Difference between revisions of "Team:UC San Diego/Modeling/Kinetics"

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                  <h3>enzyme kinetics</h3>
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<h3>The Lux System</h3>
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The bacterial lux system is principally composed of five genes - LuxA, LuxB, LuxC, LuxD, and LuxE.  
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<center><a href="https://static.igem.org/mediawiki/2015/9/9f/UCSD_generallux.png" data-lightbox="lab2" data-title="In their host bacteria, the lux genes are not sequentially ordered, with A and B flanked by C, D, and E."><img width="700" src="https://static.igem.org/mediawiki/2015/9/9f/UCSD_generallux.png"></a></center>
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<center><i>In their host bacteria, the lux genes are not sequentially ordered, with A and B flanked by C, D, and E.</i></center>
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The proteins coded by these genes associate to form two enzymatic complexes, with LuxA+LuxB coding for luciferase itself and LuxCDE coding for a fatty acid reductase complex. This reductase complex serves to provide the substrates (fatty aldehydes) for the system’s bioluminescent reaction<sup>1</sup>. Catalyzed by luciferase, these aldehydes react with FMNH2 and oxygen, emitting a photon and producing a fatty acid, FMN, and water<sup>1</sup>. FMNH2 is then regenerated by a flavin reductase<sup>1</sup>.
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<center><a href="https://static.igem.org/mediawiki/2015/1/1a/UCSD_luciferase.png" data-lightbox="lab3" data-title="The alpha subunit of luciferase drives enzymatic activity, while the beta subunit offers structural support and stabilizes the alpha subunit as it undergoes conformational changes<sup>2</sup>."><img width="300" src="https://static.igem.org/mediawiki/2015/1/1a/UCSD_luciferase.png"></a></center>
  
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<center><i class="caption">The alpha subunit (blue) of luciferase drives enzymatic activity, while the beta subunit (red) offers structural support and stabilizes the alpha subunit as it undergoes conformational changes<sup>2</sup>.</i></center>
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To allow for continuous light output, the fatty acid reductase complex recycles the fatty acid product in the luciferase-catalyzed reaction and converts it to a the substrate aldehyde. LuxC, LuxD, and LuxE code for a reductase, transferase, and synthetase, respectively. Together, they associate into a complex consisting of four of each enzyme<sup>1</sup>.
  
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<center><a href="https://static.igem.org/mediawiki/2015/1/10/Fattyacidreductase.png" data-lightbox="lab3" data-title="Substrates are recruited by the transferase and moved to a synthetase-reductase complex. These associated enzymes produce a microenvironment that stabilizes reaction intermediates."><img width="700" src="https://static.igem.org/mediawiki/2015/1/10/Fattyacidreductase.png"></a></center>
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<center><i>Substrates are recruited by the transferase and moved to a synthetase-reductase complex. These associated enzymes produce a microenvironment that stabilizes reaction intermediates.</i></center>
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Because the luminescent yield of the system is based on the function of these two enzymatic complexes, modifying the protein levels of each enzyme allows us to control the system’s output.
 
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<h3>References</h3>
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[1] Meighen, Edward A. "Enzymes and genes from the lux operons of bioluminescent bacteria." Annual Reviews in Microbiology 42.1 (1988): 151-176. <br>
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[2] Meighen, E. A., Nicoli M. Z., and Hastings, J. W. “Functional Differences of the Nonidentical Subunits of Bacterial Luciferase, Properties of Hybrids of Native and Chemically Modified Bacterial Luciferase.” Biochemistry (2003)
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<h3>Results</h3>
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<p>PLOT</p>
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<p>TABLE</p>
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<p>DIAGRAM</p>
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<p>PLOT</p>
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<h3>Future Directions</h3>
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Revision as of 22:24, 18 September 2015

Background

The Lux System

The bacterial lux system is principally composed of five genes - LuxA, LuxB, LuxC, LuxD, and LuxE.

In their host bacteria, the lux genes are not sequentially ordered, with A and B flanked by C, D, and E.

The proteins coded by these genes associate to form two enzymatic complexes, with LuxA+LuxB coding for luciferase itself and LuxCDE coding for a fatty acid reductase complex. This reductase complex serves to provide the substrates (fatty aldehydes) for the system’s bioluminescent reaction1. Catalyzed by luciferase, these aldehydes react with FMNH2 and oxygen, emitting a photon and producing a fatty acid, FMN, and water1. FMNH2 is then regenerated by a flavin reductase1.

The alpha subunit (blue) of luciferase drives enzymatic activity, while the beta subunit (red) offers structural support and stabilizes the alpha subunit as it undergoes conformational changes2.

To allow for continuous light output, the fatty acid reductase complex recycles the fatty acid product in the luciferase-catalyzed reaction and converts it to a the substrate aldehyde. LuxC, LuxD, and LuxE code for a reductase, transferase, and synthetase, respectively. Together, they associate into a complex consisting of four of each enzyme1.


Substrates are recruited by the transferase and moved to a synthetase-reductase complex. These associated enzymes produce a microenvironment that stabilizes reaction intermediates.

Because the luminescent yield of the system is based on the function of these two enzymatic complexes, modifying the protein levels of each enzyme allows us to control the system’s output.

References

[1] Meighen, Edward A. "Enzymes and genes from the lux operons of bioluminescent bacteria." Annual Reviews in Microbiology 42.1 (1988): 151-176.
[2] Meighen, E. A., Nicoli M. Z., and Hastings, J. W. “Functional Differences of the Nonidentical Subunits of Bacterial Luciferase, Properties of Hybrids of Native and Chemically Modified Bacterial Luciferase.” Biochemistry (2003)