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

 
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Analyzing
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<h1> Analysing </h1>
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<!-- Ueberschriften -->
 
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<h2> Short summary </h2>
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<h2> Short Summary </h2>
 
<!-- Normaler Text -->
 
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<article>
 
<article>
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As part of our <a href="https://www.ncbi.nlm.nih.gov/pubmed"> toolbox</a>, structural analysis of a protein could be used to study  
+
As part of our <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox"> toolbox</a>, structural analysis of a protein could be used to study  
−
distances between noncanonical amino acids with <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#FRET">Foerster&nbsp;Resonance&nbsp;Energy&nbsp;Transfer  
+
distances between non-canonical amino acids with <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#FRET">Foerster&nbsp;Resonance&nbsp;Energy&nbsp;Transfer  
−
(FRET)</a>. This provides measuring distances between specific incorporated amino acids in
+
(FRET)</a>. This provides measuring distances within specific incorporated amino acids in
 
the target protein to gain insight into protein folding or structural changes under  
 
the target protein to gain insight into protein folding or structural changes under  
 
different conditions.  
 
different conditions.  
 
<br>
 
<br>
−
To demonstrate this tool we are developing a <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#prion">prion</a> detection assay. We use the yeast  
+
To demonstrate this tool, we developed a <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#prion">prion</a> detection assay. We used the yeast  
−
prion <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#sup35">Sup35</a> as a model protein and incorporate to non&#x2011;canonical amino acids  
+
prion <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#Sup35">Sup35</a> as a model protein and incorporate two non&#x2011;canonical amino acids  
−
(<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#AcF">p-acetophenylalanine</a> and <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#PrK">propargyllysine</a>). After the purification of the recombinant  
+
(<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#AcF">p-acetophenylalanine</a> and <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#PrK">propargyllysine</a>). After purification, the recombinant  
 
produced Sup35 could be labeled with two different fluorophores (<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#Cy3Cy5">Cyanin 3 and Cyanin 5</a>).
 
produced Sup35 could be labeled with two different fluorophores (<a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#Cy3Cy5">Cyanin 3 and Cyanin 5</a>).
−
The emission spectra of the fluorophores depend on their distance between each other.  
+
The emission spectra of the fluorophores depend on their distance.  
 
When this test protein gets in contact with prions, the prions conformational changes  
 
When this test protein gets in contact with prions, the prions conformational changes  
 
result in the change of the fluorophores spectra. Therefore, the test prion could be  
 
result in the change of the fluorophores spectra. Therefore, the test prion could be  
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<!-- Ueberschriften -->
 
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<h2> Structural analysis with noncanonical amino acids </h2>
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<h2> Structural Analysis with Non-canonical Amino Acids </h2>
 
<article>
 
<article>
 
The structure of proteins could be detected through protein crystallography.   
 
The structure of proteins could be detected through protein crystallography.   
−
However, there are a lot of problems when it comes to highly flexible proteins or  
+
However, there are some problems when it comes to highly flexible proteins, or  
−
proteins which change their structure under different conditions. To analyze these
+
proteins which change their structure within different conditions. To analyze these
−
proteins and the changes in their conformation we want to establish a tool that allows
+
proteins and the changes in their conformation we want to establish a tool, that allows
−
to detect changes in protein conformation.  For the detection of these changes two  
+
to detect changes in protein conformation.  For the detection of those changes, two  
−
amino acids are incorporated at specific positions in the protein. These amino acids  
+
amino acids are incorporated at specific positions into the protein. These amino acids  
−
could then be labeled with chromophores, enabeling the measurement of the proteins  
+
could then be labeled with chromophores, enabling the measurement of the proteins  
−
distances with <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#FRET">Foerster Resonance Energy Transfer (FRET)</a>[Aramburu 2017, Kim 2013].
+
distances with <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox/analysing#FRET">Foerster Resonance Energy Transfer (FRET)</a>(Lembke, 2011, Kim <i>et al.</i>, 2013).
 
