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Modeling promoter search by E. coli RNA polymerase: One-dimensional diffusion in a sequence-dependent energy landscape

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dc.contributor.author Weindl J.
dc.contributor.author Dawy Z.
dc.contributor.author Hanus P.
dc.contributor.author Zech J.
dc.contributor.author Mueller J.C.
dc.contributor.editor
dc.date 2009
dc.date.accessioned 2017-10-04T11:06:41Z
dc.date.available 2017-10-04T11:06:41Z
dc.date.issued 2009
dc.identifier 10.1016/j.jtbi.2009.05.006
dc.identifier.isbn
dc.identifier.issn 00225193
dc.identifier.uri http://hdl.handle.net/10938/14068
dc.description.abstract We present a biophysical model of promoter search by Escherichia coli RNA polymerase. We use an unconventional weight matrix derived from promoter strength data to extract the energy landscape common to a large set of known promoters. This exhibits a continuous strengthening of the binding energy when approaching the transcription start site from either side. During promoter search, the RNA polymerase slides along the DNA double helix (one-dimensional diffusion) after randomly binding to it. We discuss the possibility that the sliding has a sequence-dependent component, which implies that the energy landscape influences the movement with respect to speed, direction and efficiency. Based on this assumption, we relate the obtained energy landscape around the promoters to the one-dimensional diffusion of the RNA polymerase. Our analytical results suggest that the sequence-dependent random walk slows down and gets directed upon entering a region of 500 bp around the transcription start site, which significantly increases the efficiency of promoter search. These results may explain how the RNA polymerase is able to find the promoter in biologically relevant times out of a vast excess of non-target sites. Moreover, they provide evidence for a sequence-dependent component of one-dimensional diffusion. © 2009 Elsevier Ltd. All rights reserved.
dc.format.extent
dc.format.extent Pages: (628-634)
dc.language English
dc.publisher LONDON
dc.relation.ispartof Publication Name: Journal of Theoretical Biology; Publication Year: 2009; Volume: 259; no. 3; Pages: (628-634);
dc.relation.ispartofseries
dc.relation.uri
dc.source Scopus
dc.subject.other
dc.title Modeling promoter search by E. coli RNA polymerase: One-dimensional diffusion in a sequence-dependent energy landscape
dc.type Article
dc.contributor.affiliation Weindl, J., Institute for Communications Engineering, Technische Universität München, Arcisstraße 21, 80290 München, Germany
dc.contributor.affiliation Dawy, Z., Department of Electrical and Computer Engineering, American University of Beirut, P.O. Box 11-0236, Riad El-Solh, Beirut, Lebanon
dc.contributor.affiliation Hanus, P., Institute for Communications Engineering, Technische Universität München, Arcisstraße 21, 80290 München, Germany
dc.contributor.affiliation Zech, J., MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
dc.contributor.affiliation Mueller, J.C., Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, 82305 Starnberg, Germany
dc.contributor.authorAddress Weindl, J.; Institute for Communications Engineering, Technische Universität München, Arcisstraße 21, 80290 München, Germany; email: johanna.weindl@mytum.de
dc.contributor.authorCorporate University: American University of Beirut; Faculty: Faculty of Engineering and Architecture; Department: Electrical and Computer Engineering;
dc.contributor.authorDepartment Electrical and Computer Engineering
dc.contributor.authorDivision
dc.contributor.authorEmail johanna.weindl@mytum.de; zaher.dawy@aub.edu.lb; pavol.hanus@tum.de; juergen.zech@csc.mrc.ac.uk; mueller@orn.mpg.de
dc.contributor.authorFaculty Faculty of Engineering and Architecture
dc.contributor.authorInitials Weindl, J
dc.contributor.authorInitials Dawy, Z
dc.contributor.authorInitials Hanus, P
dc.contributor.authorInitials Zech, J
dc.contributor.authorInitials Mueller, JC
dc.contributor.authorOrcidID
dc.contributor.authorReprintAddress Weindl, J (reprint author), Tech Univ Munich, Inst Commun Engn, Arcisstr 21, D-80290 Munich, Germany.
