{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T22:11:26Z","timestamp":1762639886663,"version":"3.32.0"},"reference-count":23,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2015,8,1]],"date-time":"2015-08-01T00:00:00Z","timestamp":1438387200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2015,8,1]],"date-time":"2015-08-01T00:00:00Z","timestamp":1438387200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2015,8]]},"abstract":"<jats:p>Lac repressor, the first discovered transcriptional regulator, has been shown to confer multiple modes of binding to its operator sites depending on the central spacer length. Other homolog members in the LacI\/GalR family (PurR and YcjW) cannot bind their operator sites with similar structural flexibility. To decipher the underlying mechanism for this unique property, we used Spec\u2010seq approach combined with site\u2010directed mutagenesis to quantify the DNA binding specificity of multiple hybrids of lacI and PurR. We find that lac repressor\u2019s recognition di\u2010residues YQ and its hinge helix loop regions are both critical for its structural flexibility. Also, specificity profiling of the whole lac operator suggests that a simple additive model from single variants suffice to predict other multivariant sites\u2019 energy reasonably well, and the genome occupancy model based on this specificity data correlates well with in vivo lac repressor binding profile.<\/jats:p>","DOI":"10.1007\/s40484-015-0044-z","type":"journal-article","created":{"date-parts":[[2015,5,29]],"date-time":"2015-05-29T18:51:44Z","timestamp":1432925504000},"page":"69-80","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["A quantitative understanding of lac repressor\u2019s binding specificity and flexibility"],"prefix":"10.1002","volume":"3","author":[{"given":"Zheng","family":"Zuo","sequence":"first","affiliation":[{"name":"Department of Genetics and Center for Genomic Sciences and Systems Biology School of Medicine Washington University St. Louis MO 63108 USA"}]},{"given":"Yiming","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Genetics and Center for Genomic Sciences and Systems Biology School of Medicine Washington University St. Louis MO 63108 USA"}]},{"given":"Gary D.","family":"Stormo","sequence":"additional","affiliation":[{"name":"Department of Genetics and Center for Genomic Sciences and Systems Biology School of Medicine Washington University St. Louis MO 63108 USA"}]}],"member":"311","published-online":{"date-parts":[[2015,8]]},"reference":[{"doi-asserted-by":"publisher","key":"e_1_2_8_2_2","DOI":"10.1016\/S0022\u20102836(61)80072\u20107"},{"doi-asserted-by":"publisher","key":"e_1_2_8_3_2","DOI":"10.1016\/j.crvi.2005.04.004"},{"doi-asserted-by":"publisher","key":"e_1_2_8_4_2","DOI":"10.1073\/pnas.70.12.3581"},{"doi-asserted-by":"publisher","key":"e_1_2_8_5_2","DOI":"10.1534\/genetics.114.170100"},{"doi-asserted-by":"publisher","key":"e_1_2_8_6_2","DOI":"10.1016\/0022\u20102836(85)90106\u20108"},{"doi-asserted-by":"publisher","key":"e_1_2_8_7_2","DOI":"10.1006\/jmbi.1997.0920"},{"doi-asserted-by":"publisher","key":"e_1_2_8_8_2","DOI":"10.1093\/nar\/27.4.1063"},{"doi-asserted-by":"publisher","key":"e_1_2_8_9_2","DOI":"10.1093\/nar\/gkf578"},{"doi-asserted-by":"publisher","key":"e_1_2_8_10_2","DOI":"10.1007\/s40484\u2010013\u20100012\u20104"},{"doi-asserted-by":"publisher","key":"e_1_2_8_11_2","DOI":"10.1126\/science.1131007"},{"doi-asserted-by":"publisher","key":"e_1_2_8_12_2","DOI":"10.1093\/nar\/gkp894"},{"doi-asserted-by":"publisher","key":"e_1_2_8_13_2","DOI":"10.1093\/protein\/gzp051"},{"doi-asserted-by":"publisher","key":"e_1_2_8_14_2","DOI":"10.1021\/bi00641a005"},{"doi-asserted-by":"publisher","key":"e_1_2_8_15_2","DOI":"10.1073\/pnas.1418978111"},{"doi-asserted-by":"publisher","key":"e_1_2_8_16_2","DOI":"10.1126\/science.7973627"},{"doi-asserted-by":"publisher","key":"e_1_2_8_17_2","DOI":"10.1126\/science.271.5253.1247"},{"doi-asserted-by":"publisher","key":"e_1_2_8_18_2","DOI":"10.1016\/j.jmb.2009.05.022"},{"doi-asserted-by":"publisher","key":"e_1_2_8_19_2","DOI":"10.1002\/pro.389"},{"doi-asserted-by":"publisher","key":"e_1_2_8_20_2","DOI":"10.1021\/cr0304065"},{"doi-asserted-by":"publisher","key":"e_1_2_8_21_2","DOI":"10.1016\/0022\u20102836(70)90219\u20106"},{"doi-asserted-by":"publisher","key":"e_1_2_8_22_2","DOI":"10.1126\/science.1101270"},{"doi-asserted-by":"publisher","key":"e_1_2_8_23_2","DOI":"10.1128\/JB.02038\u201012"},{"doi-asserted-by":"publisher","key":"e_1_2_8_24_2","DOI":"10.1093\/nar\/gkq1110"}],"container-title":["Quantitative Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s40484-015-0044-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s40484-015-0044-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1007\/s40484-015-0044-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,3]],"date-time":"2025-01-03T09:57:58Z","timestamp":1735898278000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1007\/s40484-015-0044-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8]]},"references-count":23,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2015,8]]}},"alternative-id":["10.1007\/s40484-015-0044-z"],"URL":"https:\/\/doi.org\/10.1007\/s40484-015-0044-z","archive":["Portico"],"relation":{},"ISSN":["2095-4689","2095-4697"],"issn-type":[{"type":"print","value":"2095-4689"},{"type":"electronic","value":"2095-4697"}],"subject":[],"published":{"date-parts":[[2015,8]]}}}