<br>
 
<br>
−
The first step is the incorporation of the noncanonical amino acids. In proteins
+
The first step is the incorporation of the non-canonical amino acids. In proteins which
−
naturally containing no cysteins (cysteines are the only canonical amino acids that
+
contain no cysteines naturally (cysteines are the only canonical amino acids, that
 
could be labeled specific) or in which the exchanges of cysteines does not influence  
 
could be labeled specific) or in which the exchanges of cysteines does not influence  
−
the structure only one ncAA and one cysteine at specific points need to be incorporated
+
the structure, only one ncAA and one cysteine at specific points need to be incorporated
−
to be labeled. In proteins that contain cysteine two ncAAs need to be incorporated for  
+
to be labeled. In proteins that contain cysteines, two ncAAs need to be incorporated for  
−
the labeling [Kim 2013].  
+
the labeling (Kim <i>et al.</i>, 2013).  
 
<br>
 
<br>
−
Noncanonical amino acids could be incorporated by <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/translational_system/translational_mechanism">orthogonal tRNA/aaRS synthetases</a> in
+
Non-canonical amino acids could be incorporated by <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/translational_system/translational_mechanism">orthogonal tRNA/aaRS pairs</a> using the amber stop codon. However, this allows only the incorporation of one  
−
response to the amber stop codon. However, this allows only the incorporation of one  
+
non-canonical amino acid. To incorporate the second amino acid, another orthogonal  
−
noncanonical amino acid. To incorporate the second amino acid, another orthogonal  
+
amino acid has to be used for the incorporation. Another codon that could be repurposed is the rarely used leucine codon CUA. With the use of this and the amber codon, two different ncAAs could be used. For structural analysis, the amino acids are specific labeled with chromophores. This labeling (shown in figure 1)
−
amino acid could be used for the incorporation in response to a rarely used leucine  
+
is possible due to the functional groups of the amino acids, which could  
−
codon. For structural analysis the amino acids are specific labeled with chromophores.
+
−
This labeling is possible due to the functional groups of the amino acids which could  
+
 
form a covalent bond to the fluorophores in a chemical reaction.  
 
form a covalent bond to the fluorophores in a chemical reaction.  
−
After the protein is labeled the fluorescence of the chromophores could be measured to  
+
After the protein is labeled, the fluorescence of the chromophores could be measured to  
−
draw conclusions on the distance of the ncAA from each other [Brustad 2008, Kim 2013].
+
draw conclusions on the distance of the ncAAs from each other (Brustad <i>et al.</i>, 2008, Kim <i>et al.</i>, 2013).
 
</article>
 
</article>
 
<div class="figure large">
 
<div class="figure large">
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acids is propargyllysine. The propargyl group of PrK could form a covalent bond to
 
acids is propargyllysine. The propargyl group of PrK could form a covalent bond to
 
acidic groups in a click chemistry reaction. PrK is commercially available or could
 
acidic groups in a click chemistry reaction. PrK is commercially available or could
−
be synthesized chemically in two steps starting with Boc&#x2011;I&#x2011;Lys&#x2011;OH [Lemke5].  
+
be synthesized chemically in two steps starting with Boc&#x2011;I&#x2011;Lys&#x2011;OH (Kim <i>et al.</i>, 2013).  
 
The click chemistry reaction is performed at neutral pH, native buffers and
 
The click chemistry reaction is performed at neutral pH, native buffers and
 
temperatures of 4°&nbsp;C to 37&nbsp;°C. However, for the click&#x2011;chemistry reaction copper
 
temperatures of 4°&nbsp;C to 37&nbsp;°C. However, for the click&#x2011;chemistry reaction copper
−
is required which is toxic for living cells, So PrK could not be used for <i> in
+
is required which is toxic for living cells, so PrK could not be used for <i> in
−
vivo </i> labeling [Kim 2013].
+
vivo </i> labeling (Kim <i>et al.</i>, 2013).
 
