Difference between revisions of "Team:Bielefeld-CeBiTec/Project/toolbox/fusing"

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<article>
 
<article>
 
Fusing proteins is normally limited to the C&#x2011;&nbsp;or&nbsp;N&#x2011;terminus of a protein.  
 
Fusing proteins is normally limited to the C&#x2011;&nbsp;or&nbsp;N&#x2011;terminus of a protein.  
−
The incorporation of noncanonical amino acids that could be fused to each  
+
The incorporation of non-canonical amino acids that could be fused to each  
 
other or to surfaces enables several additional applications. This tool facilitates  
 
other or to surfaces enables several additional applications. This tool facilitates  
 
immobilization of proteins and improved stability of protein polymer networks.  
 
immobilization of proteins and improved stability of protein polymer networks.  
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can be applied for different applications like modern biomaterials in medicine and industry  
 
can be applied for different applications like modern biomaterials in medicine and industry  
 
(Rnjak-Kovacina&nbsp;<i>et&nbsp;al.</i>,&nbsp;2011). The amino acids N<sup>ε</sup>&#x2011;L&#x2011;cysteinyl&#x2011;L&#x2011;lysine (CL)  
 
(Rnjak-Kovacina&nbsp;<i>et&nbsp;al.</i>,&nbsp;2011). The amino acids N<sup>ε</sup>&#x2011;L&#x2011;cysteinyl&#x2011;L&#x2011;lysine (CL)  
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and N<sup>γ</sup>&#x2011;2&#x2011;cyanobenzothiazol&#x2011;6&#x2011;yl&#x2011;L&#x2011;asparagine (CBT-Asp)  
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and N<sup>γ</sup>&#x2011;2&#x2011;cyanobenzothiazol&#x2011;6&#x2011;yl&#x2011;L&#x2011;asparagine (CBT&#x2011;asparagine)  
 
comprise key parts of this tool. Both amino acids can bind specificly to each other resulting in the formation  
 
comprise key parts of this tool. Both amino acids can bind specificly to each other resulting in the formation  
 
of a covalent bond between their side chains. We plan to use this covalent bond to increase the stability of  
 
of a covalent bond between their side chains. We plan to use this covalent bond to increase the stability of  
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While terminus dependent binding systems for proteins are already in use, there are only a  
 
While terminus dependent binding systems for proteins are already in use, there are only a  
 
few systems for terminus independent binding systems. We want to expand the number of those  
 
few systems for terminus independent binding systems. We want to expand the number of those  
−
systems. Our aim is to incorporate two noncanonical amino acids, which are able to build a  
+
systems. Our aim is to incorporate two non-canonical amino acids, which are able to build a  
−
specific bond to each other. According to the synthesis of luciferin for the firefly luciferase  
+
specific bond to each other. According to the synthesis of D-luciferin for the firefly luciferase  
 
of <i>Photinus&nbsp;pyralis</i>, we decided to use the specific binding of 1,2&#x2011;aminothiols  
 
of <i>Photinus&nbsp;pyralis</i>, we decided to use the specific binding of 1,2&#x2011;aminothiols  
 
and the cyano group of cyanobenzothiazole&nbsp;(CBT). Figure 1 shows the biosynthesis of luciferin  
 
and the cyano group of cyanobenzothiazole&nbsp;(CBT). Figure 1 shows the biosynthesis of luciferin  
−
and the mechanism of the binding reaction of CBT and 1,2&#x2011;aminothiol.
+
and the mechanism of the binding reaction of 1,2&#x2011;aminothiol and CBT.
 
</article>
 
</article>
 
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<article>
 
<article>
 
By synthesis of amino acids with side chains containing CBT and a 1,2&#x2011;aminothiol, polypeptides  
 
By synthesis of amino acids with side chains containing CBT and a 1,2&#x2011;aminothiol, polypeptides  
−
binding to each other should be produced. These amino acids are CL and CBT&#x2011;Asp. The binding  
+
binding to each other should be produced. These amino acids are CL and CBT&#x2011;asparagine. The binding  
 
mechanism of both amino acids are shown in figure 2.
 
mechanism of both amino acids are shown in figure 2.
 
