The Binding Process of a Nonspecific Enzyme with DNA
Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colic...
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| Veröffentlicht in: | Biophysical journal 2011-09, Vol.101 (5), p.1139-1147 |
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| creator | Chen, Chuanying Pettitt, B. Montgomery |
| description | Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from
Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways. |
| doi_str_mv | 10.1016/j.bpj.2011.07.016 |
| format | Article |
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Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.</description><identifier>ISSN: 0006-3495</identifier><identifier>EISSN: 1542-0086</identifier><identifier>DOI: 10.1016/j.bpj.2011.07.016</identifier><identifier>PMID: 21889451</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>60 APPLIED LIFE SCIENCES ; Amino Acid Motifs ; Base Pairing ; BASIC BIOLOGICAL SCIENCES ; Binding sites ; Brownian motion ; colicins ; Colicins - chemistry ; Colicins - metabolism ; Deoxyribonucleases - metabolism ; Deoxyribonucleic acid ; DNA ; DNA - chemistry ; DNA - metabolism ; E coli ; Environmental Molecular Sciences Laboratory ; ENZYMES ; ESCHERICHIA COLI ; Escherichia coli - enzymology ; landscapes ; molecular dynamics ; Molecular Dynamics Simulation ; NUCLEASES ; Nucleic Acid ; Protein Binding ; Protein Structure, Tertiary ; PROTEINS ; SIMULATION ; Static Electricity ; Substrate Specificity ; Thermodynamics ; TRANSIENTS ; WATER</subject><ispartof>Biophysical journal, 2011-09, Vol.101 (5), p.1139-1147</ispartof><rights>2011 Biophysical Society</rights><rights>Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.</rights><rights>Copyright Biophysical Society Sep 7, 2011</rights><rights>2011 by the Biophysical Society. 2011 Biophysical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c560t-70a22342b1eb444eaded5f2a7244282b9ec3277f92c63380f938d5fb195d16123</citedby><cites>FETCH-LOGICAL-c560t-70a22342b1eb444eaded5f2a7244282b9ec3277f92c63380f938d5fb195d16123</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/PMC3164187/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.bpj.2011.07.016$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,3550,27924,27925,45995,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21889451$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1038378$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Chuanying</creatorcontrib><creatorcontrib>Pettitt, B. Montgomery</creatorcontrib><creatorcontrib>Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)</creatorcontrib><title>The Binding Process of a Nonspecific Enzyme with DNA</title><title>Biophysical journal</title><addtitle>Biophys J</addtitle><description>Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from
Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>Amino Acid Motifs</subject><subject>Base Pairing</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Binding sites</subject><subject>Brownian motion</subject><subject>colicins</subject><subject>Colicins - chemistry</subject><subject>Colicins - metabolism</subject><subject>Deoxyribonucleases - metabolism</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>DNA - metabolism</subject><subject>E coli</subject><subject>Environmental Molecular Sciences Laboratory</subject><subject>ENZYMES</subject><subject>ESCHERICHIA COLI</subject><subject>Escherichia coli - enzymology</subject><subject>landscapes</subject><subject>molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>NUCLEASES</subject><subject>Nucleic Acid</subject><subject>Protein Binding</subject><subject>Protein Structure, Tertiary</subject><subject>PROTEINS</subject><subject>SIMULATION</subject><subject>Static Electricity</subject><subject>Substrate