</article>
 
</article>
 
<div class="contentline">
 
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                         <li> MW: 228.25 g mol<sup>-1</sup>
 
                         <li> MW: 228.25 g mol<sup>-1</sup>
 
                         <li> Storage:          4 °C
 
                         <li> Storage:          4 °C
−
                         <li> Source: <a https://www.sichem.de/de/sc-8002.html>Sichem</a>
+
                         <li> Source: <a href="https://www.sichem.de/de/sc-8002.html">Sichem</a>
 
                         <li> Prize: 1g - £300.00
 
                         <li> Prize: 1g - £300.00
 
                         <li> Function:          Propargyl group for click-chemistry reaction
 
                         <li> Function:          Propargyl group for click-chemistry reaction
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is p&#x2011;acetylphenylalanine. The ketone group of AcF is able to build a covalent bond to a
 
is p&#x2011;acetylphenylalanine. The ketone group of AcF is able to build a covalent bond to a
 
hydroxylamine coupled dye in a hydrazide reaction. This reaction is carried out at low  
 
hydroxylamine coupled dye in a hydrazide reaction. This reaction is carried out at low  
−
pH&#x2011;values which causes problems with certain proteins[Kim 2013].
+
pH&#x2011;values which causes problems with certain proteins (Kim <i>et al.</i>, 2013).
 
</article>
 
</article>
 
<div class="contentline">
 
<div class="contentline">
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Foerster Resonance Energy Transfer or Fluorescence Energy Transfer, short FRET,  
 
Foerster Resonance Energy Transfer or Fluorescence Energy Transfer, short FRET,  
 
describes an energy transfer between two chromophores. During this process the donor  
 
describes an energy transfer between two chromophores. During this process the donor  
−
chromophore is excited and transfers the energy to the acceptor chromophore if they  
+
chromophore is excited by light of a certain wavelength and transfers the energy to the acceptor chromophore if they  
 
are within a certain distance to each other. In biochemistry, FRET is mostly used as  
 
are within a certain distance to each other. In biochemistry, FRET is mostly used as  
 
measurement tool with the help of fluorescent dyes. Using FRET, the measuring of
 
measurement tool with the help of fluorescent dyes. Using FRET, the measuring of
−
distances from 1 to 10&nbsp;nm is possible [Brustad 2006].
+
distances from 1 to 10&nbsp;nm is possible (Brustad <i>et al.</i>, 2006). The FRET process is shown in Figure 4.
 
</article>
 
</article>
 
 
 
<div class="figure large">
 
<div class="figure large">
−
<img class="figure image" src="HIER DEN LINK ZUM BILD.jpg">
+
<img class="figure image" src="https://static.igem.org/mediawiki/2017/8/84/T--Bielefeld-CeBiTec--SVI_FRET_Animation.gif">
 
<p class="figure subtitle"><b>Figure 4: Animations of a FRET fluorophore pair </b><br> Animation of the distance dependent energy transfer of two fluorophores.</p>
 
<p class="figure subtitle"><b>Figure 4: Animations of a FRET fluorophore pair </b><br> Animation of the distance dependent energy transfer of two fluorophores.</p>
 
</div>
 
</div>
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<br>
 
<br>
 
<article>
 
<article>
−
E  FRET efficency <br>
+
E  FRET efficiency <br>
 
r  intermolecular distance <br>
 
r  intermolecular distance <br>
 
R<sub>0</sub> Foerster distance for a given dye pair
 
R<sub>0</sub> Foerster distance for a given dye pair
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Cyanin&nbsp;3 (Cy3) in combination with Cyanin&nbsp;5 (Cy5) is a chromophore pair which is  
 
Cyanin&nbsp;3 (Cy3) in combination with Cyanin&nbsp;5 (Cy5) is a chromophore pair which is  
 
suitable for FRET measurements. Cy3 operates as the donor dye and Cy5 as the acceptor
 
suitable for FRET measurements. Cy3 operates as the donor dye and Cy5 as the acceptor
−
dye. The extinction and emission spectra of both chromophores is shown in Figure&nbsp;5[Kim 2013].
+
dye. The extinction and emission spectra of both chromophores is shown in Figure&nbsp;5 (Kim <i>et al.</i>, 2013).
 
