User:Eric Martz/Sandbox 0: Difference between revisions

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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>. ~~A dramatic~~ protein ~~knot~~, ~~discovered in 2000~~<~~ref name="taylor2000"~~ />, ~~is illustrated 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. 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.

<tr>

<td colspan="2"><center>Knots Occurring in Proteins</center></td>

</tr><tr>

<td>[[Image:Overhand knot.jpg]]</td>

<td>[[Image:Figure-of-eight-knot.jpg]]</td>

</tr><tr>

<td>Trefoil (overhand, [http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 3<sub>1</sub>]) knot.</td>

<td>Figure-of-eight ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 4<sub>1</sub>]) knot.</td>

</tr><tr>

</tr><tr>

<td>[[Image:Three-twist knot.jpg]]</td>

<td>[[Image:Stevedores knot.jpg]]</td>

</tr><tr>

<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>

</tr></table>

__TOC__

==Figure-of-eight knot in acetohydroxy acid isomeroreductase==

<table class="wikitable" align="right" width="260"><tr><td>[[Image:Overhand knot.jpg]]</td><td>[[Image:Figure-of-eight-knot.jpg]]</td></tr><tr><td>Trefoil (overhand, [http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 3<sub>1</sub>]) knot.</td><td>Figure-of-eight knot ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 4<sub>1</sub>])</td></tr></table>

William R. Taylor developed an algorithm for detecting knots in protein backbones, which he reported in 2000<ref name="taylor2000">PMID: 10972297</ref>. He scanned 3,440 sequence-different published protein structures from the [[Protein Data Bank]]. Only eight genuine knots were found, most of which were simple [http://en.wikipedia.org/wiki/Trefoil_knot trefoil knots] ([http://en.wikipedia.org/wiki/Overhand_knot overhand knots]) and had been previously described. However several knots were detected in proteins not previously recognized as knotted. One was in acetohydroxy acid isomeroreductase ("AAIR", [[1yve]], [[1qmg]]) , and was particularly interesting because of how deeply it sits in the folded protein backbone (far away from the ends) and because it is a more complicated [http://en.wikipedia.org/wiki/Figure-eight_knot_(mathematics) figure-of-eight knot].

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Taylor states "Pulling the ends of a given piece of string will usually decide whether it is knotted or not. Because we hold the ends, the string and our body form a closed circle and there is no danger of untying the knot as it is pulled." "The ends of protein chains (being charged) tend to lie on the surface ...." "An alternative approach is to invert the problem: rather than extending the termini outwards, these can be left fixed and the rest of the protein made to shrink around them. This was done [mathematically] by contracting the protein as if it were a rubber band."<ref name="taylor2000" />

<applet load='Insert PDB code or filename here' size='400' frame='true' align='right' caption='~~Insert caption here~~'

<applet load='Insert PDB code or filename here' size='400' frame='true' align='right' caption='Reductoisomerase [[1yve]] containing a figure-of-eight knot.'

scene='User:Eric_Martz/Sandbox_0/1yve_chain_i_rockets/2' />

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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.

*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>.

*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]]).

*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).

*Mathematical shrinking, while fixing the positions of the ends, <scene name='User:Eric_Martz/Sandbox_0/1tph_noknot_morph/3'>reveals that no knot is present</scene>.

Subsequent to Taylor's work, figure-of-eight knots were found in three other ketol acid reductoisomerases, as well as in several phytochromes, a transcriptional regulator, and a virus core protein (see [http://pknot.life.nctu.edu.tw/table_new.php list at the pKnot server]). Also, more complex knots were found, described below.

==Knot Servers==

These protein knot servers offer rotatable 3D graphics.

These protein knot servers offer rotatable 3D graphics showing simplified knots.

*[http://pknot.life.nctu.edu.tw/ pKnot]<ref>PMID: 17526524</ref>.

===pKnot===

*Server: [http://pknot.life.nctu.edu.tw/ pKnot]<ref>PMID: 17526524</ref>.

*Generates a morph "movie" of shrinking (holding the ends fixed), which can be played in OpenAstexViewer, or downloaded as a multiple-model PDB file, e.g. for animation in [[Jmol]].

*Visualization: appears to be in [http://www.openastexviewer.net/web/ OpenAstexViewer]. In Safari (but not in Firefox) on OS X, moving away from the browser tab containing the viewer causes the view to disappear when you return, and any options you checked to be lost.

*Lists all knots in the [[PDB]] categorized by knot type (click the small link ''Knot table'' near the upper left of the main page, in a black bar). List includes core sequence range, and depth (but the "depth" is a single value not defined on the server). "Length" in the list appears to be the length of the entire protein chain, not the length of the knotted portion.

*Upload PDB file: YES, and you can specify a sequence range for analysis.

*[http://knots.mit.edu knots.mit.edu]<ref>PMID: 17517776</ref>.

===knots.mit.edu===

*Server: [http://knots.mit.edu knots.mit.edu]<ref>PMID: 17517776</ref>.

*Visualization: Jmol showing the chain with the knotted region colored, and the simplified knot (no movie).

*Lists knots (a shorter list than at the pKnot server). List includes core sequence range plus other numbers that are not labeled. "Length" in the list appears to be the length of the entire protein chain, not the length of the knotted portion.

*Upload PDB file: YES.

==Notes==

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==Methods==

Please see [[Knots in Proteins - Methods]].

Please see [[Knots in Proteins: Methods]].

