User:Eric Martz/Sandbox 0 - Revision history

Eric Martz at 15:49, 8 April 2018

Eric Martz — Sun, 08 Apr 2018 15:49:16 GMT

←Older revision		Revision as of 15:49, 8 April 2018
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-	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.

Eric Martz at 15:48, 8 April 2018

Eric Martz — Sun, 08 Apr 2018 15:48:47 GMT

←Older revision		Revision as of 15:48, 8 April 2018
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-	Proposed Article Title: Knots in Proteins	+	Proposed Article Title: [[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.

Eric Martz: /* Figure-of-eight knot in acetohydroxy acid isomeroreductase */

Eric Martz — Sun, 08 Apr 2018 15:48:18 GMT

Figure-of-eight knot in acetohydroxy acid isomeroreductase

←Older revision		Revision as of 15:48, 8 April 2018
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	*<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 - Methods\|Animation Methods]]).	+	*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).

Eric Martz: /* Methods */

Eric Martz — Fri, 28 Sep 2012 22:55:02 GMT

Methods

←Older revision		Revision as of 22:55, 28 September 2012
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	==Methods==		==Methods==
-	Please see [[Knots in Proteins - Methods]].	+	Please see [[Knots in Proteins: Methods]].

	==Content Attribution==		==Content Attribution==

Eric Martz: /* Content Attribution */

Eric Martz — Fri, 11 Feb 2011 15:19:53 GMT

Content Attribution

←Older revision		Revision as of 15:19, 11 February 2011
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	==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 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.		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.

Eric Martz: /* Content Attribution */

Eric Martz — Fri, 11 Feb 2011 15:19:17 GMT

Content Attribution

←Older revision		Revision as of 15:19, 11 February 2011
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	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 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 ~~above~~ 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]).	+	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 />

Eric Martz at 14:56, 8 November 2010

Eric Martz — Mon, 08 Nov 2010 14:56:38 GMT

←Older revision		Revision as of 14:56, 8 November 2010
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	<td>[[Image:Stevedores knot.jpg]]</td>		<td>[[Image:Stevedores knot.jpg]]</td>
	</tr><tr>		</tr><tr>
-	<td>Three-twist [http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 5<sub>2</sub>]) knot.</td>	+	<td>Three-twist ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 5<sub>2</sub>]) knot.</td>
	<td>Stevedore's ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 6<sub>1</sub>]) knot.</td>		<td>Stevedore's ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 6<sub>1</sub>]) knot.</td>
	</tr></table>		</tr></table>

Eric Martz at 13:30, 21 October 2010

Eric Martz — Thu, 21 Oct 2010 13:30:00 GMT

←Older revision		Revision as of 13:30, 21 October 2010
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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. 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.
		+

	<table class="wikitable" align="right" width="260">		<table class="wikitable" align="right" width="260">

Eric Martz at 13:28, 21 October 2010

Eric Martz — Thu, 21 Oct 2010 13:28:53 GMT

←Older revision		Revision as of 13:28, 21 October 2010
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	</tr></table>		</tr></table>

-		+	__TOC__
-		+	{{Clear}}
	==Figure-of-eight knot in acetohydroxy acid isomeroreductase==		==Figure-of-eight knot in acetohydroxy acid isomeroreductase==

Eric Martz at 13:25, 21 October 2010

Eric Martz — Thu, 21 Oct 2010 13:25:21 GMT

←Older revision		Revision as of 13:25, 21 October 2010
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	<table class="wikitable" align="right" width="260">		<table class="wikitable" align="right" width="260">
	<tr>		<tr>
		+	<td colspan="2"><center>Knots Occurring in Proteins</center></td>
		+	</tr><tr>
	<td>[[Image:Overhand knot.jpg]]</td>		<td>[[Image:Overhand knot.jpg]]</td>
	<td>[[Image:Figure-of-eight-knot.jpg]]</td>		<td>[[Image:Figure-of-eight-knot.jpg]]</td>