{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T10:31:55Z","timestamp":1762252315776,"version":"3.37.3"},"reference-count":47,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2015,12,26]],"date-time":"2015-12-26T00:00:00Z","timestamp":1451088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100005237","name":"Helen Hay Whitney Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100005237","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2016,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Proper maintenance of RNA structure and dynamics is essential to maintain cellular health. Multiple families of RNA chaperones exist in cells to modulate RNA structure, RNA\u2013protein complexes, and RNA granules. The largest of these families is the DEAD\u2010box proteins, named after their catalytic Asp\u2010Glu\u2010Ala\u2010Asp motif. The human DEAD\u2010box protein DDX3 is implicated in diverse biological processes including translation initiation and is mutated in numerous cancers. Like many DEAD\u2010box proteins, DDX3 is essential to cellular health and exhibits dosage sensitivity, such that both decreases and increases in protein levels can be lethal. Therefore, chemical inhibition would be an ideal tool to probe the function of DDX3. However, most DEAD\u2010box protein active sites are extremely similar, complicating the design of specific inhibitors. Here, we show that a chemical genetic approach best characterized in protein kinases, known as analog\u2010sensitive chemical inhibition, is viable for DDX3 and possibly other DEAD\u2010box proteins. We present an expanded active\u2010site mutant that is tolerated <jats:italic>in vitro<\/jats:italic> and <jats:italic>in vivo<\/jats:italic>, and is sensitive to chemical inhibition by a novel bulky inhibitor. Our results highlight a course towards analog sensitive chemical inhibition of DDX3 and potentially the entire DEAD\u2010box protein family.<\/jats:p>","DOI":"10.1002\/pro.2857","type":"journal-article","created":{"date-parts":[[2015,12,9]],"date-time":"2015-12-09T18:46:37Z","timestamp":1449686797000},"page":"638-649","source":"Crossref","is-referenced-by-count":14,"title":["Analog sensitive chemical inhibition of the <scp>DEAD<\/scp>\u2010box protein <scp>DDX<\/scp>3"],"prefix":"10.1002","volume":"25","author":[{"given":"Stephen N.","family":"Floor","sequence":"first","affiliation":[{"name":"Department of Molecular and Cell Biology University of California Berkeley California"},{"name":"Howard Hughes Medical Institute, University of California Berkeley Berkeley, California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Krister J.","family":"Barkovich","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Pharmacology University of California San Francisco California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kendall J.","family":"Condon","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology University of California Berkeley California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevan M.","family":"Shokat","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Pharmacology University of California San Francisco California"},{"name":"Howard Hughes Medical Institute, University of California San Francisco California"},{"name":"Department of Chemistry University of California Berkeley California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer A.","family":"Doudna","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology University of California Berkeley California"},{"name":"Howard Hughes Medical Institute, University of California Berkeley Berkeley, California"},{"name":"Department of Chemistry University of California Berkeley California"},{"name":"Innovative Genomics Initiative, University of California Berkeley Berkeley, California"},{"name":"Lawrence Berkeley National Laboratory Physical Biosciences Division Berkeley California"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2015,12,26]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3154"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.4161\/rna.4.3.5445"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1042\/BJ20110739"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2011.08.008"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201308087"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10879"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.04.017"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2013.09.024"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.00560-10"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn454"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.10.5201"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.191601.115"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.275.5305.1468"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11284"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2014.02.004"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11329"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11213"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3358"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1111\/bjh.13211"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11378"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1109016"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-13-3310"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1208130"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.15252\/emmm.201404368"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi972430g"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0811115106"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-397918-6.00008-2"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.07.030"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.274.44.31373"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.16.9106"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M115.700625"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2013.05.006"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-60327-355-8_18"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1991.tb00753.x"},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.201100166"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep09982"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.6026\/97320630010144"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi0508946"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1015312108"},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1328"},{"key":"e_1_2_7_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-396546-2.00020-6"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.10.11.5707"},{"key":"e_1_2_7_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2006.02.004"},{"key":"e_1_2_7_45_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(98)70198-8"},{"key":"e_1_2_7_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(03)00006-6"},{"key":"e_1_2_7_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2006.00060.x"},{"key":"e_1_2_7_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp033"}],"container-title":["Protein Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpro.2857","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpro.2857","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.2857","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T14:20:00Z","timestamp":1694787600000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.2857"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,26]]},"references-count":47,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,3]]}},"alternative-id":["10.1002\/pro.2857"],"URL":"https:\/\/doi.org\/10.1002\/pro.2857","archive":["Portico"],"relation":{},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"type":"print","value":"0961-8368"},{"type":"electronic","value":"1469-896X"}],"subject":[],"published":{"date-parts":[[2015,12,26]]}}}