{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:43:19Z","timestamp":1767962599256,"version":"3.49.0"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2015,10,23]],"date-time":"2015-10-23T00:00:00Z","timestamp":1445558400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004541","type":"journal-article","created":{"date-parts":[[2015,10,23]],"date-time":"2015-10-23T20:19:38Z","timestamp":1445631578000},"page":"e1004541","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["An Exploration of the Universe of Polyglutamine Structures"],"prefix":"10.1371","volume":"11","author":[{"given":"\u00c0ngel","family":"G\u00f3mez-Sicilia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mateusz","family":"Sikora","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marek","family":"Cieplak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariano","family":"Carri\u00f3n-V\u00e1zquez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,10,23]]},"reference":[{"issue":"1","key":"ref1","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1146\/annurev.bi.59.070190.005043","article-title":"The classification and origins of protein folding patterns","volume":"59","author":"C Chothia","year":"1990","journal-title":"Annual Review of Biochemistry"},{"issue":"6379","key":"ref2","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/357543a0","article-title":"One thousand families for the molecular biologist","volume":"357","author":"C Chothia","year":"1992","journal-title":"Nature"},{"issue":"D1","key":"ref3","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gks1211","article-title":"New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures","volume":"41","author":"I Sillitoe","year":"2013","journal-title":"Nucleic Acids Research"},{"issue":"11","key":"ref4","doi-asserted-by":"crossref","first-page":"e1000957","DOI":"10.1371\/journal.pcbi.1000957","article-title":"Exploring the universe of protein structures beyond the Protein Data Bank","volume":"6","author":"P Cossio","year":"2010","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"ref5","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Y Zhang","year":"2004","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"ref6","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bar009","article-title":"UniProt Knowledgebase: a hub of integrated protein data","volume":"2011","author":"M Magrane","year":"2011","journal-title":"Database"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1016\/0092-8674(95)90542-1","article-title":"Targeted disruption of the Huntington\u2019s disease gene results in embryonic lethality and behavioral and morphological changes in heterozygotes","volume":"81","author":"J Nasir","year":"1995","journal-title":"Cell"},{"issue":"5529","key":"ref8","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1126\/science.1059581","article-title":"Loss of Huntingtin-Mediated BDNF Gene Transcription in Huntington\u2019s Disease","volume":"293","author":"C Zuccato","year":"2001","journal-title":"Science"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1006\/exnr.1998.6832","article-title":"Wild-Type and Mutant Huntingtins Function in Vesicle Trafficking in the Secretory and Endocytic Pathways","volume":"152","author":"J Velier","year":"1998","journal-title":"Experimental Neurology"},{"issue":"9","key":"ref10","doi-asserted-by":"crossref","first-page":"5204","DOI":"10.1074\/jbc.273.9.5204","article-title":"Analysis of Strand Slippage in DNA Polymerase Expansions of CAG\/CTG Triplet Repeats Associated with Neurodegenerative Disease","volume":"273","author":"J Petruska","year":"1998","journal-title":"Journal of Biological Chemistry"},{"issue":"5","key":"ref11","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/S0896-6273(02)00872-3","article-title":"Polyglutamine Pathogenesis: Emergence of Unifying Mechanisms for Huntington\u2019s Disease and Related Disorders","volume":"35","author":"CA Ross","year":"2002","journal-title":"Neuron"},{"issue":"135","key":"ref12","article-title":"Mood disorders in Huntington\u2019s disease: from behavior to cellular and molecular mechanisms","volume":"8","author":"P Pla","year":"2014","journal-title":"Frontiers in Behavioral Neuroscience"},{"issue":"4\u20135","key":"ref13","first-page":"441","article-title":"Polyglutamine (PolyQ) Diseases: Genetics to Treatments","volume":"23","author":"HC Fan","journal-title":"Cell Transplantation"},{"issue":"3","key":"ref14","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.gde.2005.04.003","article-title":"The other trinucleotide repeat: polyalanine expansion disorders","volume":"15","author":"A Albrecht","year":"2005","journal-title":"Current Opinion in Genetics & Development"},{"issue":"suppl 2","key":"ref15","doi-asserted-by":"crossref","first-page":"R235","DOI":"10.1093\/hmg\/ddh251","article-title":"Polyalanine