{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T00:26:57Z","timestamp":1779323217315,"version":"3.51.4"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2006,9,15]],"date-time":"2006-09-15T00:00:00Z","timestamp":1158278400000},"content-version":"unspecified","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.0020122","type":"journal-article","created":{"date-parts":[[2006,9,12]],"date-time":"2006-09-12T21:37:41Z","timestamp":1158097061000},"page":"e122","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":320,"title":["Intricate Knots in Proteins: Function and Evolution"],"prefix":"10.1371","volume":"2","author":[{"given":"Peter","family":"Virnau","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leonid A","family":"Mirny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mehran","family":"Kardar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2006,9,15]]},"reference":[{"key":"pcbi-0020122-b001","doi-asserted-by":"crossref","first-page":"15102","DOI":"10.1021\/ja052438a","article-title":"Knots in globule and coil phases of a model polyethylene.","volume":"127","year":"2005","journal-title":"J Am Chem Soc"},{"key":"pcbi-0020122-b002","doi-asserted-by":"crossref","first-page":"5924","DOI":"10.1021\/ma00098a057","article-title":"Knots in Hamilton cycles.","volume":"27","year":"1994","journal-title":"Macromolecules"},{"key":"pcbi-0020122-b003","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.polymer.2003.10.073","article-title":"Fractal and statistical properties of large compact polymers: A computational study.","volume":"45","year":"2004","journal-title":"Polymer"},{"key":"pcbi-0020122-b004","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nsb0494-213","article-title":"Are there knots in proteins?","volume":"1","year":"1994","journal-title":"Nat Struct Mol Bio"},{"key":"pcbi-0020122-b005","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/nsb0397-166","article-title":"Fit to be tied.","volume":"4","year":"1997","journal-title":"Nat Struct Mol Bio"},{"key":"pcbi-0020122-b006","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","year":"2000","journal-title":"Nature"},{"key":"pcbi-0020122-b007","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/421025a","article-title":"Protein knots\u2014A tangled problem.","volume":"421","year":"2003","journal-title":"Nature"},{"key":"pcbi-0020122-b008","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1371\/journal.pcbi.0020045","article-title":"Statistics of knots, geometry of conformations, and evolution of proteins.","volume":"2","year":"2006","journal-title":"PLOS Comp Biol"},{"key":"pcbi-0020122-b009","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: A structural classification of proteins database for the investigation of sequences and structures.","volume":"247","year":"1995","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b010","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1110\/ps.051791305","article-title":"The crystal structure of a bacterial Class II ketol-acid reductolsomerase: Domain conservation and evolution.","volume":"14","year":"2005","journal-title":"Protein Sci"},{"key":"pcbi-0020122-b011","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1038\/nature04118","article-title":"A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.","volume":"438","year":"2005","journal-title":"Nature"},{"key":"pcbi-0020122-b012","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0020122-b013","unstructured":"AdamsCC\n\t\t\t\t\t1994\n\t\t\t\t\tThe knot book: An elementary introduction to the mathematical theory of knots\n\t\t\t\t\tNew York W. H. Freeman. 306 p."},{"key":"pcbi-0020122-b014","first-page":"4201","article-title":"Topological features of protein structures: Knots and links.","volume":"177","year":"1995","journal-title":"J Am Chem Soc"},{"key":"pcbi-0020122-b015","doi-asserted-by":"crossref","first-page":"8945","DOI":"10.1021\/ja961147m","article-title":"A real knot in protein.","volume":"118","year":"1996","journal-title":"J Am Chem Soc"},{"key":"pcbi-0020122-b016","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1016\/S0022-2836(02)00539-9","article-title":"Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution.","volume":"320","year":"2002","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b017","doi-asserted-by":"crossref","first-page":"14366","DOI":"10.1074\/jbc.C500005200","article-title":"Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: A novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.","volume":"280","year":"2005","journal-title":"J Biol Chem"},{"key":"pcbi-0020122-b018","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1074\/jbc.M410770200","article-title":"Structure of the ubiquitin hydrolase Uch-L3 complexed with a suicide substrate.","volume":"280","year":"2005","journal-title":"J Biol Chem"},{"key":"pcbi-0020122-b019","doi-asserted-by":"crossref","first-page":"3877","DOI":"10.1093\/emboj\/18.14.3877","article-title":"Structural basis for the specificity of ubiquitin C-terminal hydrolases.","volume":"18","year":"1999","journal-title":"EMBO J"},{"key":"pcbi-0020122-b020","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1126\/science.273.5275.595","article-title":"Mapping the protein universe.","volume":"273","year":"1996","journal-title":"Science"},{"key":"pcbi-0020122-b021","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1016\/S1097-2765(01)00407-5","article-title":"Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome.","volume":"8","year":"2001","journal-title":"Mol Cell"},{"key":"pcbi-0020122-b022","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/81018","article-title":"Opening doors into the