{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T05:00:20Z","timestamp":1771563620269,"version":"3.50.1"},"reference-count":31,"publisher":"Proceedings of the National Academy of Sciences","issue":"42","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2007,10,16]]},"abstract":"<jats:p>Transfer RNA (tRNA) transiently occupies the hybrid P\/E state (P\/E-tRNA) when mRNA\u2013tRNA are translocated in the ribosome. In this study, we characterize the structure of P\/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P\/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3\u2032) arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P\/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P\/E-tRNA and characterizes its interactions with the translocating ribosome.<\/jats:p>","DOI":"10.1073\/pnas.0708094104","type":"journal-article","created":{"date-parts":[[2007,10,10]],"date-time":"2007-10-10T00:53:57Z","timestamp":1191977637000},"page":"16540-16545","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":34,"title":["Transfer RNA in the hybrid P\/E state: Correlating molecular dynamics simulations with cryo-EM data"],"prefix":"10.1073","volume":"104","author":[{"given":"Wen","family":"Li","sequence":"first","affiliation":[{"name":"*Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509;"}]},{"given":"Joachim","family":"Frank","sequence":"additional","affiliation":[{"name":"*Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509;"},{"name":"Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509; and"},{"name":"Department of Biomedical Sciences, University at Albany, State University of New York, Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509"}]}],"member":"341","published-online":{"date-parts":[[2007,10,16]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1117230"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.08.032"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1060089"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1131127"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/334362a0"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0014-5793(02)02327-X"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2007.01.014"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/35018597"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/cdf326"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb1003"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(03)00476-8"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.150.3.447"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(03)00478-1"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0403884101"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2007.01.022"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2005.10.007"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3950"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.285.5430.1074"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.270.5241.1464"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2294806"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2003.09.029"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7600102"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0503456102"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(71)90362-7"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2184703"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.285.5436.2095"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2006.08.011"},{"key":"e_1_3_4_28_2","volume-title":"AMBER7","author":"Case DA","year":"1999","unstructured":"DA Case, DA Pearlman, JW Caldwell, TE Cheatham, WS Ross, CL Simmerling, TA Darden, KM Merz, RV Stanton, AL Cheng, et al. 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