expansions in human","volume":"13","author":"J Amiel","year":"2004","journal-title":"Human Molecular Genetics"},{"issue":"5","key":"ref16","doi-asserted-by":"crossref","first-page":"e1001335","DOI":"10.1371\/journal.pbio.1001335","article-title":"Common features at the start of the neurodegeneration cascade","volume":"10","author":"R Herv\u00e1s","year":"2012","journal-title":"PLoS Biol"},{"issue":"17","key":"ref17","doi-asserted-by":"crossref","first-page":"4553","DOI":"10.1021\/jp067873l","article-title":"A bias-exchange approach to protein folding","volume":"111","author":"S Piana","year":"2007","journal-title":"The Journal of Physical Chemistry B"},{"issue":"28","key":"ref18","first-page":"283201","article-title":"Mechanical stretching of proteins\u2014a theoretical survey of the Protein Data Bank","volume":"19","author":"JI Su\u0142kowska","year":"2007","journal-title":"Journal of Physics: Condensed Matter"},{"issue":"10","key":"ref19","doi-asserted-by":"crossref","first-page":"e1000547","DOI":"10.1371\/journal.pcbi.1000547","article-title":"Mechanical strength of 17,134 model proteins and cysteine slipknots","volume":"5","author":"M Sikora","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S0076-6879(10)72010-3","article-title":"Single-molecule fluorescence studies of intrinsically disordered proteins","volume":"472","author":"ACM Ferreon","year":"2010","journal-title":"Methods in Enzymology"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation","volume":"4","author":"B Hess","year":"2008","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"10","key":"ref22","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/j.cpc.2009.05.011","article-title":"PLUMED: A portable plugin for free-energy calculations with molecular dynamics","volume":"180","author":"M Bonomi","year":"2009","journal-title":"Computer Physics Communications"},{"issue":"19","key":"ref23","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","article-title":"A second generation force field for the simulation of proteins, nucleic acids, and organic molecules","volume":"117","author":"WD Cornell","year":"1995","journal-title":"Journal of the American Chemical Society"},{"issue":"16","key":"ref24","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.1021\/jp961992r","article-title":"The GB\/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii","volume":"101","author":"D Qiu","year":"1997","journal-title":"The Journal of Physical Chemistry A"},{"issue":"9","key":"ref25","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1021\/ct900202f","article-title":"A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1","volume":"5","author":"F Pietrucci","year":"2009","journal-title":"Journal of Chemical Theory and Computation"},{"key":"ref26","article-title":"Comparative Protein Structure Modeling Using Modeller","author":"N Eswar","year":"2002"},{"key":"ref27","article-title":"Methods of conjugate gradients for solving linear systems","volume":"vol. 49","author":"MR Hestenes","year":"1952"},{"issue":"34","key":"ref28","doi-asserted-by":"crossref","first-page":"10259","DOI":"10.1021\/jp305065c","article-title":"Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations","volume":"116","author":"MS Miettinen","year":"2012","journal-title":"The Journal of Physical Chemistry B"},{"issue":"3","key":"ref29","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1371\/journal.pcbi.0010030","article-title":"Molecular origin of polyglutamine aggregation in neurodegenerative diseases","volume":"1","author":"SD Khare","year":"2005","journal-title":"PLoS Comput Biol"},{"issue":"16","key":"ref30","doi-asserted-by":"crossref","first-page":"165102","DOI":"10.1063\/1.3383244","article-title":"Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations","volume":"132","author":"R Laghaei","year":"2010","journal-title":"The Journal of Chemical Physics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1021\/la502465m","article-title":"Proteins at Air\u2013Water Interfaces: A Coarse-Grained Model","volume":"30","author":"M Cieplak","year":"2014","journal-title":"Langmuir"},{"issue":"44","key":"ref32","doi-asserted-by":"crossref","first-page":"445601","DOI":"10.1088\/0957-4484\/22\/44\/445601","article-title":"Linker-mediated assembly of gold nanoparticles into multimeric motifs","volume":"22","author":"M Sikora","year":"2011","journal-title":"Nanotechnology"},{"issue":"Database issue","key":"ref33","doi-asserted-by":"crossref","first-page":"D411","DOI":"10.1093\/nar\/gkq1105","article-title":"A series of PDB related databases for everyday needs","volume":"39","author":"RP Joosten","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1006\/jmbi.1999.2829","article-title":"The packing density in proteins: standard radii and volumes","volume":"290","author":"J Tsai","year":"1999","journal-title":"Journal of Molecular