ); précédent : 002F40; suivant : 002F42Thermodynamics of sequence-specific protein-DNA interactions
Auteurs : Torleif H Rd ; Thomas Lundb CkSource :
- Biophysical Chemistry [ 0301-4622 ] ; 1996.
Abstract
The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.
Url:
DOI: 10.1016/S0301-4622(96)02197-7
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The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.</div></front></TEI><istex><corpusName>elsevier</corpusName><author><json:item><name>Torleif Härd</name><affiliations><json:string>Dept. of Biochemistry and Biotechnology, Royal Institute of Technology, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</json:string></affiliations></json:item><json:item><name>Thomas Lundbäck</name><affiliations><json:string>Dept. of Biosciences, Karolinska Institutet, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Thermodynamics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Molecular recognition</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DNA-protein interactions</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Sequence specificity</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Noncovalent interactions</value></json:item></subject><language><json:string>eng</json:string></language><abstract>The molecular recognition processes in sequence-specific protein-DNA interactions are complex. 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The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.</p></abstract><textClass><keywords scheme="keyword"><list><head>Keywords</head><item><term>Thermodynamics</term></item><item><term>Molecular recognition</term></item><item><term>DNA-protein interactions</term></item><item><term>Sequence specificity</term></item><item><term>Noncovalent interactions</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1996-06-11">Registration</change><change when="1996">Published</change></revisionDesc></teiHeader></istex:fulltextTEI></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla"><item-info><jid>BIOCHE</jid><aid>96021977</aid><ce:pii>S0301-4622(96)02197-7</ce:pii><ce:doi>10.1016/S0301-4622(96)02197-7</ce:doi><ce:copyright type="unknown" year="1996"></ce:copyright></item-info><head><ce:title>Thermodynamics of sequence-specific protein-DNA interactions</ce:title><ce:author-group><ce:author><ce:given-name>Torleif</ce:given-name><ce:surname>Härd</ce:surname><ce:cross-ref refid="COR1"><ce:sup>∗</ce:sup></ce:cross-ref><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Thomas</ce:given-name><ce:surname>Lundbäck</ce:surname><ce:cross-ref refid="AFF2"><ce:sup>b</ce:sup></ce:cross-ref></ce:author><ce:affiliation id="AFF1"><ce:label>a</ce:label><ce:textfn>Dept. of Biochemistry and Biotechnology, Royal Institute of Technology, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</ce:textfn></ce:affiliation><ce:affiliation id="AFF2"><ce:label>b</ce:label><ce:textfn>Dept. of Biosciences, Karolinska Institutet, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</ce:textfn></ce:affiliation><ce:correspondence id="COR1"><ce:label>∗</ce:label><ce:text>Corresponding author.</ce:text></ce:correspondence></ce:author-group><ce:date-received day="4" month="4" year="1996"></ce:date-received><ce:date-accepted day="11" month="6" year="1996"></ce:date-accepted><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>Thermodynamics</ce:text></ce:keyword><ce:keyword><ce:text>Molecular recognition</ce:text></ce:keyword><ce:keyword><ce:text>DNA-protein interactions</ce:text></ce:keyword><ce:keyword><ce:text>Sequence specificity</ce:text></ce:keyword><ce:keyword><ce:text>Noncovalent interactions</ce:text></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Thermodynamics of sequence-specific protein-DNA interactions</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Thermodynamics of sequence-specific protein-DNA interactions</title></titleInfo><name type="personal"><namePart type="given">Torleif</namePart><namePart type="family">Härd</namePart><affiliation>Dept. of Biochemistry and Biotechnology, Royal Institute of Technology, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</affiliation><description>Corresponding author.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Thomas</namePart><namePart type="family">Lundbäck</namePart><affiliation>Dept. of Biosciences, Karolinska Institutet, Center for Structural Biochemistry, NOVUM, 141 57 Huddinge, Sweden</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article"></genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1996</dateIssued><dateValid encoding="w3cdtf">1996-06-11</dateValid><copyrightDate encoding="w3cdtf">1996</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.</abstract><subject><genre>Keywords</genre><topic>Thermodynamics</topic><topic>Molecular recognition</topic><topic>DNA-protein interactions</topic><topic>Sequence specificity</topic><topic>Noncovalent interactions</topic></subject><relatedItem type="host"><titleInfo><title>Biophysical Chemistry</title></titleInfo><titleInfo type="abbreviated"><title>BIOCHE</title></titleInfo><genre type="Journal">journal</genre><originInfo><dateIssued encoding="w3cdtf">19961129</dateIssued></originInfo><identifier type="ISSN">0301-4622</identifier><identifier type="PII">S0301-4622(00)X0020-8</identifier><part><date>19961129</date><detail type="volume"><number>62</number><caption>vol.</caption></detail><detail type="issue"><number>1–3</number><caption>no.</caption></detail><extent unit="issue pages"><start>1</start><end>165</end></extent><extent unit="pages"><start>121</start><end>139</end></extent></part></relatedItem><identifier type="istex">6867A4EEB5C6A964B5E1D4C26993BB17CC56CF79</identifier><identifier type="DOI">10.1016/S0301-4622(96)02197-7</identifier><identifier type="PII">S0301-4622(96)02197-7</identifier><recordInfo><recordContentSource>ELSEVIER</recordContentSource></recordInfo></mods></metadata><enrichments><istex:catWosTEI uri="https://api.istex.fr/document/6867A4EEB5C6A964B5E1D4C26993BB17CC56CF79/enrichments/catWos"><teiHeader><profileDesc><textClass><classCode scheme="WOS">CHEMISTRY, PHYSICAL</classCode><classCode scheme="WOS">BIOCHEMISTRY & MOLECULAR BIOLOGY</classCode><classCode scheme="WOS">BIOPHYSICS</classCode></textClass></profileDesc></teiHeader></istex:catWosTEI></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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