</article>
 
</article>
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<img class="figure image" src="https://static.igem.org/mediawiki/2017/f/f5/T--Bielefeld-CeBiTec--27-08-17-Specific_binding_CL_CBT-Asp.png">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/f/f5/T--Bielefeld-CeBiTec--27-08-17-Specific_binding_CL_CBT-Asp.png">
 
<p class="figure subtitle">
 
<p class="figure subtitle">
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<b>Figure 2: Specific binding reaction of CL and CBT&#x2011;Asp.</b>
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<b>Figure 2: Specific binding reaction of CL and CBT-asparagine.</b>
 
</p>
 
</p>
 
</div>
 
</div>
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<article>
 
<article>
 
We synthesized CL in our lab and provide the community with a validated protocol. Currently, we are  
 
We synthesized CL in our lab and provide the community with a validated protocol. Currently, we are  
−
trying to synthesize CBT&#x2011;Asp. Details of our synthesis protocol are described in the
+
trying to synthesize CBT&#x2011;asparagine. Details of our synthesis protocol are described in the
 
<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Notebook/Methods">method&nbsp;section</a>.
 
<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Notebook/Methods">method&nbsp;section</a>.
 
</article>
 
</article>
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chain of lysine so that CL contains a free 1,2-aminothiol group  
 
chain of lysine so that CL contains a free 1,2-aminothiol group  
 
(Nguyen&nbsp;<i>et&nbsp;al.</i>,&nbsp;2011). This is an important characteristic for the  
 
(Nguyen&nbsp;<i>et&nbsp;al.</i>,&nbsp;2011). This is an important characteristic for the  
−
specific binding between the CL and the CBT&#x2011;Asp.  
+
specific binding between the CL and the CBT&#x2011;asparagine.  
 
<ul>
 
<ul>
 
<li>Name: N<sup>ε</sup>-L-cysteinyl-L-lysine</li>
 
<li>Name: N<sup>ε</sup>-L-cysteinyl-L-lysine</li>
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</div>
 
</div>
 
<div class="half right">
 
<div class="half right">
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<div class="figure large">
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<div class="figure medium">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/2/22/T--Bielefeld-CeBiTec--27-08-17-CL_structure.png">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/2/22/T--Bielefeld-CeBiTec--27-08-17-CL_structure.png">
 
<p class="figure subtitle">
 
<p class="figure subtitle">
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</div>
 
</div>
  
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<h3>N<sup>γ</sup>&#x2011;2&#x2011;cyanobenzothiazol&#x2011;6&#x2011;yl&#x2011;L&#x2011;asparagine</h3>
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<h3>N<sup>γ</sup>-2-cyanobenzothiazol-6-yl-L-asparagine</h3>
 
<!-- Zwei Divs nebeneinander - Hier kann man Bilder oder articles einfuegen -->
 
<!-- Zwei Divs nebeneinander - Hier kann man Bilder oder articles einfuegen -->
 
<div class="contentline">
 
<div class="contentline">
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<img class="figure image" src="https://static.igem.org/mediawiki/2017/6/64/T--Bielefeld-CeBiTec--27-08-17-CBT-Asp_structure.png">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/6/64/T--Bielefeld-CeBiTec--27-08-17-CBT-Asp_structure.png">
 
<p class="figure subtitle">
 
<p class="figure subtitle">
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<b>Figure 4: Structure of CBT&#x2011;Asp.</b>
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<b>Figure 4: Structure of CBT&#x2011;asparagine.</b>
 
</p>
 
</p>
 
</div>
 
</div>
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<div class="half right">
 
<div class="half right">
 
<article>
 
<article>
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CBT-Asp is a completely novel amino acid, which we are synthesizing on our own. The synthesis is based on coupling the amino group of 6-Amino-CBT to the carboxyl  
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CBT&#x2011;asparagine is a completely novel amino acid, which we are synthesizing on our own. The synthesis is based on coupling the amino group of 6-Amino-CBT to the carboxyl  
−
group of the side chain of L-asparagine. The cyano group of the         CBT enables the specific binding of the CBT&#x2011;Asp to 1,2-aminothiols.
+
group of the side chain of L-asparagine. The cyano group of the CBT enables the specific binding of the CBT&#x2011;asparagine to 1,2-aminothiols.
 
