Difference between revisions of "Team:Bielefeld-CeBiTec/Applied Design"

Latest revision as of 03:37, 2 November 2017

Applied Design

Short summary

Terminus independent specific fusion of two or more peptides is a major challenge in synthetic biology and beyond. Inspired by the highly specific condensation reaction of D‑luciferin from the firefly Photinus pyralis, we came up with a sophisticated solution, combining organic chemistry, computational modelling, and molecular biology. Based on our own design, we synthesized the novel synthetic amino acid N^γ‑cyanobenzothiazolyl‑L‑asparagine‑(CBT‑asparagine). The cyano group of CBT‑asparagine undergoes a condensation reaction with the 1,2‑aminothiol group of N^ε‑L‑cysteinyl‑L‑lysine (CL). Through in silico simulation, we predicted different aminoacyl tRNA synthetase sequences to incorporate CBT‑asparagine into proteins of interest. This system offers a new way for the production of fusion proteins and polymerized polypeptides.

Searching for Interesting Non-Canonical Amino Acids

During our search for interesting non‑canonical amino acids which we could use for our project, we found CL. It was first synthesized and described by Nguyen et al. (2011). It is proposed that CL enables the highly specific binding between peptides and ligands containing a cyanobenzothiazole residue. CL itself consists of L‑cysteine coupled by its carboxy group to the amino group of the side chain of L‑lysine. As a result, it contains a free 1,2‑aminothiol group at its side chain. According to the highly specific condensation reaction of 1,2‑aminothiols and cyanobenzothiazole‑derivatives (CBT-derivatives), which is common for the biosynthesis of D‑Luciferin (see Figure 1), the substrate of the firefly luciferase of P. pyralis, CL can undergo the same condensation reaction with CBT‑derivatives (see Figure 2).

Figure 1: Synthesis of D‑Luciferin.
The 1,2‑aminothiol group of D‑cysteine and the 6‑hydroxybenzothiazole‑2‑carbonitrile undergo the condensation reaction under physiological conditions to build D‑luciferin (Liang et al., 2010).

Figure 2: The condensation reaction of CL and a CBT‑derivative.
The 1,2‑aminothiol group of the side chain of CL and the cyano group of the CBT‑derivative undergo the same condensation reaction under physiological conditions like D‑cysteine and 6‑hydroxybenzothiazole‑2‑carbonitrile.

So far, CL was used to label proteins with CBT‑derivatives bound to fluorescent chemicals and proteins. Inspired by the rapid and highly specific condensation reaction which takes place under physiological conditions, we thought about a possibility to synthesize a novel amino acid which enables the highly specific binding between peptides using CBT as a side chain and CL as the counterpart.

Designing a Novel Amino Acid

To synthesize a novel amino acid, we needed the right reagents for the reaction. First, it was important to find a CBT‑derivative which could be coupled to the side chain of a canonical amino acid. To use common methods of peptide synthesis, we needed two educts one containing a free carboxy group and one containing a free amino group. There are different canonical amino acids containing one of these two groups at their side chains. All canonical eligible amino acids with a free amino group at their side chain are lysine, asparagine and glutamine. Because of the long carbon chain at the side chain of lysine it would be too difficult to generate a well working aminoacyl‑tRNA synthetase for a novel amino acid consisting of lysine and a CBT‑derivative. To get an amino acid as small as possible containing a CBT-derivative at its side chain, asparagine and its derivative aspartic acid which contains a free carboxy group at its side chain were the best choices for an educt for the synthesis of a novel amino acid. As CBT-derivative we chose 6‑amino‑2‑cyanobenzothiazole (ACBT) which has a free amino group at its benzene ring (see Figure 3). Its free amino group ACBT requires an aspartic acid for the coupling reaction to synthesize the novel amino acid.

Figure 3: Structure of ACBT.
The amino group at the benzene ring can be used for the coupling reaction and the cyano group at the thiazole ring enables the condensation reaction.

Synthesizing a Novel Amino Acid

Due to the high price of ACBT, we synthesized it first on ourselves using 2‑chloro‑6‑nitrobenzothiazole (Cl-NBT) as educt. According to Hauser et al. (2016), we produced ACBT by the nucleophilic substitution of the chlorine atom with a cyano group and the reduction of the nitro group to an amino group. Figure 4 shows the schematic synthesis of ACBT with Cl‑NBT as the educt.