</article>
 
</article>
 
 
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For the labeling of the noncanonical amino acids with these chromophores a functional
 
For the labeling of the noncanonical amino acids with these chromophores a functional
 
group is required to build a covalent bond in chemical conjugation. PrK could be  
 
group is required to build a covalent bond in chemical conjugation. PrK could be  
−
labeled with Cy3&#x2011;azide and AcF with Cy5&#x2011;hydrazide. Both chromophores are inexpensible
+
labeled with Cy3&#x2011;azide and AcF with Cy5&#x2011;hydrazide. Both chromophores are relatively advantageously priced
−
in comparison to other chromophore pairs and above commercially available from <a href"https://de.lumiprobe.com/"> Lumiprobe</a>.
+
in comparison to other chromophore pairs and commercially available from <a href="https://de.lumiprobe.com/"> Lumiprobe</a>.
 
</article>
 
</article>
 
</div>
 
</div>
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<div class="content">
 
<div class="content">
 
 
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<h2> Prion detection assembly
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<h2> Prion Detection Assay
 
 
 
<span class="anchor-jump" id="prion"></span>
 
<span class="anchor-jump" id="prion"></span>
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<article>
 
<article>
 
Prions are proteins that could infect other proteins to change their conformation.
 
Prions are proteins that could infect other proteins to change their conformation.
−
Often this causes a loss of function and aggregation of these proteins. Prions are  
+
This is often causing a loss of function and aggregation of these proteins. Prions are  
 
the cause for diseases like transmissible spongiform encephalopathies (TSEs),  
 
the cause for diseases like transmissible spongiform encephalopathies (TSEs),  
−
neurodegenerative disorders that effect humans and animals [Wickner 2015].  
+
neurodegenerative disorders that effect humans and animals (Wickner <i>et al.</i>, 2015).  
 
</article>
 
</article>
 
 
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(amino acids 124&#x2011;250) is highly charged and provides the solubility to the native form  
 
(amino acids 124&#x2011;250) is highly charged and provides the solubility to the native form  
 
of Sup35. In the prion form the M region changes its conformation to a beta&#x2011;sheet rich  
 
of Sup35. In the prion form the M region changes its conformation to a beta&#x2011;sheet rich  
−
conformation, while the N&#x2011;section stays nearly unchanged in its conformation. [Mukhopadhyay 2007,Wickner 2015]
+
conformation, while the N&#x2011;section stays nearly unchanged in its conformation (Mukhopadhyay <i>et al.</i>, 2007; Wickner <i>et al.</i>, 2015).
 
</article>
 
</article>
 
 
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            <h2> References </h2>
 +
<b>Brustad, E. M., Lembke, E. A., Schultz, P. G., Dentz, A. A.</b>(2008). A General and Efficient Method for the Site-Specific Dual-Labeling of Proteins
 +
for Single Molecule Fluorescence Resonance Energy Transfer. American Chemical Society. <b>130</b>: 17664-17665..<br><br>
 +
<b>Kim, J., Seo, M., Lee, S., Cho, K., Yang, A., Woo, K., Kim, H., Park, H.</b>(2012). Simple and Efficient Strategy for Site-Specific Dual Labeling of
 +
Proteins for Single-Molecule Fluorescence Resonance Energy
 +
Transfer Analysis. Analytical Chemistry.<b>85</b>: 1468-1474. <br><br>
 +
<b>Lembke, E. a.</b>(2011). Site-Specific Labeling of Proteins for Single-Molecule
 +
FRET Measurements Using Genetically Encoded
 +
Ketone Functionalities. Bioconjugation Proocols: Strategies and Methods in Molecular Biology. <b>751</b>: 3-15.<br><br>
 +
<b>Mukhopadhyay, S., Krishnan, R., Lembke, E. A., Lindquist, S., Deniz, A. A.</b>(2007)A natively unfolded yeast prion monomer adopts
 +
an ensemble of collapsed and rapidly
 +
fluctuating structures.PNAS.<b>104(8)</b>:2649-2654.<br><br>
 +
<b>Wickner, R. B., Shewmaker, F. P., Bateman, D. A., Edskes, H. K., Gorkovsky, A., Dayani, Y., Bezsonov, E. E.</b>82015) Yeast Prions: Structure, Biology, and Prion-Handling Systems. Microbiology and Molecular Reviews. <b>79(1)</b>:1-17.<br><br>
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Latest revision as of 10:21, 1 November 2017

