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

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<h3>Introduction</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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<h3>Chemical Reaction Network</h3>
  
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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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<p>ALDEHYDE SYNTH PATHWAY</p>
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<p>LIGHT PRODUCTION PATHWAY</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<h3>Modeling</h3>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>LIST OF ASSUMPTIONS</p>
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<p>SYSTEM OF EQUATIONS</p>
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<h3>Induction Curves and Parameter Sensitivity</h3>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>FIGURES</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>FIGURES</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<h3>Model Reduction</h3>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>FIGURE</p>
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<p>SYSTEM OF EQUATIONS</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<h3>Velocity Equations</h3>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>EQUATIONS</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>EQUATIONS</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<h3>Results</h3>
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<p>FIGURES</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<p>FIGURES</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
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<h3>Future Directions</h3>
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<p>Parameter Table</p>
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<p>Enzyme Table</p>
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<p>Cofactor Table</p>
  
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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>
 
<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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Revision as of 22:25, 18 September 2015

post image

Introduction

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Chemical Reaction Network

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ALDEHYDE SYNTH PATHWAY

LIGHT PRODUCTION PATHWAY

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Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.

Modeling

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LIST OF ASSUMPTIONS

SYSTEM OF EQUATIONS

Induction Curves and Parameter Sensitivity

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.

FIGURES

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FIGURES

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.

Model Reduction

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FIGURE

SYSTEM OF EQUATIONS

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Velocity Equations

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EQUATIONS

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EQUATIONS

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Results

FIGURES

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FIGURES

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.

Future Directions

Parameter Table

Enzyme Table

Cofactor Table

References

REFERENCES