{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T05:32:41Z","timestamp":1792647161768,"version":"4.5.0"},"reference-count":45,"publisher":"National Academy of Sciences","issue":"20","license":[{"start":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T00:00:00Z","timestamp":1747180800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["DK-0292023"],"award-info":[{"award-number":["DK-0292023"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2025,5,20]]},"abstract":"<jats:p>\n                    The bacterial transcriptional regulator RfaH comprises structurally and functionally distinct N- (NTD) and C- (CTD) terminal domains. The latter switches from a helical hairpin packed against the NTD to a five-stranded \u03b2-roll upon displacement by RNA polymerase binding. Here, we use exchange-based NMR to probe fold-switching intermediates sampled by the isolated CTD. In addition to the predominant (~76 to 77%), semistable \u03b2-roll conformation (state A), we identify four structurally and kinetically distinct states: A\u2032, B, B\u2032, and B\u2033. State B is NMR observable with an occupancy of ~23%, exchanges slowly (\u03c4\n                    <jats:sub>ex<\/jats:sub>\n                    ~ 300 ms) with the major A species, and comprises a largely unfolded ensemble with transient occupancy of helical (\u03b15*) and \u03b2-hairpin (\u03b21*\/\u03b22*) elements. Backbone chemical shift-based structure predictions using the program CS-ROSETTA suggest that the two transient structural elements within the B state may interact with one another to form a semicompact structure. A\u2032 (~0.35%) is an off-pathway state that exchanges rapidly (\u03c4\n                    <jats:sub>ex<\/jats:sub>\n                    ~ 1 ms) with state A and likely entails a minor localized conformational change in the \u03b21\/\u03b22 loop. State B\u2032 (~0.3%) exchanges rapidly (\u03c4\n                    <jats:sub>ex<\/jats:sub>\n                    ~ 1.2 ms) with state B and exhibits downfield\n                    <jats:sup>15<\/jats:sup>\n                    N backbone shifts (relative to B) in the \u03b15* region indicative of reduced helicity. Finally state B\u2033 (~0.05%) exchanges rapidly (\u03c4\n                    <jats:sub>ex<\/jats:sub>\n                    ~ 0.8 to 1 ms) with either B\u2032 (linear model) or B (branched model), displays significant differences in absolute\n                    <jats:sup>15<\/jats:sup>\n                    N chemical shift from states B and B\u2032, and likely represents a further intermediate with increased helicity along the fold-switching pathway.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2506441122","type":"journal-article","created":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T11:28:01Z","timestamp":1747222081000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":9,"title":["Unraveling structural transitions and kinetics along the fold-switching pathway of the RfaH C-terminal domain using exchange-based NMR"],"prefix":"10.1073","volume":"122","author":[{"given":"Mengli","family":"Cai","sequence":"first","affiliation":[{"name":"Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH","place":["Bethesda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfa","family":"Ying","sequence":"additional","affiliation":[{"name":"Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH","place":["Bethesda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan M.","family":"Lopez","sequence":"additional","affiliation":[{"name":"Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH","place":["Bethesda"]},{"name":"Departmento de Ciencia\u2013Quimica, Centro de Espectroscopia de Resonancia Magn\u00e9tica Nuclear, Pontificia Universidad Cat\u00f3lica del Per\u00fa","place":["Lima 32, Per\u00fa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Huang","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH","place":["Bethesda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3809-1027","authenticated-orcid":false,"given":"G. Marius","family":"Clore","sequence":"additional","affiliation":[{"name":"Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH","place":["Bethesda"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2025,5,14]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-70-3-527"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1042\/BST20160367"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23010189"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.05.042"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd8700"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31532-9"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2024.102807"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2007.02.021"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.05.017"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08567-6"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-024-01372-w"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.4c00258"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.76630"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583514000122"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2018.09.028"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00003a021"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja3001419"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-017-0099-4"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmr.2014.01.008"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1021\/ar00028a001"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008392405740"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-009-9333-z"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-2239-0_2"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00014a071"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-011-9508-2"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0800256105"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2004.01.013"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2006.03.034"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja982592f"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2005.08.006"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja991789k"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00381a009"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmre.1998.1419"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00168a070"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00484a006"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1744152"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201713172"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00197809"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-019-00286-w"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-006-9120-z"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-016-0072-7"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp074793o"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1716098114"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1915948116"},{"key":"e_1_3_4_45_2","unstructured":"M. Cai G. M. Clore Complete set of 15N-CEST and 15N-CPMG relaxation dispersion data together with Matlab fitting scripts for the paper entitled: \u201cUnraveling structural transitions and kinetics along the fold switching pathway of the RfaH C-terminal domain using exchange-based NMR. Figshare. https:\/\/doi.org\/10.6084\/m9.figshare.28629485.v1. Deposited 19 March 2025."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2506441122","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T11:28:03Z","timestamp":1747222083000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2506441122"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,14]]},"references-count":45,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2025,5,20]]}},"alternative-id":["10.1073\/pnas.2506441122"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2506441122","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,14]]},"assertion":[{"value":"2025-03-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-04-15","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-05-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2506441122"}}