dc.contributor.authorResearcherID
dc.contributor.authorUniversity American University of Beirut
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dc.description.citedCount 2
dc.description.citedTotWOSCount 1
dc.description.citedWOSCount 1
dc.format.extentCount 7
dc.identifier.articleNo
dc.identifier.coden JTBIA
dc.identifier.pubmedID 19463831
dc.identifier.scopusID 67649982898
dc.identifier.url
dc.publisher.address 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND
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dc.relation.ispartofConferenceCode
dc.relation.ispartofConferenceDate
dc.relation.ispartofConferenceHosting
dc.relation.ispartofConferenceLoc
dc.relation.ispartofConferenceSponsor
dc.relation.ispartofConferenceTitle
dc.relation.ispartofFundingAgency
dc.relation.ispartOfISOAbbr J. Theor. Biol.
dc.relation.ispartOfIssue 3
dc.relation.ispartOfPart
dc.relation.ispartofPubTitle Journal of Theoretical Biology
dc.relation.ispartofPubTitleAbbr J. Theor. Biol.
dc.relation.ispartOfSpecialIssue
dc.relation.ispartOfSuppl
dc.relation.ispartOfVolume 259
dc.source.ID WOS:000274798000023
dc.type.publication Journal
dc.subject.otherAuthKeyword Binding energy
dc.subject.otherAuthKeyword Facilitated target location
dc.subject.otherAuthKeyword Protein-DNA interaction
dc.subject.otherAuthKeyword Random walk
dc.subject.otherAuthKeyword Sliding model
dc.subject.otherChemCAS RNA polymerase, 9014-24-8
dc.subject.otherChemCAS Bacterial Proteins
dc.subject.otherChemCAS DNA-Directed RNA Polymerases, 2.7.7.6
dc.subject.otherIndex RNA polymerase
dc.subject.otherIndex coliform bacterium
dc.subject.otherIndex DNA
dc.subject.otherIndex modeling
dc.subject.otherIndex protein
dc.subject.otherIndex random walk method
dc.subject.otherIndex article
dc.subject.otherIndex bacterial genetics
dc.subject.otherIndex DNA helix
dc.subject.otherIndex Escherichia coli
dc.subject.otherIndex gene sequence
dc.subject.otherIndex mathematical model
dc.subject.otherIndex nonhuman
dc.subject.otherIndex priority journal
dc.subject.otherIndex promoter region
dc.subject.otherIndex transcription initiation site
dc.subject.otherIndex Bacterial Proteins
dc.subject.otherIndex Diffusion
dc.subject.otherIndex DNA-Directed RNA Polymerases
dc.subject.otherIndex Escherichia coli
dc.subject.otherIndex Genes, Bacterial
dc.subject.otherIndex Models, Genetic
dc.subject.otherIndex Promoter Regions, Genetic
dc.subject.otherIndex Templates, Genetic
dc.subject.otherIndex Transcription Initiation Site
dc.subject.otherIndex Transcriptional Activation
dc.subject.otherIndex Escherichia coli
dc.subject.otherKeywordPlus FACILITATED TARGET LOCATION
dc.subject.otherKeywordPlus REPRESSOR-OPERATOR INTERACTION
dc.subject.otherKeywordPlus PROTEIN-DNA INTERACTION
dc.subject.otherKeywordPlus ESCHERICHIA-COLI
dc.subject.otherKeywordPlus DRIVEN MECHANISMS
dc.subject.otherKeywordPlus BINDING PROTEINS
dc.subject.otherKeywordPlus NUCLEIC-ACIDS
dc.subject.otherKeywordPlus TRANSLOCATION
dc.subject.otherKeywordPlus TRANSCRIPTION
dc.subject.otherKeywordPlus SPECIFICITY
dc.subject.otherWOS Biology
dc.subject.otherWOS Mathematical and Computational Biology


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