User:Eric Martz/Sandbox 0

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*[[:Category:Knot]]
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*[[:Category: Knottin]]
*[[:Category: C-terminal knot]]
*[[:Category: C-terminal knot]]
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*[[:Category:Cystine knot]]
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*[[:Category: Cystine knot]]
*[[:Category: Cystin-knot]]
*[[:Category: Cystin-knot]]
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*[[:Category: Cysteine knot]]
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*[[:Category: Cysteine-knot motif]]
*[[:Category: Inhibitory cystine knot]]
*[[:Category: Inhibitory cystine knot]]
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*[[:Category: Inhibitor cystine knot]]
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*[[:Category: Inhibitor cystine knot motif]]
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*[[:Category: Cystine knot motif]]
*[[:Category: Topological knot]]
*[[:Category: Topological knot]]
*[[:Category: Trefoil knot]]
*[[:Category: Trefoil knot]]

Revision as of 18:52, 25 September 2010

Proposed Article Title: Knots in Proteins

Insert caption here

Drag the structure with the mouse to rotate

A piece of string, or a protein chain, is deemed to contain a knot when pulling on the ends would leave a knot. When the ends of most folded protein chains are "pulled", they resolve to a straight chain between the pulled ends: no knot remains. Knots in protein chains are rare, and the mechanisms by which they form and their functions remain subjects of experimentation and discussion[1][2][3][4]. A dramatic protein knot, discovered in 2000[1], is illustrated here.

"Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date."[5].

ends on surface, why? [6]

Because knotted proteins are so rare, efforts have been made to disfavor knotted models when attempting to predict a protein fold[7][8].

Knot servers with 3D graphics [9][10] knots.mit.edu pKnot

physical pulling of ends? "the presence of the knot does not automatically indicate a superstable protein"[11]

"an unusually formed deep trefoil knot that stabilizes this region"[12] "The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot."[13]

"As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers."[14] folding [15]

  • noncovalent pseudoknots [16]
  • cyclotide cyclic cystine knots[18]
  • 1mxi Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

Content Attribution

Animations and models used in this article were developed in August, 2000 by User:Eric Martz at Knots in Proteins, where the animations utilized the now defunct MDL Chime plugin.

Notes & References

  1. ↑ 1.0 1.1 Taylor WR. A deeply knotted protein structure and how it might fold. Nature. 2000 Aug 24;406(6798):916-9. PMID:10972297 doi:10.1038/35022623
  2. ↑ Taylor WR. Protein knots and fold complexity: some new twists. Comput Biol Chem. 2007 Jun;31(3):151-62. Epub 2007 Mar 24. PMID:17500039 doi:10.1016/j.compbiolchem.2007.03.002
  3. ↑ Dzubiella J. Sequence-specific size, structure, and stability of tight protein knots. Biophys J. 2009 Feb;96(3):831-9. PMID:19186124 doi:10.1016/j.bpj.2008.10.019
  4. ↑ Mallam AL, Morris ER, Jackson SE. Exploring knotting mechanisms in protein folding. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18740-5. Epub 2008 Nov 17. PMID:19015517
  5. ↑ Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: Function and evolution. PLoS Comput Biol. 2006 Sep 15;2(9):e122. Epub 2006 Jul 28. PMID:16978047 doi:10.1371/journal.pcbi.0020122
  6. ↑ Hovmoller S, Zhou T. Why are both ends of the polypeptide chain on the outside of proteins? Proteins. 2004 May 1;55(2):219-22. PMID:15048814 doi:10.1002/prot.20011
  7. ↑ Khatib F, Rohl CA, Karplus K. Pokefind: a novel topological filter for use with protein structure prediction. Bioinformatics. 2009 Jun 15;25(12):i281-8. PMID:19478000 doi:10.1093/bioinformatics/btp198
  8. ↑ Khatib F, Weirauch MT, Rohl CA. Rapid knot detection and application to protein structure prediction. Bioinformatics. 2006 Jul 15;22(14):e252-9. PMID:16873480 doi:22/14/e252
  9. ↑ Lai YL, Yen SC, Yu SH, Hwang JK. pKNOT: the protein KNOT web server. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W420-4. Epub 2007 May 25. PMID:17526524 doi:10.1093/nar/gkm304
  10. ↑ Kolesov G, Virnau P, Kardar M, Mirny LA. Protein knot server: detection of knots in protein structures. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W425-8. Epub 2007 May 21. PMID:17517776 doi:10.1093/nar/gkm312
  11. ↑ Bornschlogl T, Anstrom DM, Mey E, Dzubiella J, Rief M, Forest KT. Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophys J. 2009 Feb 18;96(4):1508-14. PMID:19217867 doi:10.1016/j.bpj.2008.11.012
  12. ↑ Wagner JR, Brunzelle JS, Forest KT, Vierstra RD. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature. 2005 Nov 17;438(7066):325-31. PMID:16292304 doi:http://dx.doi.org/10.1038/nature04118
  13. ↑ Sulkowska JI, Sulkowski P, Szymczak P, Cieplak M. Stabilizing effect of knots on proteins. Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19714-9. Epub 2008 Dec 8. PMID:19064918
  14. ↑ Sulkowska JI, Sulkowski P, Onuchic J. Dodging the crisis of folding proteins with knots. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3119-24. Epub 2009 Feb 11. PMID:19211785
  15. ↑ Gloss LM. Tying the knot that binds. Structure. 2007 Jan;15(1):2-4. PMID:17223526 doi:10.1016/j.str.2006.12.001
  16. ↑ Taylor WR, Xiao B, Gamblin SJ, Lin K. A knot or not a knot? SETting the record 'straight' on proteins. Comput Biol Chem. 2003 Feb;27(1):11-5. PMID:12798035
  17. ↑ Andersson FI, Pina DG, Mallam AL, Blaser G, Jackson SE. Untangling the folding mechanism of the 5(2)-knotted protein UCH-L3. FEBS J. 2009 May;276(9):2625-35. Epub 2009 Mar 24. PMID:19476499 doi:10.1111/j.1742-4658.2009.06990.x
  18. ↑ Rosengren KJ, Daly NL, Plan MR, Waine C, Craik DJ. Twists, knots, and rings in proteins. Structural definition of the cyclotide framework. J Biol Chem. 2003 Mar 7;278(10):8606-16. Epub 2002 Dec 12. PMID:12482868 doi:10.1074/jbc.M211147200

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis

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