<ul>
 
<ul>
 
<li>Name: N<sup>γ</sup>&#x2011;2&#x2011;cyanobenzothiazol&#x2011;6&#x2011;yl&#x2011;L&#x2011;asparagine</li>
 
<li>Name: N<sup>γ</sup>&#x2011;2&#x2011;cyanobenzothiazol&#x2011;6&#x2011;yl&#x2011;L&#x2011;asparagine</li>
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<li>Short: CBT-Asp
+
<li>Short: CBT&#x2011;asparagine
 
<li>Molecular Weight: 290.30 g mol<sup>-1</sup></li>
 
<li>Molecular Weight: 290.30 g mol<sup>-1</sup></li>
 
<li>Storage: -20 – 4 °C</li>
 
<li>Storage: -20 – 4 °C</li>
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<article>
 
<article>
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By incorporation of CL and CBT&#x2011;Asp between the silk and the elastin repeats, we receive a strengthened polymer network  
+
By incorporation of CL and CBT&#x2011;asparagine between the silk and the elastin repeats, we receive a strengthened polymer network  
 
with covalent bonds (Figure 7).
 
with covalent bonds (Figure 7).
 
</article>
 
</article>
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with two copies of the goi (Figure 5).  
 
with two copies of the goi (Figure 5).  
 
</article>
 
</article>
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<div class="figure medium">
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<div class="figure large">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/5/59/T--Bielefeld-CeBiTec--27-08-17-PRe-RDL_McDaniel2010.png">
 
<img class="figure image" src="https://static.igem.org/mediawiki/2017/5/59/T--Bielefeld-CeBiTec--27-08-17-PRe-RDL_McDaniel2010.png">
 
<p class="figure subtitle">
 
<p class="figure subtitle">
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<b>Figure 8: Scheme of the PRe-RDL (McDaniel&nbsp;<i>et&nbsp;al.</i>,&nbsp;2010).</b>
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<b>Figure 8: Scheme of the PRe-RDL (McDaniel&nbsp;<i>et&nbsp;al.</i>,&nbsp;2010).</b> </p>
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</p>
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</div>
 
</div>
 
 

Revision as of 06:00, 31 October 2017

Fusing

Short summary

Fusing proteins is normally limited to the C‑ or N‑terminus of a protein. The incorporation of non-canonical amino acids that could be fused to each other or to surfaces enables several additional applications. This tool facilitates immobilization of proteins and improved stability of protein polymer networks. Furthermore, they lead to enhanced efficiency of pathways by combining enzymes of one pathway or for any other system where colocalization is beneficial.
As proof of concept, we work on enhanced stability of a protein polymer. This networks can be applied for different applications like modern biomaterials in medicine and industry (Rnjak-Kovacina et al., 2011). The amino acids Nε‑L‑cysteinyl‑L‑lysine (CL) and Nγ‑2‑cyanobenzothiazol‑6‑yl‑L‑asparagine (CBT‑asparagine) comprise key parts of this tool. Both amino acids can bind specificly to each other resulting in the formation of a covalent bond between their side chains. We plan to use this covalent bond to increase the stability of silk elastin like proteins (SELPs). The strengthened polymer network would be a perfect material to produce biological wound bindings which are very thin and they would be able to interact with the natural tissue matrix (Boateng et al., 2008).

Terminus independent fusion proteins

While terminus dependent binding systems for proteins are already in use, there are only a few systems for terminus independent binding systems. We want to expand the number of those systems. Our aim is to incorporate two non-canonical amino acids, which are able to build a specific bond to each other. According to the synthesis of D-luciferin for the firefly luciferase of Photinus pyralis, we decided to use the specific binding of 1,2‑aminothiols and the cyano group of cyanobenzothiazole (CBT). Figure 1 shows the biosynthesis of luciferin and the mechanism of the binding reaction of 1,2‑aminothiol and CBT.

Figure 1: Reaction of the 1,2‑aminothiol of cysteine and CBT to luciferin (Liang et al., 2010).

By synthesis of amino acids with side chains containing CBT and a 1,2‑aminothiol, polypeptides binding to each other should be produced. These amino acids are CL and CBT‑asparagine. The binding mechanism of both amino acids are shown in figure 2.

Figure 2: Specific binding reaction of CL and CBT-asparagine.

Nε-L-cysteinyl-L-lysine

We synthesized CL in our lab and provide the community with a validated protocol. Currently, we are trying to synthesize CBT‑asparagine. Details of our synthesis protocol are described in the method section.
CL is an amino acid consisting of cysteine and lysine. The cysteine was coupled to the side chain of lysine so that CL contains a free 1,2-aminothiol group (Nguyen et al., 2011). This is an important characteristic for the specific binding between the CL and the CBT‑asparagine.
  • Name: Nε-L-cysteinyl-L-lysine
  • Short: CL
  • Molecular Weight: 249.33 g mol-1
  • Storage: -20 – 4 °C
  • Function: Terminus independent binding system

Figure 3: Structure of CL.

