{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:38:55Z","timestamp":1767181135675,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007867","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T00:00:00Z","timestamp":1591315200000}}],"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2020,5,26]],"date-time":"2020-05-26T00:00:00Z","timestamp":1590451200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007867","type":"journal-article","created":{"date-parts":[[2020,5,26]],"date-time":"2020-05-26T13:39:24Z","timestamp":1590500364000},"page":"e1007867","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5566-6035","authenticated-orcid":true,"given":"Arumay","family":"Pal","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9929-973X","authenticated-orcid":true,"given":"Yaakov","family":"Levy","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,5,26]]},"reference":[{"key":"pcbi.1007867.ref001","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nrm2144","article-title":"The folding and evolution of multidomain proteins","volume":"8","author":"JH Han","year":"2007","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi.1007867.ref002","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1006\/jmbi.2001.4776","article-title":"Domain combinations in archaeal, eubacterial and eukaryotic proteomes","volume":"310","author":"G Apic","year":"2001","journal-title":"Journal of Molecular Biology"},{"key":"pcbi.1007867.ref003","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.tibs.2004.09.006","article-title":"The power of two: protein dimerization in biology","volume":"29","author":"NJ Marianayagam","year":"2004","journal-title":"Trends in Biochemical Sciences"},{"key":"pcbi.1007867.ref004","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1128\/MCB.12.2.455","article-title":"Segments of the Pou Domain Influence One Anothers DNA-Binding Specificity","volume":"12","author":"R Aurora","year":"1992","journal-title":"Molecular and Cellular Biology"},{"key":"pcbi.1007867.ref005","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/ng0696-141","article-title":"PAX6 missense mutation in isolated foveal hypoplasia","volume":"13","author":"N Azuma","year":"1996","journal-title":"Nature Genetics"},{"key":"pcbi.1007867.ref006","doi-asserted-by":"crossref","first-page":"13497","DOI":"10.1021\/jacs.6b08416","article-title":"Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA","volume":"138","author":"MY Tsai","year":"2016","journal-title":"Journal of the American Chemical Society"},{"key":"pcbi.1007867.ref007","doi-asserted-by":"crossref","first-page":"e87922","DOI":"10.1371\/journal.pone.0087922","article-title":"Concentration-Dependent Exchange of Replication Protein A on Single-Stranded DNA Revealed by Single-Molecule Imaging","volume":"9","author":"B Gibb","year":"2014","journal-title":"PLoS One"},{"key":"pcbi.1007867.ref008","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.bpj.2010.06.007","article-title":"Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker","volume":"99","author":"D Vuzman","year":"2010","journal-title":"Biophys J"},{"key":"pcbi.1007867.ref009","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1016\/j.jmb.2016.04.004","article-title":"Structural and Dynamics Studies of Pax5 Reveal Asymmetry in Stability and DNA Binding by the Paired Domain","volume":"428","author":"C Perez-Borrajero","year":"2016","journal-title":"Journal of Molecular Biology"},{"key":"pcbi.1007867.ref010","doi-asserted-by":"crossref","first-page":"E1724","DOI":"10.1073\/pnas.1121500109","article-title":"Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1","volume":"109","author":"L Zandarashvili","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007867.ref011","doi-asserted-by":"crossref","first-page":"58","DOI":"10.4161\/trns.23584","article-title":"Speed-stability paradox in DNA-scanning by zinc-finger proteins","volume":"4","author":"J Iwahara","year":"2013","journal-title":"Transcription"},{"key":"pcbi.1007867.ref012","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1002\/ijch.201400107","article-title":"The \"Monkey-Bar\" Mechanism for Searching for the DNA Target Site: The Molecular Determinants","volume":"54","author":"D Vuzman","year":"2014","journal-title":"Israel Journal of Chemistry"},{"key":"pcbi.1007867.ref013","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1016\/j.jmb.2009.11.056","article-title":"Searching DNA via a \"Monkey Bar\" mechanism: the significance of disordered tails","volume":"396","author":"D Vuzman","year":"2010","journal-title":"J Mol Biol"},{"key":"pcbi.1007867.ref014","doi-asserted-by":"crossref","first-page":"E5142","DOI":"10.1073\/pnas.1507726112","article-title":"Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble","volume":"112","author":"L Zandarashvili","year":"2015","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pcbi.1007867.ref015","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1093\/nar\/gkg161","article-title":"Structural classification of zinc fingers: survey and summary","volume":"31","author":"SS Krishna","year":"2003","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref016","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: function, expression and evolution","volume":"10","author":"JM Vaquerizas","year":"2009","journal-title":"Nature Reviews Genetics"},{"key":"pcbi.1007867.ref017","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.biophys.29.1.183","article-title":"DNA recognition by Cys(2)His(2) zinc finger proteins","volume":"29","author":"SA Wolfe","year":"2000","journal-title":"Annual Review of Biophysics and Biomolecular Structure"},{"key":"pcbi.1007867.ref018","doi-asserted-by":"crossref","first-page":"4800","DOI":"10.1093\/nar\/gku132","article-title":"An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins","volume":"42","author":"A