Analyzing

Short Summary

As part of our toolbox, structural analysis of a protein could be used to study distances between non-canonical amino acids with Foerster Resonance Energy Transfer (FRET). This provides measuring distances within specific incorporated amino acids in the target protein to gain insight into protein folding or structural changes under different conditions.
To demonstrate this tool, we developed a prion detection assay. We used the yeast prion Sup35 as a model protein and incorporate two non‑canonical amino acids (p-acetophenylalanine and propargyllysine). After purification, the recombinant produced Sup35 could be labeled with two different fluorophores (Cyanin 3 and Cyanin 5). The emission spectra of the fluorophores depend on their distance. When this test protein gets in contact with prions, the prions conformational changes result in the change of the fluorophores spectra. Therefore, the test prion could be used to detect prions in medical samples.

Structural Analysis with Non-canonical Amino Acids

The structure of proteins could be detected through protein crystallography. However, there are some problems when it comes to highly flexible proteins, or proteins which change their structure within different conditions. To analyze these proteins and the changes in their conformation we want to establish a tool, that allows to detect changes in protein conformation. For the detection of those changes, two amino acids are incorporated at specific positions into the protein. These amino acids could then be labeled with chromophores, enabling the measurement of the proteins distances with Foerster Resonance Energy Transfer (FRET)(Lembke, 2011, Kim et al., 2013).
The first step is the incorporation of the non-canonical amino acids. In proteins which contain no cysteines naturally (cysteines are the only canonical amino acids, that could be labeled specific) or in which the exchanges of cysteines does not influence the structure, only one ncAA and one cysteine at specific points need to be incorporated to be labeled. In proteins that contain cysteines, two ncAAs need to be incorporated for the labeling (Kim et al., 2013).
Non-canonical amino acids could be incorporated by orthogonal tRNA/aaRS pairs using the amber stop codon. However, this allows only the incorporation of one non-canonical amino acid. To incorporate the second amino acid, another orthogonal amino acid has to be used for the incorporation. Another codon that could be repurposed is the rarely used leucine codon CUA. With the use of this and the amber codon, two different ncAAs could be used. For structural analysis, the amino acids are specific labeled with chromophores. This labeling (shown in figure 1) is possible due to the functional groups of the amino acids, which could form a covalent bond to the fluorophores in a chemical reaction. After the protein is labeled, the fluorescence of the chromophores could be measured to draw conclusions on the distance of the ncAAs from each other (Brustad et al., 2008, Kim et al., 2013).

Figure 1: Target protein labeled with fluorophores.
The ncAAs AcF and PrK are incorporated in the target protein. After bi-orthgonal chemical conjugation the ncAAs are coupled with the fluorescent dyes cyanin 3 (Cy3) and cyanin 5 (Cy5).