Nγ-2-cyanobenzothiazol-6-yl-L-asparagine

Figure 4: Structure of CBT‑asparagine.

CBT‑asparagine is a completely novel amino acid, which we are synthesizing on our own. The synthesis is based on coupling the amino group of 6-Amino-CBT to the carboxyl group of the side chain of L-asparagine. The cyano group of the CBT enables the specific binding of the CBT‑asparagine to 1,2-aminothiols.
  • Name: Nγ‑2‑cyanobenzothiazol‑6‑yl‑L‑asparagine
  • Short: CBT‑asparagine
  • Molecular Weight: 290.30 g mol-1
  • Storage: -20 – 4 °C
  • Function: Terminus independent binding system

Silk Elastin like Proteins

This specific binding can improve the stability of SELPs. These are linear polypeptides with repeats of silk and elastin consensus sequences. They show brought application and possibilities in medicine, tissue engineering and industry (Rnjak-Kovacina et al., 2011). The silk consensus sequence is GAGAGS and the elastin consensus sequence is VPAVG. The consensus sequences can interact with each other and are able to form non-covalent hydrogen bonds. This results in a polymer network based on hydrogen bonds with a β-sheet structure. Figure 5 shows the schematic structure of a SELP polymer network.

Figure 5: Schematic structure of a SELP polymer network.
Silk consensus sequences are shown in green, elastin consensus sequences are red and the blue lines show the hydrogen bonds of the consensus sequences.

According to the work of Collins et al. (2013), we decided to use a sequence with nine repeats of five repeats of the silk consensus sequence and nine repeats of the elastin consensus sequence (see figure 6).

Figure 6: Schematic sequence of the SELP (Collins et al., 2013).
Silk consensus sequences are green and elastin consensus sequences are red.

By incorporation of CL and CBT‑asparagine between the silk and the elastin repeats, we receive a strengthened polymer network with covalent bonds (Figure 7).

Figure 7: Schematic structure of a SELP polymer network.

PRe-RDL

The gene sequence for these SELPs has a high GC content and contains a high number of repeats leading to issues during synthesis. Therefore, Recursive Directional Ligation by Plasmid Reconstruction (PRe RDL) can be applied to address this challenge. Pre-RDL uses three restriction sites of a parent plasmid which contains the gene of interest (goi) and the subsequently ligation of fragments of two different restricted parent plasmids. The first step involves the restriction of a parent plasmid at the 3'-end of the goi and in the backbone. The second step is the restriction of a parent plasmid at the 5'-end of the goi and at the same position of the backbone as in the first step. The final step is the ligation of both generated fragments containing the goi. The result is a plasmid with two copies of the goi (Figure 5).

Figure 8: Scheme of the PRe-RDL (McDaniel et al., 2010).

References

Boateng, J., Matthews, K.H., Stevens, H.N.E., and Eccleston, G.M. (2008). Wound Healing Dressings and Drug Delivery Systems: A Review. J. Pharm. Sci. 97.

Collins, T., Azevedo-silva, J., Costa, A., Branca, F., Machado, R., and Casal, M. (2013). Batch production of a silk-elastin-like protein in E . coli BL21 ( DE3 ): key parameters for optimisation. Microb. Cell Fact. 12: 1–16.

Liang, G., Ren, H., and Rao, J. (2010). A biocompatible condensation reaction for controlled assembly of nanostructures in living cells. Nat. Chem. 2: 54–60.

McDaniel, J.R., Mackay, J.A., Quiroz, F.G., and Chilkoti, A. (2010). Recursive Directional Ligation by Plasmid Reconstruction allows Rapid and Seamless Cloning of Oligomeric Genes. 11: 944–952.

Nguyen, D.P., Elliott, T., Holt, M., Muir, T.W., and Chin, J.W. (2011). Genetically Encoded 1,2-Aminothiols Facilitate Rapid and Site-Specific Protein Labeling via a Bio-orthogonal Cyanobenzothiazole Condensation. J. Am. Chem. Soc. 133: 11418–11421.

Rnjak-Kovacina, J., Daamen, W.F., Pierna, M., Rodríguez-Cabello, J.C., and Weiss, A.S. (2011). Elastin Biopolymers. Compr. Biomater.: 329–346.