Biology"},{"issue":"182","key":"ref35","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1080\/14786446408643668","article-title":"L. on the calculation of the equilibrium and stiffness of frames","volume":"27","author":"JC Maxwell","year":"1864","journal-title":"The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Sciences"},{"issue":"6","key":"ref36","doi-asserted-by":"crossref","first-page":"e63640","DOI":"10.1371\/journal.pone.0063640","article-title":"Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure","volume":"8","author":"M Cieplak","year":"2013","journal-title":"PloS One"},{"issue":"7","key":"ref37","doi-asserted-by":"crossref","first-page":"3174","DOI":"10.1529\/biophysj.107.127233","article-title":"Selection of optimal variants of G\u014d-like models of proteins through studies of stretching","volume":"95","author":"JI Su\u0142kowska","year":"2008","journal-title":"Biophysical Journal"},{"issue":"4","key":"ref38","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1006\/jmbi.1998.1645","article-title":"Contact order, transition state placement and the refolding rates of single domain proteins","volume":"277","author":"KW Plaxco","year":"1998","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1002\/prot.22479","article-title":"N-terminal strands of filamin Ig domains act as a conformational switch under biological forces","volume":"78","author":"BA Kesner","year":"2010","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/S0006-3495(03)74867-X","article-title":"Universality classes in folding times of proteins","volume":"84","author":"M Cieplak","year":"2003","journal-title":"Biophysical Journal"},{"issue":"1","key":"ref41","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.bbrc.2010.10.133","article-title":"Hopping around an entropic barrier created by force","volume":"403","author":"R Berkovich","year":"2010","journal-title":"Biochemical and Biophysical Research Communications"},{"issue":"5315","key":"ref42","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1126\/science.276.5315.1109","article-title":"Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM","volume":"276","author":"M Rief","year":"1997","journal-title":"Science"},{"issue":"7","key":"ref43","doi-asserted-by":"crossref","first-page":"3694","DOI":"10.1073\/pnas.96.7.3694","article-title":"Mechanical and chemical unfolding of a single protein: A comparison","volume":"96","author":"M Carrion-Vazquez","year":"1999","journal-title":"Proceedings of the National Academy of Sciences USA"},{"issue":"5","key":"ref44","doi-asserted-by":"crossref","first-page":"058106","DOI":"10.1103\/PhysRevLett.100.058106","article-title":"Tightening of knots in proteins","volume":"100","author":"JI Su\u0142kowska","year":"2008","journal-title":"Physical Review Letters"},{"issue":"6798","key":"ref45","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/35022623","article-title":"A deeply knotted protein structure and how it might fold","volume":"406","author":"WR Taylor","year":"2000","journal-title":"Nature"},{"issue":"9","key":"ref46","doi-asserted-by":"crossref","first-page":"e122","DOI":"10.1371\/journal.pcbi.0020122","article-title":"Intricate knots in proteins: Function and evolution","volume":"2","author":"P Virnau","year":"2006","journal-title":"PLoS Computational Biology"},{"issue":"26","key":"ref47","doi-asserted-by":"crossref","first-page":"E1715","DOI":"10.1073\/pnas.1205918109","article-title":"Conservation of complex knotting and slipknotting patterns in proteins","volume":"109","author":"JI Su\u0142kowska","year":"2012","journal-title":"Proceedings of the National Academy of Sciences USA"},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"Journal of Molecular Graphics"},{"issue":"4","key":"ref49","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/nsmb1215","article-title":"A toxic monomeric conformer of the polyglutamine protein","volume":"14","author":"Y Nagai","year":"2007","journal-title":"Nature Structural & Molecular Biology"},{"issue":"51","key":"ref50","doi-asserted-by":"crossref","first-page":"18219","DOI":"10.1073\/pnas.1421313111","article-title":"Overexpression of Q-rich prion-like proteins suppresses polyQ cytotoxicity and alters the polyQ interactome","volume":"111","author":"L Ripaud","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004541","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,31]],"date-time":"2019-08-31T21:42:35Z","timestamp":1567287755000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004541"}},"subtitle":[],"editor":[{"given":"Guanghong","family":"Wei","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,10,23]]},"references-count":50,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2015,10,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004541","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,10,23]]}}}