User:Eric Martz/Sandbox 0
From Proteopedia
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<applet load='Insert PDB code or filename here' size='300' frame='true' align='right' caption='Insert caption here' /> | <applet load='Insert PDB code or filename here' size='300' frame='true' align='right' caption='Insert caption here' /> | ||
| - | 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 | + | 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 discussion<ref name="taylor2000">PMID: 10972297</ref><ref name="taylor2007">PMID: 17500039</ref><ref>PMID: 19186124</ref><ref>PMID: 19015517</ref>. A dramatic protein knot, discovered in 2000<ref name="taylor2000" />, is illustrated here. |
Because knotted proteins are so rare, efforts have been made to disfavor knotted models when attempting to predict a protein fold<ref>PMID: 19478000</ref>. | Because knotted proteins are so rare, efforts have been made to disfavor knotted models when attempting to predict a protein fold<ref>PMID: 19478000</ref>. | ||
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"an unusually formed deep trefoil knot that stabilizes this region"<ref>PMID: 16292304</ref> | "an unusually formed deep trefoil knot that stabilizes this region"<ref>PMID: 16292304</ref> | ||
| + | "The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot."<ref>PMID: 19064918</ref> | ||
"As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers."<ref>PMID: 19211785</ref> | "As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers."<ref>PMID: 19211785</ref> | ||
Revision as of 00:46, 1 September 2009
Proposed Article Title: Knots in Proteins
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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 discussion[1][2][3][4]. A dramatic protein knot, discovered in 2000[1], is illustrated here.
Because knotted proteins are so rare, efforts have been made to disfavor knotted models when attempting to predict a protein fold[5].
physical pulling of ends? "the presence of the knot does not automatically indicate a superstable protein"[6]
"an unusually formed deep trefoil knot that stabilizes this region"[7] "The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot."[8]
"As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers."[9]
noncovalent pseudoknots [10]
??[11]
Notes & References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
