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

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Fusing

Short summary

Fusing proteins is normally limited to the C- or N-terminus of a protein. The incorporation of noncanonical 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 N^ε-L-cysteinyl-L-lysine (CL) and N^γ 2 cyanobenzothiazol 6 yl L asparagine (CBT-Asp) 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 noncanonical amino acids, which are able to build a specific bond to each other. According to the synthesis of 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 CBT and 1,2-aminothiol.

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-Asp. The binding mechanism of both amino acids are shown in figure 2.

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

N^ε-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-Asp. Details of our synthesis protocol are described in the method section (link to methods).

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-Asp.

Figure 3: Structure of CL.
Name: N^ε-L-cysteinyl-L-lysine
Molecular Weight: 249.33 g mol^-1
Storage: -20 – 4 °C

N^γ 2 cyanobenzothiazol-6-yl-L-asparagine

CBT-Asp is a completely novel amino acid, which we are synthesizing on our own. to the synthesis is based on coupling the amino group of CBT to the carboxyl group of the side chain of L-asparagine. The cyano group of the cyanobenzothiazol enables the specific binding of the CBT-Asp to 1,2-aminothiols.

Figure 4: Structure of CBT-Asp.
Name: N^γ-2-cyanobenzothiazol-6-yl-L-asparagine
Molecular Weight: 290.30 g mol^-1
Storage: -20 – 4 °C

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-Asp 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). We applied Pre-RDL to build a plasmid with the described SELP gene sequence.

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

Boateng, J., Matthews, K.H., Stevens, H.N.E., Eccleston, G.M., 2008. Wound Healing Dressings and Drug Delivery Systems: A Review. J. Pharm. Sci. 97. doi:10.1002/jps21210

Collins, T., Azevedo-silva, J., Costa, A., Branca, F., Machado, R., 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. doi:10.1186/1475-2859-12-21

Liang, G., Ren, H., Rao, J., 2010. A biocompatible condensation reaction for controlled assembly of nanostructures in living cells. Nat. Chem. 2, 54–60. doi:10.1038/nchem.480

McDaniel, J.R., Mackay, J.A., Quiroz, F.G., Chilkoti, A., 2010. Recursive Directional Ligation by Plasmid Reconstruction allows Rapid and Seamless Cloning of Oligomeric Genes 11, 944–952. doi:10.1021/bm901387t.Recursive

Nguyen, D.P., Elliott, T., Holt, M., Muir, T.W., 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. doi:10.1021/ja203111c

Rnjak-Kovacina, J., Daamen, W.F., Pierna, M., Rodríguez-Cabello, J.C., Weiss, A.S., 2011. Elastin Biopolymers. Compr. Biomater. 329–346. doi:http://dx.doi.org/10.1016/B978-0-08-055294-1.00071-4

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 		<article>
-		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.
+		Fusing proteins is normally limited to the C- or N-terminus of a protein. The incorporation of noncanonical 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.
 <br>
 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 N<sup>ε</sup>-L-cysteinyl-L-lysine (CL) and N<sup>γ</sup> 2 cyanobenzothiazol 6 yl L asparagine (CBT-Asp) 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).
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 <h3>Terminus independent fusion proteins</h3>
 <article>
-		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 luciferin for the firefly luciferase of <i>Photinus pyralis</i>, 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 CBT and 1,2-aminothiol.
+		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 noncanonical amino acids, which are able to build a specific bond to each other. According to the synthesis of luciferin for the firefly luciferase of <i>Photinus pyralis</i>, 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 CBT and 1,2-aminothiol.
 		</article>
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