User:Eric Martz/Sandbox 0: Difference between revisions

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 (4₁, 5₂, 6₁) are discussed below.

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

<tr>

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

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

<td colspan="2">&nbsp;</td>

</tr><tr>

</tr><tr>

<td>Stevedore's ([http://en.wikipedia.org/wiki/Crossing_number_(knot_theory) 6₁]) knot.</td>

</tr></table>

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

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" />

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

*<scene name='User:Eric_Martz/Sandbox_0/1yve_chain_i_knot_only/2'>Only the knot-containing segment 312-545</scene> is shown here.

{{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).

==Knot Servers==

*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]].

*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.

==Methods==

==Content Attribution==

==Notes & References==

<references />