proteasome.","volume":"7","year":"2000","journal-title":"Nat Struct Mol Bio"},{"key":"pcbi-0020122-b023","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1073\/pnas.0409634102","article-title":"Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020122-b024","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1006\/jmbi.1998.2249","article-title":"Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments.","volume":"285","year":"1999","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b025","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1046\/j.1365-3040.1997.d01-107.x","article-title":"Phytochrome degradation.","volume":"20","year":"1997","journal-title":"Plant Cell Environ"},{"key":"pcbi-0020122-b026","doi-asserted-by":"crossref","first-page":"3405","DOI":"10.1093\/emboj\/16.12.3405","article-title":"The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution.","volume":"16","year":"1997","journal-title":"EMBO J"},{"key":"pcbi-0020122-b027","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1080\/07391102.1996.10508887","article-title":"Flexible loop in the structure of S-adenosylmethionine synthetase crystallized in the tetragonal modification.","volume":"13","year":"1996","journal-title":"J Biomol Struct Dyn"},{"key":"pcbi-0020122-b028","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1006\/jmbi.2000.3858","article-title":"The crystal structure of tetrameric methionine adenosyltransferase from rat liver reveals the methionine-binding site.","volume":"300","year":"2000","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b029","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/prot.340090107","article-title":"Database of homology-derived protein structures.","volume":"9","year":"1991","journal-title":"Proteins: Struct Funct Genet"},{"key":"pcbi-0020122-b030","doi-asserted-by":"crossref","first-page":"2974","DOI":"10.1128\/JB.188.8.2974-2982.2006","article-title":"Acetylornithine transcarbamylase: A novel enzyme in arginine biosynthesis.","volume":"188","year":"2006","journal-title":"J Bacteriol"},{"key":"pcbi-0020122-b031","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1002\/(SICI)1097-0134(20000601)39:4<271::AID-PROT10>3.0.CO;2-E","article-title":"Crystal structure of human ornithine transcarbamylase complexed with carbamyl phosphate and L-Norvaline at 1.9 A resolution.","volume":"39","year":"2000","journal-title":"Proteins: Struct Funct Genet"},{"key":"pcbi-0020122-b032","doi-asserted-by":"crossref","first-page":"2801","DOI":"10.1073\/pnas.95.6.2801","article-title":"The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures.","volume":"95","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020122-b033","doi-asserted-by":"crossref","first-page":"5373","DOI":"10.1073\/pnas.032095099","article-title":"Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.","volume":"99","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020122-b034","doi-asserted-by":"crossref","unstructured":"Janse van RensburgEJSumnersDWWassermannEWhittingtonSG\n\t\t\t\t\t1992\n\t\t\t\t\tMath Gen\n\t\t\t\t\t25\n\t\t\t\t\t6557\n\t\t\t\t\t6566","DOI":"10.1088\/0305-4470\/25\/24\/010"},{"key":"pcbi-0020122-b035","doi-asserted-by":"crossref","first-page":"6245","DOI":"10.1103\/PhysRevE.55.6245","article-title":"Universality in random knotting.","volume":"55","year":"1997","journal-title":"Phys Rev E"},{"key":"pcbi-0020122-b036","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1063\/1.460889","article-title":"Self-entanglement in ring polymers.","volume":"95","year":"1991","journal-title":"J Chem Phys"},{"key":"pcbi-0020122-b037","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1016\/j.jmb.2004.12.055","article-title":"Folding studies on a knotted protein.","volume":"346","year":"2005","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b038","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1016\/j.jmb.2006.04.032","article-title":"Probing nature's knots: The folding pathway of a knotted homodimeric protein.","volume":"359","year":"2006","journal-title":"J Mol Biol"},{"key":"pcbi-0020122-b039","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1021\/ma048779a","article-title":"Linear random knots and their scaling behavior.","volume":"38","year":"2005","journal-title":"Macromolecules"},{"key":"pcbi-0020122-b040","doi-asserted-by":"crossref","first-page":"4675","DOI":"10.1073\/pnas.0510403103","article-title":"Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1.","volume":"103","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020122-b041","first-page":"2256","article-title":"Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.","volume":"D60","year":"2004","journal-title":"Acta Cryst"},{"key":"pcbi-0020122-b042","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1126\/science.2530630","article-title":"The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl-terminal hydrolase.","volume":"246","year":"1989","journal-title":"Science"},{"key":"pcbi-0020122-b043","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD\u2014Visual molecular dynamics.","volume":"14","year":"1996","journal-title":"J Molec Graphics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020122","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T21:48:44Z","timestamp":1588801724000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020122"}},"subtitle":[],"editor":[{"given":"Robert B","family":"Russell","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2006,9,15]]},"references-count":43,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2006,9,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0020122","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,9,15]]}}}