{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T02:01:24Z","timestamp":1782266484240,"version":"3.54.5"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2010,4,1]],"date-time":"2010-04-01T00:00:00Z","timestamp":1270080000000},"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.1000731","type":"journal-article","created":{"date-parts":[[2010,4,1]],"date-time":"2010-04-01T15:20:28Z","timestamp":1270135228000},"page":"e1000731","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":163,"title":["A Stevedore's Protein Knot"],"prefix":"10.1371","volume":"6","author":[{"given":"Daniel","family":"B\u00f6linger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna I.","family":"Su\u0142kowska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiao-Ping","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonid A.","family":"Mirny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehran","family":"Kardar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 N.","family":"Onuchic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Virnau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2010,4,1]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1002\/prot.340210302","article-title":"Funnels, Pathways, and the Energy Landscape of Protein-Folding - a Synthesis.","volume":"21","author":"JD Bryngelson","year":"1995","journal-title":"Proteins Struct Funct Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"8721","DOI":"10.1073\/pnas.89.18.8721","article-title":"Protein Folding Funnels - a Kinetic Approach to the Sequence Structure Relationship.","volume":"89","author":"PE Leopold","year":"1992","journal-title":"PNAS"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nsb0494-213","article-title":"Are there knots in proteins?","volume":"1","author":"ML Mansfield","year":"1994","journal-title":"Nature Struct Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/nsb0397-166","article-title":"Fit to be tied.","volume":"4","author":"ML Mansfield","year":"1997","journal-title":"Nature Struct Biol"},{"key":"ref5","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"},{"key":"ref6","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","author":"RC Lua","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1074","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 Comput Biol"},{"key":"ref8","doi-asserted-by":"crossref","DOI":"10.5948\/UPO9781614440239","article-title":"Knot theory.","author":"C Livingston","year":"1993"},{"key":"ref9","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","author":"AL Mallam","year":"2005","journal-title":"J Mol Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1016\/j.jmb.2006.04.032","article-title":"Probing Nature&apos;s Knots: The Folding Pathway of a Knotted Homodimeric Protein.","volume":"359","author":"AL Mallam","year":"2006","journal-title":"J Mol Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.jmb.2006.11.014","article-title":"A comparison of the folding of two knotted proteins: YbeA and YibK.","volume":"366","author":"AL Mallam","year":"2007","journal-title":"J Mol Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1016\/j.molcel.2008.03.019","article-title":"Knotted fusion proteins reveal unexpected possibilities in protein folding.","volume":"30","author":"AL Mallam","year":"2008","journal-title":"Mol Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1016\/j.bpj.2008.11.012","article-title":"Tightening the Knot in Phytochrome by Single-Molecule Atomic Force Microscopy.","volume":"96","author":"T Bornschlogl","year":"2009","journal-title":"Biophys J"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1016\/j.jmb.2007.02.035","article-title":"The folding mechanics of a knotted protein.","volume":"368","author":"S Wallin","year":"2007","journal-title":"J Mol Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1073\/pnas.0811147106","article-title":"Dodging the crisis of folding proteins with knots.","volume":"106","author":"JI Sulkowska","year":"2009","journal-title":"PNAS"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"058106","DOI":"10.1103\/PhysRevLett.100.058106","article-title":"Tightening of knots in proteins.","volume":"100","author":"JI Sulkowska","year":"2008","journal-title":"Phys Rev Lett"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"121107","DOI":"10.1063\/1.2968554","article-title":"Translocation of a knotted polypeptide through a pore.","volume":"129","author":"L Huang","year":"2008","journal-title":"J Chem Phys"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.bpj.2008.10.019","article-title":"Sequence-Specific Size, Structure, and Stability of Tight Protein Knots.","volume":"96","author":"J Dzubiella","year":"2009","journal-title":"Biophys J"},{"key":"ref19","article-title":"Jamming proteins with slipknots and their free energy landscape.","author":"JI Sulkowska","year":"2009","journal-title":"Phys Rev Lett: 268103"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"16057","DOI":"10.1073\/pnas.0801343105","article-title":"Extracting function from a beta-trefoil folding motif (vol 105, pg 10384, 2008).","volume":"105","author":"S Gosavi","year":"2008","journal-title":"PNAS"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.jmb.2006.07.054","article-title":"A framework for describing topological frustration in models of protein folding.","volume":"362","author":"TS Norcross","year":"2006","journal-title":"J Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.cbpa.2007.10.002","article-title":"Knotted and topologically complex proteins as models for studying folding and stability.","volume":"11","author":"T Yeates","year":"2007","journal-title":"Curr Opin Chem Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.jmb.2007.07.042","article-title":"Identification of rare slipknots in proteins and their implications for stability and folding.","volume":"373","author":"NP King","year":"2007","journal-title":"J Mol Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1038\/nrm2446","article-title":"From the first protein structures to our current knowledge of protein folding: delights and scepticisms.","volume":"9","author":"AR Fersht","year":"2008","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.jmb.2008.02.035","article-title":"The crystal structure of Dehl reveals a new alpha-haloacid dehalogenase fold and active-site mechanism.","volume":"378","author":"JW Schmidberger","year":"2008","journal-title":"J Mol Biol"},{"key":"ref27","article-title":"Kumarevel TS, Karthe P, Kuramitsu S, Yokoyama S (to be published) Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus jannaschii."},{"key":"ref28","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","author":"AG Murzin","year":"1995","journal-title":"J Mol Biol"},{"key":"ref29","article-title":"Lu J, Glover JNM (to be published) Crystal structure of plasmid pTiC58 VirC2"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"9621","DOI":"10.1073\/pnas.0802494105","article-title":"Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.","volume":"105","author":"AMM van Roon","year":"2008","journal-title":"PNAS"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.compbiolchem.2007.03.002","article-title":"Protein knots and fold complexity: Some new twists.","volume":"31","author":"WR Taylor","year":"2007","journal-title":"Comput Biol Chem"},{"key":"ref32","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":"Biophys J"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1006\/jmbi.2000.3693","article-title":"Topological and energetic factors: What determines the structural details of the transition state ensemble and \u201cen-route\u201d intermediates for protein folding? An investigation for small globular proteins.","volume":"298","author":"C Clementi","year":"2000","journal-title":"J Mol Biol"},{"key":"ref34","article-title":"in preparation.","author":"JK Noel","year":"2010"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"19714","DOI":"10.1073\/pnas.0805468105","article-title":"Stabilizing effect of knots on proteins.","volume":"105","author":"JI Sulkowska","year":"2008","journal-title":"PNAS"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1006\/jmbi.1996.0704","article-title":"How to derive a protein folding potential? A new approach to an old problem.","volume":"264","author":"LA Mirny","year":"1996","journal-title":"J Mol Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"W425","DOI":"10.1093\/nar\/gkm312","article-title":"Protein knot server: detection of knots in protein structures.","volume":"35","author":"G Kolesov","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref38","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":"J Mol Graphics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000731","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,3]],"date-time":"2020-06-03T08:56:15Z","timestamp":1591174575000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000731"}},"subtitle":[],"editor":[{"given":"William","family":"Taylor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2010,4,1]]},"references-count":38,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2010,4,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000731","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.3078974.2762077","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,1]]}}}