{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T04:07:57Z","timestamp":1793506077075,"version":"4.5.0"},"reference-count":39,"publisher":"National Academy of Sciences","issue":"19","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2010,5,11]]},"abstract":"\n Protein folding mechanisms are probed experimentally using single-point mutant perturbations. The relative effects on the folding (\n \u03d5<\/jats:italic>\n -values) and unfolding (1\u00a0-\u00a0\n \u03d5<\/jats:italic>\n ) rates are used to infer the detailed structure of the transition-state ensemble (TSE). Here we analyze kinetic data on >\u00a0800 mutations carried out for 24 proteins with simple kinetic behavior. We find two surprising results: (\n i<\/jats:italic>\n ) all mutant effects are described by the equation:\n \n \n <\/jats:inline-formula>\n . Therefore all data are consistent with a single\n \u03d5<\/jats:italic>\n -value (0.24) with accuracy comparable to experimental precision, suggesting that the structural information in conventional\n \u03d5<\/jats:italic>\n -values is low. (\n ii<\/jats:italic>\n )\n \u03d5<\/jats:italic>\n -values change with stability, increasing in mean value and spread from native to unfolding conditions, and thus cannot be interpreted without proper normalization. We eliminate stability effects calculating the\n \u03d5<\/jats:italic>\n -values at the mutant denaturation midpoints; i.e., conditions of zero stability (\n \u03d5<\/jats:italic>\n 0<\/jats:sup>\n ). We then show that the intrinsic variability is\n \u03d5<\/jats:italic>\n 0<\/jats:sup>\n \u00a0=\u00a00.36\u00a0\u00b1\u00a00.11, being somewhat larger for \u03b2-sheet-rich proteins than for \u03b1-helical proteins. Importantly, we discover that\n \u03d5<\/jats:italic>\n 0<\/jats:sup>\n -values are proportional to how many of the residues surrounding the mutated site are local in sequence. High\n \u03d5<\/jats:italic>\n 0<\/jats:sup>\n -values correspond to protein surface sites, which have few nonlocal neighbors, whereas core residues with many tertiary interactions produce the lowest\n \u03d5<\/jats:italic>\n 0<\/jats:sup>\n -values. These results suggest a general mechanism in which the TSE at zero stability is a broad conformational ensemble stabilized by local interactions and without specific tertiary interactions, reconciling\n \u03d5<\/jats:italic>\n -values with many other empirical observations.\n <\/jats:p>","DOI":"10.1073\/pnas.1000988107","type":"journal-article","created":{"date-parts":[[2010,4,23]],"date-time":"2010-04-23T22:26:22Z","timestamp":1272061582000},"page":"8611-8616","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":105,"title":["Insights into protein folding mechanisms from large scale analysis of mutational effects"],"prefix":"10.1073","volume":"107","author":[{"given":"Athi N.","family":"Naganathan","sequence":"first","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas, Consejo Superior de Investigaciones Cient\u00edficas, Ramiro de Maeztu 9, Madrid 28040, Spain; and"},{"name":"Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas, Consejo Superior de Investigaciones Cient\u00edficas, Ramiro de Maeztu 9, Madrid 28040, Spain; and"},{"name":"Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2010,4,23]]},"reference":[{"key":"e_1_3_2_1_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(92)90561-W"},{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm1126"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583506004185"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00839a053"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1995.0616"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.81.5237"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.20.11305"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.12.018"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0808600105"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3693"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)00620-7"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/35054591"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.10.016"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.2174\/0929866053005809"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.051870506"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1997.1612"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.4873"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.26.14854"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308497101"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(03)00171-2"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja0669878"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0810218105"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi973111s"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0402684101"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.07.059"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.20.11311"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja0761939"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.physchem.48.1.545"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.12.6170"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja0689740"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.2976\/1.2988030"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20172"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi060025w"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2613"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(03)00436-4"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.97.12.6509"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00199a029"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3233(08)60546-X"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature04859"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1000988107","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,13]],"date-time":"2022-04-13T23:15:37Z","timestamp":1649891737000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1000988107"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,23]]},"references-count":39,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2010,5,11]]}},"alternative-id":["10.1073\/pnas.1000988107"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1000988107","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.4148956.3931054","asserted-by":"object"}]},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,23]]},"assertion":[{"value":"2010-04-23","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}