==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 ~~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==

@@ 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>. A dramatic protein knot, discovered in 2000<ref name="taylor2000" />, is illustrated 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. 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">
+<tr>
+<td colspan="2"><center>Knots Occurring in Proteins</center></td>
+</tr><tr>
+<td>[[Image:Overhand knot.jpg]]</td>
+<td>[[Image:Figure-of-eight-knot.jpg]]</td>
+</tr><tr>
+<td>Trefoil (overhand, [http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 3<sub>1</sub>]) knot.</td>
+<td>Figure-of-eight ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 4<sub>1</sub>]) knot.</td>
+</tr><tr>
+<td colspan="2">&nbsp;</td>
+</tr><tr>
+<td>[[Image:Three-twist knot.jpg]]</td>
+<td>[[Image:Stevedores knot.jpg]]</td>
+</tr><tr>
+<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>
+</tr></table>
+__TOC__
+{{Clear}}
 ==Figure-of-eight knot in acetohydroxy acid isomeroreductase==
-<table class="wikitable" align="right" width="260"><tr><td>[[Image:Overhand knot.jpg]]</td><td>[[Image:Figure-of-eight-knot.jpg]]</td></tr><tr><td>Trefoil (overhand, [http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 3<sub>1</sub>]) knot.</td><td>Figure-of-eight knot ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 4<sub>1</sub>])</td></tr></table>
 William R. Taylor developed an algorithm for detecting knots in protein backbones, which he reported in 2000<ref name="taylor2000">PMID: 10972297</ref>. He scanned 3,440 sequence-different published protein structures from the [[Protein Data Bank]]. Only eight genuine knots were found, most of which were simple [http://en.wikipedia.org/wiki/Trefoil_knot trefoil knots] ([http://en.wikipedia.org/wiki/Overhand_knot overhand knots]) and had been previously described. However several knots were detected in proteins not previously recognized as knotted. One was in acetohydroxy acid isomeroreductase ("AAIR", [[1yve]], [[1qmg]]) , and was particularly interesting because of how deeply it sits in the folded protein backbone (far away from the ends) and because it is a more complicated [http://en.wikipedia.org/wiki/Figure-eight_knot_(mathematics) figure-of-eight knot].
@@ Line 11: / Line 31: @@
 Taylor states "Pulling the ends of a given piece of string will usually decide whether it is knotted or not. Because we hold the ends, the string and our body form a closed circle and there is no danger of untying the knot as it is pulled." "The ends of protein chains (being charged) tend to lie on the surface ...." "An alternative approach is to invert the problem: rather than extending the termini outwards, these can be left fixed and the rest of the protein made to shrink around them. This was done [mathematically] by contracting the protein as if it were a rubber band."<ref name="taylor2000" />
-<applet load='Insert PDB code or filename here' size='400' frame='true' align='right' caption='Insert caption here'
+<applet load='Insert PDB code or filename here' size='400' frame='true' align='right' caption='Reductoisomerase [[1yve]] containing a figure-of-eight knot.'
 scene='User:Eric_Martz/Sandbox_0/1yve_chain_i_rockets/2' />
@@ Line 20: / 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.
-*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>.
+*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}}
 *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).
 *Mathematical shrinking, while fixing the positions of the ends, <scene name='User:Eric_Martz/Sandbox_0/1tph_noknot_morph/3'>reveals that no knot is present</scene>.
+Subsequent to Taylor's work, figure-of-eight knots were found in three other ketol acid reductoisomerases, as well as in several phytochromes, a transcriptional regulator, and a virus core protein (see [http://pknot.life.nctu.edu.tw/table_new.php list at the pKnot server]). Also, more complex knots were found, described below.
 ==Knot Servers==
-These protein knot servers offer rotatable 3D graphics.
+These protein knot servers offer rotatable 3D graphics showing simplified knots.
-*[http://pknot.life.nctu.edu.tw/ pKnot]<ref>PMID: 17526524</ref>.
+===pKnot===
+*Server: [http://pknot.life.nctu.edu.tw/ pKnot]<ref>PMID: 17526524</ref>.
+*Generates a morph "movie" of shrinking (holding the ends fixed), which can be played in OpenAstexViewer, or downloaded as a multiple-model PDB file, e.g. for animation in [[Jmol]].
+*Visualization: appears to be in [http://www.openastexviewer.net/web/ OpenAstexViewer]. In Safari (but not in Firefox) on OS X, moving away from the browser tab containing the viewer causes the view to disappear when you return, and any options you checked to be lost.
+*Lists all knots in the [[PDB]] categorized by knot type (click the small link ''Knot table'' near the upper left of the main page, in a black bar). List includes core sequence range, and depth (but the "depth" is a single value not defined on the server). "Length" in the list appears to be the length of the entire protein chain, not the length of the knotted portion.
+*Upload PDB file: YES, and you can specify a sequence range for analysis.
-*[http://knots.mit.edu knots.mit.edu]<ref>PMID: 17517776</ref>.
+===knots.mit.edu===
+*Server: [http://knots.mit.edu knots.mit.edu]<ref>PMID: 17517776</ref>.
+*Visualization: Jmol showing the chain with the knotted region colored, and the simplified knot (no movie).
+*Lists knots (a shorter list than at the pKnot server). List includes core sequence range plus other numbers that are not labeled. "Length" in the list appears to be the length of the entire protein chain, not the length of the knotted portion.
+*Upload PDB file: YES.
 ==Notes==
@@ Line 71: / Line 102: @@
 ==Methods==
-Please see [[Knots in Proteins - Methods]].
+Please see [[Knots in Proteins: Methods]].
 ==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 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==
 <references />

User:Eric Martz/Sandbox 0: Difference between revisions

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