Gupta","year":"2014","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref019","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/nature03556","article-title":"Highly efficient endogenous human gene correction using designed zinc-finger nucleases","volume":"435","author":"FD Urnov","year":"2005","journal-title":"Nature"},{"key":"pcbi.1007867.ref020","doi-asserted-by":"crossref","first-page":"6493","DOI":"10.1093\/nar\/gkg853","article-title":"Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins","volume":"31","author":"CD Carvin","year":"2003","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref021","doi-asserted-by":"crossref","first-page":"16370","DOI":"10.1073\/pnas.0605633103","article-title":"Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells","volume":"103","author":"J Morton","year":"2006","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pcbi.1007867.ref022","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1021\/bi200393g","article-title":"Adding fingers to an engineered zinc finger nuclease can reduce activity","volume":"50","author":"Y Shimizu","year":"2011","journal-title":"Biochemistry"},{"key":"pcbi.1007867.ref023","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.cell.2012.12.009","article-title":"DNA-binding specificities of human transcription factors","volume":"152","author":"A Jolma","year":"2013","journal-title":"Cell"},{"key":"pcbi.1007867.ref024","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1002\/prot.24845","article-title":"A multiscale approach to simulating the conformational properties of unbound multi\u2010C 2 H 2 zinc finger proteins.","volume":"83","author":"L Liu","year":"2015","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"pcbi.1007867.ref025","doi-asserted-by":"crossref","first-page":"D452","DOI":"10.1093\/nar\/gks1167","article-title":"Zinc Finger Database (ZiFDB) v2. 0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays","volume":"41","author":"F Fu","year":"2012","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref026","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1093\/nar\/gku1395","article-title":"A systematic survey of the Cys2His2 zinc finger DNA-binding landscape","volume":"43","author":"AV Persikov","year":"2015","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref027","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/nar\/gkt890","article-title":"De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins","volume":"42","author":"AV Persikov","year":"2013","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref028","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.bpj.2009.11.021","article-title":"Probing the DNA-binding affinity and specificity of designed zinc finger proteins","volume":"98","author":"D Jantz","year":"2010","journal-title":"Biophysical journal"},{"key":"pcbi.1007867.ref029","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/nmeth.1805","article-title":"Zinc-finger nucleases: how to play two good hands","volume":"9","author":"M Isalan","year":"2012","journal-title":"Nat Methods"},{"key":"pcbi.1007867.ref030","doi-asserted-by":"crossref","first-page":"9147","DOI":"10.1093\/nar\/gkv919","article-title":"A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity","volume":"43","author":"M Garton","year":"2015","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref031","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1007\/11415770_40","article-title":"Predicting transcription factor binding sites using structural knowledge","volume":"3500","author":"T Kaplan","year":"2005","journal-title":"Research in Computational Molecular Biology, Proceedings"},{"key":"pcbi.1007867.ref032","doi-asserted-by":"crossref","first-page":"6673","DOI":"10.1093\/nar\/gkh1003","article-title":"Looking into DNA recognition: zinc finger binding specificity","volume":"32","author":"G Paillard","year":"2004","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref033","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1093\/nar\/gkq1303","article-title":"Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays","volume":"39","author":"KN Lam","year":"2011","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref034","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.cell.2018.02.058","article-title":"DNA conformation induces adaptable binding by tandem zinc finger proteins","volume":"173","author":"A Patel","year":"2018","journal-title":"Cell"},{"key":"pcbi.1007867.ref035","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"U Consortium","year":"2018","journal-title":"Nucleic acids research"},{"key":"pcbi.1007867.ref036","doi-asserted-by":"crossref","first-page":"3163","DOI":"10.1002\/pmic.201400441","article-title":"Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues, and cell\u2010lines","volume":"15","author":"M Wang","year":"2015","journal-title":"Proteomics"},{"key":"pcbi.1007867.ref037","doi-asserted-by":"crossref","first-page":"E1724","DOI":"10.1073\/pnas.1121500109","article-title":"Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1","volume":"109","author":"L Zandarashvili","year":"2012","journal-title":"Proc Natl Acad Sci USA"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007867","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T00:00:00Z","timestamp":1591315200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007867","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T13:57:28Z","timestamp":1591365448000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007867"}},"subtitle":[],"editor":[{"given":"Shi-Jie","family":"Chen","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,5,26]]},"references-count":37,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007867","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,26]]}}}