User:Eric Martz/Sandbox 0: Difference between revisions
Jump to navigation
Jump to search
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
Proposed Article Title: Knots in Proteins | Proposed Article Title: [[Knots in proteins|Knots in Proteins]] | ||
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. In this article, only knots in the peptide-bonded amino acid chain are considered; knots resulting from disulfide bonds or hydrogen bonds are excluded. Knots in protein chains are rare, and the mechanisms by which they form and their functions remain subjects of experimentation and discussion<ref name="taylor2000">PMID: 10972297</ref><ref name="taylor2007">PMID: 17500039</ref><ref>PMID: 19186124</ref><ref>PMID: 19015517</ref>. Four types of knots have been found in protein chains, examples of three of which (4<sub>1</sub>, 5<sub>2</sub>, 6<sub>1</sub>) are discussed below. | 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. In this article, only knots in the peptide-bonded amino acid chain are considered; knots resulting from disulfide bonds or hydrogen bonds are excluded. Knots in protein chains are rare, and the mechanisms by which they form and their functions remain subjects of experimentation and discussion<ref name="taylor2000">PMID: 10972297</ref><ref name="taylor2007">PMID: 17500039</ref><ref>PMID: 19186124</ref><ref>PMID: 19015517</ref>. Four types of knots have been found in protein chains, examples of three of which (4<sub>1</sub>, 5<sub>2</sub>, 6<sub>1</sub>) are discussed below. | ||
| Line 40: | Line 40: | ||
*<scene name='User:Eric_Martz/Sandbox_0/1yve_chain_i_knot_only/2'>Only the knot-containing segment 312-545</scene> is shown here. | *<scene name='User:Eric_Martz/Sandbox_0/1yve_chain_i_knot_only/2'>Only the knot-containing segment 312-545</scene> is shown here. | ||
*The ends of the knot-containing segment are fixed, while the intervening backbone mathematically <scene name='User:Eric_Martz/Sandbox_0/Knot_pull_morph_1yve/2'>shrinks revealing the knot</scene> (see [[Knots in Proteins | *The ends of the knot-containing segment are fixed, while the intervening backbone mathematically <scene name='User:Eric_Martz/Sandbox_0/Knot_pull_morph_1yve/2'>shrinks revealing the knot</scene> (see [[Knots in Proteins: Methods|Animation Methods]]). | ||
{{Template:Button_Toggle_Animation2}} | {{Template:Button_Toggle_Animation2}} | ||
*For comparision, here <scene name='User:Eric_Martz/Sandbox_0/1tph_rockets/1'>chain "1" of triosephosphate isomerase</scene> ([[1tph]]), which has a similar length (247 residues) to the knotted region of 1yve (sequence range 312-545, length 234). | *For comparision, here <scene name='User:Eric_Martz/Sandbox_0/1tph_rockets/1'>chain "1" of triosephosphate isomerase</scene> ([[1tph]]), which has a similar length (247 residues) to the knotted region of 1yve (sequence range 312-545, length 234). | ||
| Line 102: | Line 102: | ||
==Methods== | ==Methods== | ||
Please see [[Knots in Proteins | Please see [[Knots in Proteins: Methods]]. | ||
==Content Attribution== | ==Content Attribution== | ||
Animations and models used in this article were developed in August, 2000 by [[User:Eric Martz]] at [http://www.umass.edu/microbio/chime/knots/ Knots in Proteins], where the animations utilized the now defunct [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime plugin]. | Animations and models used in this article for the figure-of-eight knot were developed in August, 2000 by [[User:Eric Martz]] at [http://www.umass.edu/microbio/chime/knots/ Knots in Proteins], where the animations utilized the now defunct [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime plugin]. | ||
Data for the | Data for the figure-of-eight and unknotted comparison morphs were kindly provided by William R. Taylor ([http://mathbio.nimr.mrc.ac.uk/ Division of Mathematical Biology, National Institute for Medical Research, the Ridgeway, Mill Hill, London UK]) in 2000. | ||
==Notes & References== | ==Notes & References== | ||
<references /> | <references /> | ||