Specificity</subject><subject>Thermodynamics</subject><subject>TRANSIENTS</subject><subject>WATER</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU9vEzEQxVcIREvhA3CBFRdOCTO2d20LCamU8keqChLt2fJ6ZxNHiR3sTVH59HiVEuACJ0vj37yZea-qniLMEbB9tZp329WcAeIc5LxU7lXH2Ag2A1Dt_eoYANoZF7o5qh7lvAJA1gA-rI4YKqVFg8eVuFpS_daH3odF_SVFRznXcahtfRlD3pLzg3f1efhxu6H6ux-X9bvL08fVg8GuMz25e0-q6_fnV2cfZxefP3w6O72YuaaFcSbBMsYF65A6IQTZnvpmYFYyIZhinSbHmZSDZq7lXMGguSpAh7rpsUXGT6o3e93trttQ7yiMya7NNvmNTbcmWm_-_gl-aRbxxnBsBSpZBF7sBWIevcnOj-SWLoZAbjQIXHGpCvTybkqK33aUR7Px2dF6bQPFXTYaJCrkkv2XVErKRjOA34MP5CruUihmFUizVikxbYd7yKWYc6LhcBmCmQI2K1MCNlPABqQpldLz7E9LDh2_Ei3A8z0w2GjsIvlsrr8Whaakj6j1JPF6T1CJ7sZTmoyh4Kj3afKlj_4fC_wEXiG7_w</recordid><startdate>20110907</startdate><enddate>20110907</enddate><creator>Chen, Chuanying</creator><creator>Pettitt, B. Montgomery</creator><general>Elsevier Inc</general><general>Biophysical Society</general><general>The Biophysical Society</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</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>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20110907</creationdate><title>The Binding Process of a Nonspecific Enzyme with DNA</title><author>Chen, Chuanying ; Pettitt, B. Montgomery</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c560t-70a22342b1eb444eaded5f2a7244282b9ec3277f92c63380f938d5fb195d16123</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>60 APPLIED LIFE SCIENCES</topic><topic>Amino Acid Motifs</topic><topic>Base Pairing</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Binding sites</topic><topic>Brownian motion</topic><topic>colicins</topic><topic>Colicins - chemistry</topic><topic>Colicins - metabolism</topic><topic>Deoxyribonucleases - metabolism</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - chemistry</topic><topic>DNA - metabolism</topic><topic>E coli</topic><topic>Environmental Molecular Sciences Laboratory</topic><topic>ENZYMES</topic><topic>ESCHERICHIA COLI</topic><topic>Escherichia coli - enzymology</topic><topic>landscapes</topic><topic>molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>NUCLEASES</topic><topic>Nucleic Acid</topic><topic>Protein Binding</topic><topic>Protein Structure, Tertiary</topic><topic>PROTEINS</topic><topic>SIMULATION</topic><topic>Static Electricity</topic><topic>Substrate Specificity</topic><topic>Thermodynamics</topic><topic>TRANSIENTS</topic><topic>WATER</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Chuanying</creatorcontrib><creatorcontrib>Pettitt, B. Montgomery</creatorcontrib><creatorcontrib>Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biophysical journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Chuanying</au><au>Pettitt, B. Montgomery</au><aucorp>Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Binding Process of a Nonspecific Enzyme with DNA</atitle><jtitle>Biophysical journal</jtitle><addtitle>Biophys J</addtitle><date>2011-09-07</date><risdate>2011</risdate><volume>101</volume><issue>5</issue><spage>1139</spage><epage>1147</epage><pages>1139-1147</pages><issn>0006-3495</issn><eissn>1542-0086</eissn><abstract>Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from
Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>21889451</pmid><doi>10.1016/j.bpj.2011.07.016</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 60 APPLIED LIFE SCIENCES Amino Acid Motifs Base Pairing BASIC BIOLOGICAL SCIENCES Binding sites Brownian motion colicins Colicins - chemistry Colicins - metabolism Deoxyribonucleases - metabolism Deoxyribonucleic acid DNA DNA - chemistry DNA - metabolism E coli Environmental Molecular Sciences Laboratory ENZYMES ESCHERICHIA COLI Escherichia coli - enzymology landscapes molecular dynamics Molecular Dynamics Simulation NUCLEASES Nucleic Acid Protein Binding Protein Structure, Tertiary PROTEINS SIMULATION Static Electricity Substrate Specificity Thermodynamics TRANSIENTS WATER |
| title | The Binding Process of a Nonspecific Enzyme with DNA |
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