{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:17:02Z","timestamp":1773659822029,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Proteins of all kinds can self-assemble into highly ordered \u03b2-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods.<\/jats:p>\n               <jats:p>Results: We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between A\u03b2 and its highly-toxic \u2018Iowa\u2019 mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments.<\/jats:p>\n               <jats:p>Availability: Our tool is publically available on the web at http:\/\/amyloid.csail.mit.edu\/.<\/jats:p>\n               <jats:p>Contact: \u00a0lindquist_admin@wi.mit.edu; bab@csail.mit.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr238","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i34-i42","source":"Crossref","is-referenced-by-count":65,"title":["A method for probing the mutational landscape of amyloid structure"],"prefix":"10.1093","volume":"27","author":[{"given":"Charles W.","family":"O'Donnell","sequence":"first","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"J\u00e9r\u00f4me","family":"Waldisp\u00fchl","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"Mieszko","family":"Lis","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"Randal","family":"Halfmann","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"Srinivas","family":"Devadas","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"Susan","family":"Lindquist","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]},{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"},{"name":"1 Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, 2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, 3Department of EECS, Massachusetts Institute of Technology, Cambridge, MA 02139, 4School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada, 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, 6Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142 and 7Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512153401100_B1","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.cell.2009.02.044","article-title":"A systematic survey identifies prions and illuminates sequence features of prionogenic proteins","volume":"147","author":"Alberti","year":"2009","journal-title":"Cell"},{"key":"2023012512153401100_B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids 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