Propargyllysine (PrK)

One amino acid which provides a functional group different to the canonical amino acids is propargyllysine. The propargyl group of PrK could form a covalent bond to acidic groups in a click chemistry reaction. PrK is commercially available or could be synthesized chemically in two steps starting with Boc‑I‑Lys‑OH (Kim et al., 2013). The click chemistry reaction is performed at neutral pH, native buffers and temperatures of 4° C to 37 °C. However, for the click‑chemistry reaction copper is required which is toxic for living cells, so PrK could not be used for in vivo labeling (Kim et al., 2013).
  • Name: Propargyllysine
  • Short: PrK
  • CAS: 1428330-91-9
  • MW: 228.25 g mol-1
  • Storage: 4 °C
  • Source: Sichem
  • Prize: 1g - £300.00
  • Function: Propargyl group for click-chemistry reaction

Figure 2: Structure of PrK
Propargyllysine (PrK).

p‑Acetylphenylalanine (AcF)

Another amino acid with an additional functional group to the canonical amino acids is p‑acetylphenylalanine. The ketone group of AcF is able to build a covalent bond to a hydroxylamine coupled dye in a hydrazide reaction. This reaction is carried out at low pH‑values which causes problems with certain proteins (Kim et al., 2013).
  • Name: p‑Acetylphenylalanine
  • Short: AcF
  • CAS: 122555-04-8
  • MW: 207,23 g mol-1
  • Storage: -20 °C
  • Source: abcr
  • Prize: 1g - £509.00
  • Function: Ketone group for hydrazide reaction

Figure 3: Structure of AcF
p-Acetylphenylalanine (AcF).

Foerster Resonance Energy Transfer (FRET)

Foerster Resonance Energy Transfer or Fluorescence Energy Transfer, short FRET, describes an energy transfer between two chromophores. During this process the donor chromophore is excited by light of a certain wavelength and transfers the energy to the acceptor chromophore if they are within a certain distance to each other. In biochemistry, FRET is mostly used as measurement tool with the help of fluorescent dyes. Using FRET, the measuring of distances from 1 to 10 nm is possible (Brustad et al., 2006). The FRET process is shown in Figure 4.

Figure 4: Animations of a FRET fluorophore pair
Animation of the distance dependent energy transfer of two fluorophores.

The FRET efficiency (E) is used to estimate the intramolecular distance of molecules.
E=[1+(r/R0)6)]-1

E FRET efficiency
r intermolecular distance
R0 Foerster distance for a given dye pair

Cyanin 3 and Cyanin 5

Cyanin 3 (Cy3) in combination with Cyanin 5 (Cy5) is a chromophore pair which is suitable for FRET measurements. Cy3 operates as the donor dye and Cy5 as the acceptor dye. The extinction and emission spectra of both chromophores is shown in Figure 5 (Kim et al., 2013).

Figure 5: Spectra of the fluorophore pair
Extinction and emission spectra of Cy3 and Cy5.

For the labeling of the noncanonical amino acids with these chromophores a functional group is required to build a covalent bond in chemical conjugation. PrK could be labeled with Cy3‑azide and AcF with Cy5‑hydrazide. Both chromophores are relatively advantageously priced in comparison to other chromophore pairs and commercially available from Lumiprobe.

Prion Detection Assay

Prions

Prions are proteins that could infect other proteins to change their conformation. This is often causing a loss of function and aggregation of these proteins. Prions are the cause for diseases like transmissible spongiform encephalopathies (TSEs), neurodegenerative disorders that effect humans and animals (Wickner et al., 2015).

Sup35

Sup35 is a yeast translation termination factor from Saccharomyces cerevisiae. The prion form of Sup35 is known to form amyloids consisting of beta-sheet rich protein aggregates with beta-strands perpendicular to the long axis of the filament. The domain responsible for the conformational change is the NM region. This region of the protein contains two different sections. The N‑section (amino acids 1‑124) forms the major part of the amyloid core that that directs the protein into the prion form. The M-section (amino acids 124‑250) is highly charged and provides the solubility to the native form of Sup35. In the prion form the M region changes its conformation to a beta‑sheet rich conformation, while the N‑section stays nearly unchanged in its conformation (Mukhopadhyay et al., 2007; Wickner et al., 2015).

References

Brustad, E. M., Lembke, E. A., Schultz, P. G., Dentz, A. A.(2008). A General and Efficient Method for the Site-Specific Dual-Labeling of Proteins for Single Molecule Fluorescence Resonance Energy Transfer. American Chemical Society. 130: 17664-17665..

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