Figure 4: Schematic synthesis of ACBT with Cl‑NBT as the educt.
First, the chlorine atom of the Cl‑NBT is substituted with a cyano group (i) to give 6‑nitrobenzothiazole‑2‑carbonitrile (NBT‑CN). The second step is the reduction of the nitro group of NBT‑CN to an amino group (ii) resulting in ACBT.

With ACBT and N‑Fmoc‑aspartic acid‑OAllyl ester we could synthesize the novel amino acid CBT‑asparagine. Figure 5 and 6 show the two steps of the synthesis.

Figure 5: Schematic coupling reaction of ACBT and N‑Fmoc‑aspartic acid‑OAllyl ester.
Due to the protecting groups, only the carboxy group of N‑Fmoc‑aspartic acid‑OAllyl ester can react with the amino group of ACBT. Using isobutyl chloroformate and 4‑methylmorpholine enables the coupling reaction.

Figure 6: Deprotection of N‑Fmoc‑CBT‑asparagine‑OAllyl ester.
By adding 3x the equivalent of morpholine to the protected N‑Fmoc‑CBT‑asparagine‑OAllyl ester, we could directly remove both protecting groups resulting in the free form of the novel amino acid CBT-asparagine.

With the novel amino acid CBT‑asparagine and the CL we provide a new way of rapid highly specific binding of peptides and enzymes under physiological conditions. First in vitro tests show that the condensation reaction between CBT‑asparagine and CL (see Figure 7) takes place.

Figure 7: Schematic condensation reaction of CL and CBT‑asparagine.
The natural condensation reaction of 1,2‑aminothiols and 6‑hydroxybenzothiazole‑2‑carbonitrile provides a new way to produce fusion proteins and polymer peptides by binding both amino acids.

Modeling New Aminoacyl-tRNA Synthetases by in silico Simulation

Additionally, we generated several new aminoacyl‑tRNA synthetases based on the tyrosyl‑tRNA synthetase of Methanococcus jannaschii using the protein design software ROSETTA. Preliminary tests indicate that the modeled synthetases K2201300, K2201301, and K2201302 are able to incorporate CBT‑asparagine (for further information visit our modeling page). Further tests are needed to evluate these results. Following figure shows CBT‑asparagine in the binding site of the synthetase K2201300 (Figure 8).

Figure 8: CBT-asparagine in the binding site of K2201300.

Conclusion

We provide a new way to produce fusion proteins and polymerized peptides using the terminus independent, rapid and highly specific binding ability of CL and the novel amino acid CBT‑asparagine. With this method, it is possible to fuse peptides and enzymes using an environmentally friendly condensation reaction which is inspired by natural systems.

References

Hauser, J.R., Beard, H.A., Bayana, M.E., Jolley, K.E., Warriner, S.L., and Bon, R.S. (2016). Economical and scalable synthesis of 6-amino-2-cyanobenzothiazole. Beilstein J. Org. Chem. 12: 2019–2025.
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.
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.

