{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T07:50:51Z","timestamp":1761292251467},"reference-count":24,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2005,4,22]],"date-time":"2005-04-22T00:00:00Z","timestamp":1114128000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2005,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We have previously demonstrated that calculation of contact\u2010dependent secondary structure propensity (CSSP) is highly sensitive in detecting non\u2010native \u03b2\u2010strand propensities in the core sequences of known amyloidogenic proteins. Here we describe a CSSP method based on an artificial neural network that rapidly and accurately quantifies the influence of tertiary contacts (<jats:italic>TC<\/jats:italic>s) on secondary structure propensity in local regions of protein sequences. The present method exhibited 72% accuracy in predicting the alternate secondary structure adopted by chameleon sequences located in highly disparate <jats:italic>TC<\/jats:italic> regions. Analysis of 1930 nonhomologous protein domains reveals that the \u03b1\u2010helix and the \u03b2\u2010strand largely share the same sequence context, and that tertiary context is a major determinant of the native conformation. Conversely, it appears that the propensity of random coils for either the \u03b1\u2010helix or the \u03b2\u2010strand is largely invariant to tertiary effects. The present CSSP method successfully reproduced the amyloidogenic character observed in local regions of the human islet amyloid polypeptide (hIAPP). Furthermore, CSSP profiles were strongly correlated (<jats:italic>r<\/jats:italic> = 0.76) with the observed mutational effects on the aggregation rate of acylphosphatase. Taken together, these results provide compelling evidence in support of the present CSSP approach as a sensitive probe useful for analysis of full\u2010length proteins and for detection of core sequences that may trigger amyloid fibril formation. The combined speed and simplicity of the CSSP method lends itself to proteome\u2010wide analysis of the amyloidogenic nature of common proteins. Proteins 2005. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.20477","type":"journal-article","created":{"date-parts":[[2005,4,22]],"date-time":"2005-04-22T18:52:34Z","timestamp":1114195954000},"page":"110-117","source":"Crossref","is-referenced-by-count":23,"title":["Rapid assessment of contact\u2010dependent secondary structure propensity: Relevance to amyloidogenic sequences"],"prefix":"10.1002","volume":"60","author":[{"given":"Sukjoon","family":"Yoon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William J.","family":"Welsh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2005,4,22]]},"reference":[{"key":"e_1_2_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd769"},{"key":"e_1_2_4_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.66.1.385"},{"key":"e_1_2_4_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2634884100"},{"key":"e_1_2_4_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/380730a0"},{"key":"e_1_2_4_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19980215)30:3<228::AID-PROT2>3.0.CO;2-G"},{"key":"e_1_2_4_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(96)66033-9"},{"key":"e_1_2_4_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10082"},{"key":"e_1_2_4_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.2.644"},{"key":"e_1_2_4_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.12.5814"},{"key":"e_1_2_4_11_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.04790604"},{"key":"e_1_2_4_12_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4049"},{"key":"e_1_2_4_13_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.1645"},{"key":"e_1_2_4_14_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.03143803"},{"key":"e_1_2_4_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/18.4.815"},{"key":"e_1_2_4_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.7.3590"},{"key":"e_1_2_4_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.254"},{"key":"e_1_2_4_18_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360221211"},{"key":"e_1_2_4_19_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci970439j"},{"key":"e_1_2_4_20_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1020655417839"},{"key":"e_1_2_4_21_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM200008103430607"},{"key":"e_1_2_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00887-2"},{"key":"e_1_2_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb752"},{"key":"e_1_2_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01891"},{"key":"e_1_2_4_25_2","doi-asserted-by":"publisher","DOI":"10.1096\/fj.01-0442hyp"}],"container-title":["Proteins: Structure, Function, and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fprot.20477","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.20477","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,16]],"date-time":"2023-10-16T04:30:29Z","timestamp":1697430629000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.20477"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4,22]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2005,7]]}},"alternative-id":["10.1002\/prot.20477"],"URL":"https:\/\/doi.org\/10.1002\/prot.20477","archive":["Portico"],"relation":{},"ISSN":["0887-3585","1097-0134"],"issn-type":[{"value":"0887-3585","type":"print"},{"value":"1097-0134","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,4,22]]}}}