Team:Heidelberg/Toolbox Guide

From 2014.igem.org

(Difference between revisions)
Line 122: Line 122:
</div>
</div>
</div>
</div>
-
<!-- ko fadeVisible: data.q0A -->
+
<div data-bind="fadeVisible: data.q0A">
<h3>2. Do you want to use split inteins or sortase to circularize your protein?</h3>
<h3>2. Do you want to use split inteins or sortase to circularize your protein?</h3>
<div class="panel panel-default">
<div class="panel panel-default">
Line 150: Line 150:
</div>
</div>
</div>
</div>
-
<!-- /ko -->
+
</div>
-
<!-- ko fadeVisible: data.q1A -->
+
<div data-bind="fadeVisible: data.q1A">
<h3>3. Can your protein be easily expressed in <i>E. coli</i>?</h3>
<h3>3. Can your protein be easily expressed in <i>E. coli</i>?</h3>
<div class="panel panel-default">
<div class="panel panel-default">
Line 170: Line 170:
</div>
</div>
</div>
</div>
-
<!-- /ko -->
+
</div>
<div data-bind="fadeVisible: data.q2A() &amp;&amp; !data.useSortase()">
<div data-bind="fadeVisible: data.q2A() &amp;&amp; !data.useSortase()">
<h3>4. Which exteins do you want to use? They will remain as scars in your circular protein.</h3>
<h3>4. Which exteins do you want to use? They will remain as scars in your circular protein.</h3>
Line 237: Line 237:
</div>
</div>
-
<!-- ko fadeVisible: data.comingBack -->
+
<div data-bind="fadeVisible: data.comingBack">
-
<h3><span data-bind="text: data.useSortase() ? 5 : 6"></span>. Hello again. What is the result of <span data-bind="text: softwareName"></span>?</h3>
+
<h3><span data-bind="text: data.useSortase() ? 5 : 6"></span>. Hello again. What is the result of <span data-bind="text: softwareName"></span>?</h3>
-
<div class="panel panel-default">
+
<div class="panel panel-default">
-
<div class="radio">
+
<div class="radio">
-
<label>
+
<label>
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 0, click: data.q5A.bind(null, true)" />
+
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 0, click: data.q5A.bind(null, true)" />
-
I do not need a linker.
+
I do not need a linker.
-
</label>
+
</label>
-
</div>
+
</div>
-
<div class="radio">
+
<div class="radio">
-
<label>
+
<label>
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 1, click: data.q5A.bind(null, true)" />
+
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 1, click: data.q5A.bind(null, true)" />
-
The linker + scars are &lt; 15 amino acids in length.
+
The linker + scars are &lt; 15 amino acids in length.
-
</label>
+
</label>
-
</div>
+
</div>
-
<div class="radio">
+
<div class="radio">
-
<label>
+
<label>
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 2, click: data.q5A.bind(null, true)" />
+
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 2, click: data.q5A.bind(null, true)" />
-
The linker + scars are betweeen 16 and 30 amino acids in length.
+
The linker + scars are betweeen 16 and 30 amino acids in length.
-
</label>
+
</label>
-
</div>
+
</div>
-
<div class="radio">
+
<div class="radio">
-
<label>
+
<label>
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 3, click: data.q5A.bind(null, true)" />
+
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 3, click: data.q5A.bind(null, true)" />
-
The linker + scars are &gt; 30 amino acids in length.
+
The linker + scars are &gt; 30 amino acids in length.
-
</label>
+
</label>
 +
</div>
</div>
</div>
</div>
</div>
-
<!-- /ko -->
+
<div data-bind="fadeVisible: data.q5A">
-
<!-- ko fadeVisible: data.q5A -->
+
<h3><span data-bind="text: data.useSortase() ? 6 : 7"></span>. Have you decided to use one linker or try different linkers?</h3>
-
<h3><span data-bind="text: data.useSortase() ? 6 : 7"></span>. Have you decided to use one linker or try different linkers?</h3>
+
<div class="panel panel-default">
-
<div class="panel panel-default">
+
<div class="radio">
-
<div class="radio">
+
<label>
-
<label>
+
<input type="radio" data-bind="checked: data.testSeveral, checkedValue: false, click: data.q6A.bind(null, true)" />
-
<input type="radio" data-bind="checked: data.testSeveral, checkedValue: false, click: data.q6A.bind(null, true)" />
+
I trust <span data-bind="text: softwareName"></span>. One should be enough.
-
I trust <span data-bind="text: softwareName"></span>. One should be enough.
+
</label>
-
</label>
+
</div>
-
</div>
+
<div class="radio">
-
<div class="radio">
+
<label>
-
<label>
+
<input type="radio" data-bind="checked: data.testSeveral, checkedValue: true, click: data.q6A.bind(null, true)" />
-
<input type="radio" data-bind="checked: data.testSeveral, checkedValue: true, click: data.q6A.bind(null, true)" />
+
I want to test several linkers.  
-
I want to test several linkers.  
+
</label>
-
</label>
+
</div>
</div>
</div>
</div>
</div>
-
<!-- /ko -->
 
</div>
</div>
</div>
</div>

Revision as of 06:44, 15 October 2014


use the intein
TOOLBOX to

1. Please go to www.rcsb.org and get a pdb file of your protein. If you cannot find one, we will not be able to assist you circularizing it.

Additionally, check the DNA sequence of your proteins for EcoRI, XbaI, SpeI, PstI and BsaI recognition sites. If there are E/X/S/P sites, you might have problems to change your backbone or add a promotor. If there is a BsaI recognition site, the cloning will be more difficult.

2. Do you want to use split inteins or sortase to circularize your protein?

  • Successfully used in our project
  • High efficiency
  • In vivo circularization
  • In vitro only
  • Well-purified protein required
  • Not successfully tested yet

3. Can your protein be easily expressed in E. coli?

4. Which exteins do you want to use? They will remain as scars in your circular protein.

. If you want to save time, check manually whether the ends are close together (approx.  Å or closer). For example, you can use the Swiss-PdbViewer or PyMOL.

Please use to generate a linker for your circular protein. [LINK] This step might take up to 11 days.
NILS – hier könnte dein instruction-file-ersatz stehen
NILS – hier auch
NILS – hier immernoch
NILS – hier ebnfalls und auch gerne noch umfangreicher
Please save this link:
https://2014.igem.org/#
 Clipboard icon Copy to clipboard
In order to generate your linker, needs to know the scar amino acid sequence that is caused by circularization. In your case, it is .

. Hello again. What is the result of ?

. Have you decided to use one linker or try different linkers?