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-<div id="title" style="background-image: url(https://static.igem.org/mediawiki/2017/7/74/T--Bielefeld-CeBiTec--title-img-centrifuge.jpg);">
+<div id="title" style="background-image: url(https://static.igem.org/mediawiki/2017/7/77/T--Bielefeld-CeBiTec--title-img-toolbox2.jpg);">
-				<img src="https://static.igem.org/mediawiki/2017/7/74/T--Bielefeld-CeBiTec--title-img-centrifuge.jpg">
+				<img src="https://static.igem.org/mediawiki/2017/7/77/T--Bielefeld-CeBiTec--title-img-toolbox2.jpg">
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 <div class="contentbox">
+	<div class="bevel tr"></div>
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 		<h3>Short summary</h3>
@@ Line 24: / Line 25: @@
 			proteins of interest. This system offers a new way for the production of fusion proteins and polymerized polypeptides.
 		</div>
+	</div>
+	<div class="bevel bl"></div>
+</div>
+<div class="contentbox">
+	<div class="bevel tr"></div>
+	<div class="content">
 		<h3>Searching for Interesting Non-Canonical Amino Acids</h3>
 		<div class="article">
 			During our search for interesting non&#x2011;canonical amino acids which we could use for our project, we found CL. It was first synthesized
-			and described by Nguyen <i>et&nbsp;al</i>. (2011). Its proposed that CL enables the highly specific binding between peptides and ligands containing
+			and described by Nguyen <i>et&nbsp;al</i>. (2011). It is proposed that CL enables the highly specific binding between peptides and ligands containing
-			a cyanobenzothiazole residue. CL itself consists out of L&#x2011;cysteine coupled by its carboxy group to the amino group of the side chain of
+			a cyanobenzothiazole residue. CL itself consists of L&#x2011;cysteine coupled by its carboxy group to the amino group of the side chain of
-			L&#x2011;lysine. As a result, it contains at its side chain a free 1,2&#x2011;aminothiol group. According to the highly specific condensation reaction
+			L&#x2011;lysine. As a result, it contains a free 1,2&#x2011;aminothiol group at its side chain. According to the highly specific condensation reaction
 			of 1,2&#x2011;aminothiols and cyanobenzothiazole&#x2011;derivatives (CBT-derivatives), which is common for the biosynthesis of D&#x2011;Luciferin (see Figure
-), the substrate of the firefly luciferase of <i>P. pyralis</i>, CL can undergo the same condensation reaction with CBT&#x2011;derivatives (see
+), the substrate of the firefly luciferase of <i>P.&nbsp;pyralis</i>, CL can undergo the same condensation reaction with CBT&#x2011;derivatives (see
 			Figure 2).
 		</div>
@@ Line 47: / Line 54: @@
 		</div>
 		<div class="article">
-			So far, it was used to label proteins with CBT&#x2011;derivatives bound to fluorescent chemicals and proteins. Inspired by the rapid and
+			So far, CL was used to label proteins with CBT&#x2011;derivatives bound to fluorescent chemicals and proteins. Inspired by the rapid and
-			highly specific condensation reaction which takes place under physiological conditions we thought about a possibility to synthesize
+			highly specific condensation reaction which takes place under physiological conditions, we thought about a possibility to synthesize
-			a novel amino acid which enables the highly specific binding between peptides using CBT as side chain and CL as counterpart.
+			a novel amino acid which enables the highly specific binding between peptides using CBT as a side chain and CL as the counterpart.
 		</div>
+	</div>
+	<div class="bevel bl"></div>
+</div>
+<div class="contentbox">
+	<div class="bevel tr"></div>
+	<div class="content">
 		<h3>Designing a Novel Amino Acid</h3>
 		<div class="article">
-			To synthesize a novel amino acid, we needed the right reagents for the reaction. First, it was necessary to find a CBT&#x2011;derivative
+			To synthesize a novel amino acid, we needed the right reagents for the reaction. First, it was important to find a CBT&#x2011;derivative
-			which could be coupled to the side chain of a canonical amino acid. To use common methods of the peptide synthesis, we needed two
+			which could be coupled to the side chain of a canonical amino acid. To use common methods of peptide synthesis, we needed two
