Difference between revisions of "Part:BBa K2065001"

 
 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2065001 short</partinfo>
 
<partinfo>BBa_K2065001 short</partinfo>
  
−
CT52 is linked to mNeonGreen by a flexible GGS-10 linker to make sure the mNeonGreen is able to move towards other bound proteins. This insert is placed into a pET28a vector and  
+
This BioBrick is a coding sequence for the CT52 protein, attached to the mNeonGreen protein with a GGS10 linker in between. Because CT52 has a binding interaction for the T14-3-3 scaffold protein under influence of the small molecule fusicoccin, it can be used for assembly of proteins on this scaffold protein. mNeonGreen is a fluorescent protein and together with CT52-SmallBit and CT52-LargeBit it can be used for a BRET assay on a tetrameric T14-3-3 scaffold protein.
−
expressed by the E. Coli BL21 (DE3) bacteria.
+
 
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The part is used for BRET assays in the tetrameric scaffold together with the CT52-SsNL and CT52-LsNL. mNeonGreen-CT52 will be the acceptor that changes the wavelength of the light emitted by NanoLuc to a wavelength of 517 nm.
+
 
−
The sequence of our CT52-mNeonGreen has been verified by Starseq. It contains the prefix and suffix with  
+
==Design of the construct==
−
the correct restriction sites (EcoRI, XbaI, SpeI and PstI). mNeonGreen-CT52 is 956 bp long.
+
This parts is constructed of three subparts; CT52, a GGS10 linker and the fluorescent protein mNeonGreen. It has a molecular weight of 38 kDa. CT52 is the name for the isolated last 52 C-terminal amino acids of the plant plasma H+-ATPase PMA2 [1]. The N-terminus of CT52 is connected to a flexible GGS10 linker. This linker consists of a ten times repeating Glycine-Glycine-Serine amino acid sequence. mNeonGreen is a yellow-green fluorescent protein derived from a fluorescent protein from the Cephalochordate Branchiostoma Lanceolatum. For a fluorescence measurement, the mNeonGreen fluorophore can be excitated with a laser with a wavelength of 480 nm and read out at 517 nm. [2]
 +
 
 +
==Usage==
 +
These three subparts were inserted in a pET28a vector for protein expression, and subsequently used for an in vitro BRET assay. This BRET assay tests the ability of the tetrameric variant of the T14-3-3 scaffold protein to assemble four different proteins.
 +
 +
Because the free C-terminus of CT52 has a strong binding affinity with the T14-3-3 scaffold from the Nicotiana plumbaginifolia (Tobacco plant) and the N-terminus can be bound to another protein, CT52 was used to test the activity of the heterotetrameric T14-3-3 scaffold protein. This heterotetrameric scaffold can bind four different proteins at the same time. Therefore, three mutation sets were designed (with the Rosetta Software package) to create orthogonal bindings between T14-3-3 and CT52. The fourth binding pocket is the wildtype pocket. For more information about the designing of the mutation sets for these new binding pockets, visit our wiki (link naar het Rosetta stuk)
 +
 
 +
For this BRET assay, the CT52-mNeongreen as well as CT52-LargeBit and CT52-SmallBit were assembled on the T14-3-3 scaffold protein. CT52-mNeonGreen will be the acceptor that changes the wavelength of the light emitted by NanoLuc to a wavelength of 517 nm. This system is visible in figure 1.
 +
'[[File:T--TU-Eindhoven--BRETbb.png]]
 +
<br>
 +
''Figure 1: Schematic representaton of the BRET system with tetrameric T14-3-3 scaffold protein and the NanoBiT system linked to CT52''
 +
 
 +
==Sequence==
 +
The sequence of our CT52-mNeonGreen has been verified by StarSeq. It contains the prefix and suffix with the correct restriction sites (EcoRI, XbaI, SpeI and PstI). CT52-mNeonGreen is 956 bp long.  
 +
 
 +
[[File:T--TU-Eindhoven--mNeonGreenSnap.png]]
 +
<br>
 +
''Figure 2: Snapgene map of BBa_K2065001''
 +
 
 +
 
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
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<partinfo>BBa_K2065001 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K2065001 SequenceAndFeatures</partinfo>
  
