Team:Peking/Modeling/Luminesensor/Orthogonality

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  <h3 id="title1">Orthogonal Test <i>in silico</i></h3>
  <h3 id="title1">Orthogonal Test <i>in silico</i></h3>
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To modularize the genetic system, our <i>Luminesensor</i> is expected to be bio-orthogonal with the origin system in bacteria. LexA, a natural element from the lactin-SOS system in bacteria may cause unexpected crosstalk. In order to remove this obstacle on the application prospects of our <i>Luminesensor</i>, we use LexA408 instead of the wild-type LexA. LexA408 and LexA are bio-orthogonal with each other since the sequence of the binding sites have variations (See <a href="/Team:Peking/Project/Luminesensor/Characterization" title="">Characterization</a>).
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Our <i>Luminesensor</i> is expected to be orthogonal to endogenous SOS pathway. In order to remove this obstacle on the application prospects of our <i>Luminesensor</i>, we used LexA408 instead of wild-type LexA DNA Binding domain. LexA408 and LexA are bio-orthogonal with each other since the sequence of the binding sites have variations (See <a href="/Team:Peking/Project/Luminesensor/Characterization#title2" title="">Project Luminesensor Characterization</a>).
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By adding several nodes into the network, we constructed modeling for orthogonality test:
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By adding several nodes into the network, we constructed modeling for orthogonality <i>in silica</i> simulation(Figure 1):
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   <img src="/wiki/images/2/2c/Peking2012_LuminesensorOrthogonal.png" alt="" style="width:500px;"/>
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   <img src="/wiki/images/2/2c/Peking2012_LuminesensorOrthogonal.png" alt="Figure 1" style="width:500px;"/>
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   <p class="description">Fig 5. Kinetic Network for Orthogonal Analysis</p>
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   <p class="description" style="text-align:center;">Figure 1. Kinetic Network for Orthogonal Analysis</p>
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  <p>where</p><ul><li>
  <p>where</p><ul><li>
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  <p class="description">Tab 2. Reaction Parameters for Orthogonal Test</p>
 
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   <img src="/wiki/images/7/7b/Peking2012_LuminesensorOrthogonalEffect.png" alt="" />
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   <img src="/wiki/images/7/7b/Peking2012_LuminesensorOrthogonalEffect.png" alt="Figure 11" />
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   <p class="description">Fig 6. Orthogonal Test Result.
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   <p class="description" style="text-align:center;">Figure 2. Orthogonality Simulation Result.
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The result shows that the contrast is highly related to the orthogonality. As our <i>Luminesensor</i> is orthogonal to the endogerous LexA system, our system still works well in bacteria with endogenous LexA (See <a href="/Team:Peking/Project/Luminesensor/Characterization" title="">Characterization</a>).
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The result(Figure 2) shows that the contrast is highly related to the orthogonality. As our <i>Luminesensor</i> is orthogonal to the endogerous LexA system, our system still works well in bacteria with endogenously expressed LexA (See <a href="/Team:Peking/Project/Luminesensor/Characterization#title2" title="">Project Luminesensor Characterization</a>).
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  <h3 id="title7">Referrence</h3>
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  <h3 id="title2">Reference</h3>
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  <ul class="refer"><li id="ref1">
  <ul class="refer"><li id="ref1">
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[1] Light Activation of the LOV Protein Vivid Generates a Rapidly Exchanging Dimer. B. D. Zoltowski etc. Biochemistry
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1. Zoltowski, B.D., Crane, B.R.(2008). Light Activation of the LOV Protein Vivid Generates a Rapidly Exchanging Dimer. <i>Biochemistry</i>, 47: 7012: 7019
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[2] LexA Repressor Forms Stable Dimers in Solution. R. Mohana-Borges etc. THE JOURNAL OF BIOLOGICAL CHEMISTRY
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2. Mohana-Borges, R., Pacheco, A.B., Sousa, F.J., Foguel, D., Almeida, D.F., and Silva, J.L. (2000). LexA repressor forms stable dimers in solution. The role of specific DNA in tightening protein-protein interactions. <i>J. Biol. Chem.</i>, 275: 4708: 4712
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  </li><li id="ref3">
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[3] Mechanism-based tuning of a LOV domain photoreceptor, Brian D. Zoltowski, etc. NATURE CHEMICAL BIOLOGY
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3. Zoltowski, B.D., Vaccaro, B., and Crane, B.R. (2009). Mechanism-based tuning of a LOV domain photoreceptor. <i>Nat. Chem. Biol.</i> 5: 827: 834
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</li><li id="ref4">
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[4] Protein Vivid Generates a Rapidly Exchanging Dimer, Brian D. Zoltowski, etc. BIOCHEMISTRY
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  </li><li id="ref5">
  </li><li id="ref5">
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[5] A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli, M. Dmitrova. etc. Springer-Verlag Mol Gen Genet
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4. Dmitrova, M., Younes-Cauet, G., Oertel-Buchheit, P., Porte, D., Schnarr, M., Granger-Schnarr, M.(1998) A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in <i>Escherichia coli.</i> <i>Mol. Gen. Genet.</i>, 257: 205: 212
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Latest revision as of 05:10, 26 October 2012

Orthogonal Test in silico

Our Luminesensor is expected to be orthogonal to endogenous SOS pathway. In order to remove this obstacle on the application prospects of our Luminesensor, we used LexA408 instead of wild-type LexA DNA Binding domain. LexA408 and LexA are bio-orthogonal with each other since the sequence of the binding sites have variations (See Project Luminesensor Characterization).
By adding several nodes into the network, we constructed modeling for orthogonality in silica simulation(Figure 1):

Figure 1

Figure 1. Kinetic Network for Orthogonal Analysis

where

  • L denotes Luminesensor
  • I denotes the inner wild LexA
  • DL denotes the specific DNA binding site to Luminesensor
  • DI denotes the specific DNA binding site to wild LexA

The parameters are estimated as following:

ParameterValueUnitDescription
k61.x10-4s-1dimered LexA releasing rate constant from non-specific binding site
K61.x10-2(n mol/L)-1dimered non-specific binding equilibrium constant
Figure 11

Figure 2. Orthogonality Simulation Result.

The result(Figure 2) shows that the contrast is highly related to the orthogonality. As our Luminesensor is orthogonal to the endogerous LexA system, our system still works well in bacteria with endogenously expressed LexA (See Project Luminesensor Characterization).

Reference

  • 1. Zoltowski, B.D., Crane, B.R.(2008). Light Activation of the LOV Protein Vivid Generates a Rapidly Exchanging Dimer. Biochemistry, 47: 7012: 7019
  • 2. Mohana-Borges, R., Pacheco, A.B., Sousa, F.J., Foguel, D., Almeida, D.F., and Silva, J.L. (2000). LexA repressor forms stable dimers in solution. The role of specific DNA in tightening protein-protein interactions. J. Biol. Chem., 275: 4708: 4712
  • 3. Zoltowski, B.D., Vaccaro, B., and Crane, B.R. (2009). Mechanism-based tuning of a LOV domain photoreceptor. Nat. Chem. Biol. 5: 827: 834
  • 4. Dmitrova, M., Younes-Cauet, G., Oertel-Buchheit, P., Porte, D., Schnarr, M., Granger-Schnarr, M.(1998) A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli. Mol. Gen. Genet., 257: 205: 212
  • Totop Totop

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