 			educts one containing a free carboxy group and one containing a free amino group. There are different canonical amino acids containing
-			at their side chains one of both groups. All canonical eligible amino acids with a free amino group at their side chain are lysine,
+			one of these two groups at their side chains. All canonical eligible amino acids with a free amino group at their side chain are lysine,
 			asparagine and glutamine. Because of the long carbon chain at the side chain of lysine it would be too difficult to generate a well
 			working aminoacyl&#x2011;tRNA synthetase for a novel amino acid consisting of lysine and a CBT&#x2011;derivative. To get an amino acid as small as
-			possible containing a CBT-derivative at its side chain asparagine and its derivative aspartic acid which contains a free carboxy group
+			possible containing a CBT-derivative at its side chain, asparagine and its derivative aspartic acid which contains a free carboxy group
-			at its side chain were the best choice for an educt for the synthesis of the novel amino acid. As CBT-derivative we chose
+			at its side chain were the best choices for an educt for the synthesis of a novel amino acid. As CBT-derivative we chose
-&#x2011;amino&#x2011;2&#x2011;cyanobenzothiazole (ACBT) which has a free amino group at its benzene ring (see Figure 3). With its free amino group ACBT
+&#x2011;amino&#x2011;2&#x2011;cyanobenzothiazole (ACBT) which has a free amino group at its benzene ring (see Figure 3). Its free amino group ACBT
-			requires aspartic acid for the coupling reaction to synthesize the novel amino acid.
+			requires an aspartic acid for the coupling reaction to synthesize the novel amino acid.
 		</div>
 		<div class="figure medium">
@@ Line 69: / Line 82: @@
 			coupling reaction and the cyano group at the thiazole ring enables the condensation reaction.</p>
 		</div>
+	</div>
+	<div class="bevel bl"></div>
+</div>
+<div class="contentbox">
+	<div class="bevel tr"></div>
+	<div class="content">
 		<h3>Synthesizing a Novel Amino Acid</h3>
 		<div class="article">
 			Due to the high price of ACBT, we synthesized it first on ourselves using 2&#x2011;chloro&#x2011;6&#x2011;nitrobenzothiazole (Cl-NBT) as educt. According
-			to Hauser <i>et&nbsp;al</i>. (2016), we got ACBT by the nucleophilic substitution of the chlorine atom with a cyano group and the reduction of
+			to Hauser <i>et&nbsp;al</i>. (2016), we produced ACBT by the nucleophilic substitution of the chlorine atom with a cyano group and the reduction of
-			the nitro group to an amino group. Figure 4 shows the schematic synthesis of ACBT with Cl&#x2011;NBT as educt.
+			the nitro group to an amino group. Figure 4 shows the schematic synthesis of ACBT with Cl&#x2011;NBT as the educt.
 		</div>
 		<div class="figure large">
 			<img class="figure image" src="https://static.igem.org/mediawiki/2017/c/c1/T--Bielefeld-CeBiTec--28-10-17-CBT_syn.png">
-			<p class="figure subtitle"><b>Figure 4: Schematic synthesis of ACBT with Cl&#x2011;NBT as educt. </b><br> First, the chlorine atom of the
+			<p class="figure subtitle"><b>Figure 4: Schematic synthesis of ACBT with Cl&#x2011;NBT as the educt. </b><br> First, the chlorine atom of the
 			Cl&#x2011;NBT is substituted with a cyano group (i) to give 6&#x2011;nitrobenzothiazole&#x2011;2&#x2011;carbonitrile (NBT&#x2011;CN). The second step is the reduction
 			of the nitro group of NBT&#x2011;CN to an amino group (ii) resulting in ACBT.</p>
@@ Line 93: / Line 112: @@
 		<div class="figure large">
 			<img class="figure image" src="https://static.igem.org/mediawiki/2017/e/e6/T--Bielefeld-CeBiTec--28-10-17-CBT-asparagine_syn2.png">
-			<p class="figure subtitle"><b>Figure 6: Deprotection of <i>N</i>&#x2011;Fmoc&#x2011;CBT&#x2011;asparagine&#x2011;OAllyl ester.</b><br>By using 3x equivalent of morpholine to
+			<p class="figure subtitle"><b>Figure 6: Deprotection of <i>N</i>&#x2011;Fmoc&#x2011;CBT&#x2011;asparagine&#x2011;OAllyl ester.</b><br>By adding 3x the equivalent of morpholine to
-			the protected <i>N</i>&#x2011;Fmoc&#x2011;CBT&#x2011;asparagine&#x2011;OAllyl ester we could directly remove both protecting groups resulting in the free form of the novel
+			the protected <i>N</i>&#x2011;Fmoc&#x2011;CBT&#x2011;asparagine&#x2011;OAllyl ester, we could directly remove both protecting groups resulting in the free form of the novel