 +
==Fluorescence confirmation==
 +
The construct on which CT52-mNeonGreen was planned to be tested was created on DNA level but due to time limitations this construct was not expressed. This means mNeonGreen-CT52 has not been characterized yet.
 +
 +
===mNeonGreen-CT52===
 +
 +
<table>
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<tr>
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<th style="height:40px;" colspan="4"> Protein Specifications</th>
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</tr>
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<tr>
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<td style="font-weight:bold;" rowspan="6">General Information</td>
 +
<td colspan="2">Number of amino acids</td>
 +
<td> 344</td>
 +
</tr>
 +
<tr>
 +
<td colspan="2">Molecular weight</td>
 +
<td> 37684</td>
 +
</tr>
 +
<tr>
 +
<td colspan="2">Theoretical pi</td>
 +
<td> 5.23</td>
 +
</tr>
 +
<tr>
 +
<td colspan="2">Extinction coefficient</td>
 +
<td> 27555</td>
 +
</tr>
 +
<tr>
 +
<td colspan="2">Formula</td>
 +
<td> C<sub>1643</sub>H<sub>2521</sub>N<sub>449</sub>O<sub>544</sub>S<sub>13</sub></td>
 +
</tr>
 +
<tr>
 +
<td colspan="2">Total numbers of atons</td>
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<td> 45840 </td>
 +
</tr>
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<tr>
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<td style="font-weight:bold;" rowspan="40">Amino Acid Composition</td>
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<td style="font-weight:bold;">Amino Acid</td>
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<td style="font-weight:bold;">Frequency</td>
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<td style="font-weight:bold;">Percentage(%)</td>
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</tr>
 +
<tr>
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<td>Ala(A)</td>
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<td>18</td>
 +
<td>5.2</td>
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</tr>
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<tr>
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<td>Arg(R</td>
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<td>1</td>
 +
<td>3.2</td>
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</tr>
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<tr>
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<td>Asn(N)</td>
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<td>15</td>
 +
<td>3.3</td>
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</tr>
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<tr>
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<td>Asp(D)</td>
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<td>15</td>
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<td>3.3</td>
 +
</tr>
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<tr>
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<td>Cys(C)</td>
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<td>1</td>
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<td>0.3</td>
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</tr>
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<tr>
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<td>Gln(Q)</td>
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<td>13</td>
 +
<td>3.8</td>
 +
</tr>
 +
<tr>
 +
<td>Glu(E)</td>
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<td>31</td>
 +
<td>9.0</td>
 +
</tr>
 +
<tr>
 +
<td>Gly(G)</td>
 +
<td>44</td>
 +
<td>12.8</td>
 +
</tr>
 +
<tr>
 +
<td>His(H)</td>
 +
<td>9</td>
 +
<td>2.6</td>
 +
</tr>
 +
<tr>
 +
<td>Ile(I)</td>
 +
<td>11</td>
 +
<td>3.2</td>
 +
</tr>
 +
<tr>
 +
<td>Leu(L)</td>
 +
<td>20</td>
 +
<td>5.8</td>
 +
</tr>
 +
<tr>
 +
<td>Lys(K)</td>
 +
<td>22</td>
 +
<td>6.4</td>
 +
</tr>
 +
<tr>
 +
<td>Met(M)</td>
 +
<td>12</td>
 +
<td>3.5</td>
 +
</tr>
 +
<tr>
 +
<td>Phe(F)</td>
 +
<td>13</td>
 +
<td>3.8</td>
 +
</tr>
 +
<tr>
 +
<td>Pro(P)</td>
 +
<td>12</td>
 +
<td>3.5</td>
 +
</tr>
 +
<tr>
 +
<td>Ser(S)</td>
 +
<td>27</td>
 +
<td>7.8</td>
 +
</tr>
 +
<tr>
 +
<td>Thr(T)</td>
 +
<td>36</td>
 +
<td>10.5</td>
 +
</tr>
 +
<tr>
 +
<td>Trp(W)</td>
 +
<td>4</td>
 +
<td>1.2</td>
 +
</tr>
 +
<tr>
 +
<td>Tyr(T)</td>
 +
<td>16</td>
 +
<td>4.7</td>
 +
</tr>
 +
<tr>
 +
<td>Val(V)</td>
 +
<td>14</td>
 +
<td>4.1</td>
 +
</tr>
 +
<tr>
 +
<td>Pyl(O)</td>
 +
<td>0</td>
 +
<td>0.0</td>
 +
</tr>
 +
<tr>
 +
<td>Sec(U)</td>
 +
<td>0</td>
 +
<td>0.0</td>
 +
</tr>
 +
</table>
 +
 +
 +
==References==
 +
 +
[1] - Svennelid, F., Olsson, A., Piotrowski, M., Rosenquist, M., Ottman, C., Larsson, C.& Sommarin, M. (1999). Phosphorylation of Thr-948 at the C terminus of the plasma membrane H+-ATPase creates a binding site for the regulatory 14-3-3 protein. The Plant Cell, 11(12), 2379-2391.
  
