Difference between revisions of "Part:BBa K1598002:Experience"

(→‎Squirrel-CHN-II 2023)
(→‎Squirrel-CHN-II 2023)
 
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<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-1.png" width="80%"></html>
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-1.png" width="80%"></html>
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Results for in silico binding affinity prediction:
  
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-2.png" width="80%"></html>
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-2.png" width="80%"></html>
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The zebrafish TPH would hypothetically mediate the highest efficiency of tryptophan hydrolysis among the four selected TPHs. Our wet lab experiments and results would, furthermore, help us identify the most potent TPH enzyme to be produced in E. coli expression and used for the final product.
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In vitro enzyme activity testing:
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To measure the HTP activity, we followed the protocol listed in this part by team UCL in 2015. In the protocol, a continuous fluorometric assay for HTP activity based on the different spectral characteristics of tryptophan and 5­hydroxytryptophan is presented.
  
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-3.png" width="80%"></html>
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-3.png" width="80%"></html>
 +
 +
Results for in vitro enzyme activity testing:
  
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-4.png" width="80%"></html>
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-4.png" width="80%"></html>
  
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-5.png" width="80%"></html>
 
<html><img src="https://static.igem.wiki/teams/5009/wiki/basic-parts/homo-tph/homo-tph-5.png" width="80%"></html>
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Our wet lab experiments and results fit our in silico prediction of HTP activity and show that the zebrafish TPH has the highest efficiency of tryptophan hydrolysis among the four selected TPHs. Therefore, we will choose this strain of HTP in our final product.
 +
 +
Hence, we also submitted a new basic part ( BBa_K5009001 ) for the TPH origin from zebrafish.
 +
 +
More about our design, visit: https://2023.igem.wiki/squirrel-chn-ii/engineering
  
 
===User Reviews===
 
===User Reviews===

Latest revision as of 01:03, 12 October 2023


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K1598002

Squirrel-CHN-II 2023

To better understand the TPH activity in the intestine, we decided to use a hybrid of in silico and in vivo experiments to investigate the TPH activity. The tryptophan hydroxylases (TPH) from human, as well as from mice, zebrafish, and rabbits have been selected and analyzed for their catalytic efficiency in the rate-limiting step of producing serotonin. By predicting the binding affinity of the TPHs to the tryptophan molecule we could predict the catalytic effectiveness of the enzyme selected.

In silico binding affinity prediction: The full-length 3D structures of the four TPHs from human, mouse, zebrafish, and rabbit are acquired as the PDB files from the uniport database under the following entry numbers: P17752; P09810; Q6PBX4; P17290 for each host organism respectively. For entry numbers P09810, Q6PBX4, and P17290, the known x-ray/NMR structures of the proteins are missing. Instead, the Alphafold predicted full-length structure of the proteins was selected for further analysis.

Results for in silico binding affinity prediction:

The zebrafish TPH would hypothetically mediate the highest efficiency of tryptophan hydrolysis among the four selected TPHs. Our wet lab experiments and results would, furthermore, help us identify the most potent TPH enzyme to be produced in E. coli expression and used for the final product.

In vitro enzyme activity testing: To measure the HTP activity, we followed the protocol listed in this part by team UCL in 2015. In the protocol, a continuous fluorometric assay for HTP activity based on the different spectral characteristics of tryptophan and 5­hydroxytryptophan is presented.

Results for in vitro enzyme activity testing:

Our wet lab experiments and results fit our in silico prediction of HTP activity and show that the zebrafish TPH has the highest efficiency of tryptophan hydrolysis among the four selected TPHs. Therefore, we will choose this strain of HTP in our final product.

Hence, we also submitted a new basic part ( BBa_K5009001 ) for the TPH origin from zebrafish.

More about our design, visit: https://2023.igem.wiki/squirrel-chn-ii/engineering

User Reviews

UNIQ0651af5e2c773f65-partinfo-00000005-QINU UNIQ0651af5e2c773f65-partinfo-00000006-QINU