 			amino acid CBT-asparagine.</p>
 		</div>
 		<div class="article">
 			With the novel amino acid CBT&#x2011;asparagine and the CL we provide a new way of rapid highly specific binding of peptides and enzymes
-			under physiological conditions. First <a href="https://2017.igem.org/Results/toolbox/fusing#in_vitro"> <i>in vitro</i> tests </a> show that the condensation reaction
+			under physiological conditions. First <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing"> <i>in vitro</i> tests </a> show that the condensation reaction
 			between CBT&#x2011;asparagine and CL (see Figure 7) takes place.
 		</div>
 		<div class="figure large">
 			<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"><b>Figure 7: Schematic condensation reaction of CL and CBT&#x2011;asparagine.</b><br>According to the natural
+			<p class="figure subtitle"><b>Figure 7: Schematic condensation reaction of CL and CBT&#x2011;asparagine.</b><br>The natural
-			condensation reaction of 1,2&#x2011;aminothiols and 6&#x2011;hydroxybenzothiazole-2-carbonitrile, both amino acids can bind to each other providing
+			condensation reaction of 1,2&#x2011;aminothiols and 6&#x2011;hydroxybenzothiazole&#x2011;2&#x2011;carbonitrile provides a new way to produce fusion proteins and polymer peptides by binding both amino acids.</p>
-			incorporated into proteins a new way to produce fusion proteins and polymer peptides.</p>
 		</div>
+	</div>
+	<div class="bevel bl"></div>
+</div>
+<div class="contentbox">
+	<div class="bevel tr"></div>
+	<div class="content">
 		<h3>Modeling New Aminoacyl-tRNA Synthetases by in silico Simulation</h3>
 		<div class="article">
 			Additionally, we generated several new aminoacyl&#x2011;tRNA synthetases based on the tyrosyl&#x2011;tRNA synthetase of <i>Methanococcus jannaschii</i>
-			using the <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model#ROSETTA"> protein design software ROSETTA </a>. All of the three tested synthetases were able to incorporate the CBT&#x2011;asparagine (for
+			using the protein design software ROSETTA. Preliminary tests indicate that the modeled synthetases <a href="http://parts.igem.org/Part:BBa_K2201300">K2201300</a>, <a href="http://parts.igem.org/Part:BBa_K2201301">K2201301</a>, and <a href="http://parts.igem.org/Part:BBa_K2201302">K2201302</a> are able to incorporate CBT&#x2011;asparagine (for
-			further information visit our <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model"> modeling page </a>.
+			further information visit our <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model"> modeling page</a>). Further tests are needed to
+			evluate these results. Following figure shows CBT&#x2011;asparagine in the binding site of the synthetase <a href="http://parts.igem.org/Part:BBa_K2201300">K2201300</a> (Figure 8).
+		<div class="figure medium">
+			<img class="figure image" src="https://static.igem.org/mediawiki/2017/2/22/T--Bielefeld-CeBiTec--1-11-17--CBT-asparagin_K2201300.png">
+			<p class="figure subtitle"><b>Figure 8: CBT-asparagine in the binding site of <a href="http://parts.igem.org/Part:BBa_K2201300">K2201300</a>.</b></p>
+		</div>
 		</div>
 		<h3>Conclusion</h3>
@@ Line 118: / Line 147: @@
 			We provide a new way to produce fusion proteins and polymerized peptides using the terminus independent, rapid and highly specific
 			binding ability of CL and the novel amino acid CBT&#x2011;asparagine. With this method, it is possible to fuse peptides and enzymes using
-			an environmental friendly condensation reaction which is inspired by natural systems.
+			an environmentally friendly condensation reaction which is inspired by natural systems.
 		</div>
+	<div class="bevel bl"></div>
+	</div>
+</div>
+<div class="contentbox">
+	<div class="bevel tr"></div>
+	<div class="content">
 		<h3>References</h3>
 		<div class="article">
@@ Line 128: / Line 163: @@
 			<b>Nguyen, D.P., Elliott, T., Holt, M., Muir, T.W., and Chin, J.W.</b> (2011). Genetically Encoded 1,2-Aminothiols Facilitate Rapid and Site-Specific Protein Labeling via a Bio-orthogonal Cyanobenzothiazole Condensation. J. Am. Chem. Soc. <b>133</b>: 11418–11421.
 		</div>
-	<div class="bevel bl"></div>
 	</div>
+	<div class="bevel bl"></div>
 </div>
 </div>