 +
[2] - N.C. Shaner et al,͞A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum.,Nature Methods, vol. 10, no. 5, pp. 407-409, Mar. 2013.
 +
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K2065001 parameters</partinfo>
 
<partinfo>BBa_K2065001 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 16:31, 19 October 2016

CT52-mNeonGreen

This BioBrick is a coding sequence for the CT52 protein, attached to the mNeonGreen protein with a GGS10 linker in between. Because CT52 has a binding interaction for the T14-3-3 scaffold protein under influence of the small molecule fusicoccin, it can be used for assembly of proteins on this scaffold protein. mNeonGreen is a fluorescent protein and together with CT52-SmallBit and CT52-LargeBit it can be used for a BRET assay on a tetrameric T14-3-3 scaffold protein.


Design of the construct

This parts is constructed of three subparts; CT52, a GGS10 linker and the fluorescent protein mNeonGreen. It has a molecular weight of 38 kDa. CT52 is the name for the isolated last 52 C-terminal amino acids of the plant plasma H+-ATPase PMA2 [1]. The N-terminus of CT52 is connected to a flexible GGS10 linker. This linker consists of a ten times repeating Glycine-Glycine-Serine amino acid sequence. mNeonGreen is a yellow-green fluorescent protein derived from a fluorescent protein from the Cephalochordate Branchiostoma Lanceolatum. For a fluorescence measurement, the mNeonGreen fluorophore can be excitated with a laser with a wavelength of 480 nm and read out at 517 nm. [2]

Usage

These three subparts were inserted in a pET28a vector for protein expression, and subsequently used for an in vitro BRET assay. This BRET assay tests the ability of the tetrameric variant of the T14-3-3 scaffold protein to assemble four different proteins.

Because the free C-terminus of CT52 has a strong binding affinity with the T14-3-3 scaffold from the Nicotiana plumbaginifolia (Tobacco plant) and the N-terminus can be bound to another protein, CT52 was used to test the activity of the heterotetrameric T14-3-3 scaffold protein. This heterotetrameric scaffold can bind four different proteins at the same time. Therefore, three mutation sets were designed (with the Rosetta Software package) to create orthogonal bindings between T14-3-3 and CT52. The fourth binding pocket is the wildtype pocket. For more information about the designing of the mutation sets for these new binding pockets, visit our wiki (link naar het Rosetta stuk)

For this BRET assay, the CT52-mNeongreen as well as CT52-LargeBit and CT52-SmallBit were assembled on the T14-3-3 scaffold protein. CT52-mNeonGreen will be the acceptor that changes the wavelength of the light emitted by NanoLuc to a wavelength of 517 nm. This system is visible in figure 1. 'T--TU-Eindhoven--BRETbb.png
Figure 1: Schematic representaton of the BRET system with tetrameric T14-3-3 scaffold protein and the NanoBiT system linked to CT52

Sequence

The sequence of our CT52-mNeonGreen has been verified by StarSeq. It contains the prefix and suffix with the correct restriction sites (EcoRI, XbaI, SpeI and PstI). CT52-mNeonGreen is 956 bp long.

T--TU-Eindhoven--mNeonGreenSnap.png
Figure 2: Snapgene map of BBa_K2065001


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 964
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Fluorescence confirmation

The construct on which CT52-mNeonGreen was planned to be tested was created on DNA level but due to time limitations this construct was not expressed. This means mNeonGreen-CT52 has not been characterized yet.

mNeonGreen-CT52

Protein Specifications
General Information Number of amino acids 344
Molecular weight 37684
Theoretical pi 5.23
Extinction coefficient 27555
Formula C1643H2521N449O544S13
Total numbers of atons 45840
Amino Acid Composition Amino Acid Frequency Percentage(%)
Ala(A) 18 5.2
Arg(R 1 3.2
Asn(N) 15 3.3
Asp(D) 15 3.3
Cys(C) 1 0.3
Gln(Q) 13 3.8
Glu(E) 31 9.0
Gly(G) 44 12.8
His(H) 9 2.6
Ile(I) 11 3.2
Leu(L) 20 5.8
Lys(K) 22 6.4
Met(M) 12 3.5
Phe(F) 13 3.8
Pro(P) 12 3.5
Ser(S) 27 7.8
Thr(T) 36 10.5
Trp(W) 4 1.2
Tyr(T) 16 4.7
Val(V) 14 4.1
Pyl(O) 0 0.0
Sec(U) 0 0.0


References

[1] - Svennelid, F., Olsson, A., Piotrowski, M., Rosenquist, M., Ottman, C., Larsson, C.& Sommarin, M. (1999). Phosphorylation of Thr-948 at the C terminus of the plasma membrane H+-ATPase creates a binding site for the regulatory 14-3-3 protein. The Plant Cell, 11(12), 2379-2391.

[2] - N.C. Shaner et al,͞A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum.,Nature Methods, vol. 10, no. 5, pp. 407-409, Mar. 2013.