Team:Shenzhen/Result/YAO.Factory
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<div id="media">{{:Team:Shenzhen/Temp/media_result_yao_factory.htm}}</div> | <div id="media">{{:Team:Shenzhen/Temp/media_result_yao_factory.htm}}</div> | ||
- | <div id="intro">[[File:yao.032-001.jpg]] | + | <div id="intro"> [[File:yao.032-001.jpg]] |
</div> | </div> | ||
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<ul><p>The rate expression is defined as</p></ul> | <ul><p>The rate expression is defined as</p></ul> | ||
<ul><p>[[File:Eqn34.jpg]]</p></ul> | <ul><p>[[File:Eqn34.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 1. Parameters for acetoacetyl-CoA thiolase</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<ul><p>The rate expression is defined as</p></ul> | <ul><p>The rate expression is defined as</p></ul> | ||
<ul><p>[[File:Eqn36.jpg]]</p></ul> | <ul><p>[[File:Eqn36.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 2. Parameters for 3-hydroxy-3-methylglutaryl coenzyme A synthase</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<td><p>Saccharomyces cerevisiae </p></td> | <td><p>Saccharomyces cerevisiae </p></td> | ||
</tr> | </tr> | ||
- | </table></ | + | </table></div> |
<ul><p>For HMG-CoA Reductase, the reaction is</p></ul> | <ul><p>For HMG-CoA Reductase, the reaction is</p></ul> | ||
<ul><p>[[File:Eqn37.jpg]]</p></ul> | <ul><p>[[File:Eqn37.jpg]]</p></ul> | ||
<ul><p>The rate expression is defined as</p></ul> | <ul><p>The rate expression is defined as</p></ul> | ||
<ul><p>[[File:Eqn38.jpg]]</p></ul> | <ul><p>[[File:Eqn38.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 3. Parameters for HMG-CoA Reductase</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<ul><p>The rate expression is defined as</p></ul> | <ul><p>The rate expression is defined as</p></ul> | ||
<ul><p>[[File:Eqn40.jpg]]</p></ul> | <ul><p>[[File:Eqn40.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 4. Parameters for mevalonate kinase </p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<td><p>Enterococcus faecalis</p></td> | <td><p>Enterococcus faecalis</p></td> | ||
</tr> | </tr> | ||
- | </table></ | + | </table></div> |
<ul><p>For phosphomevalonate kinase, the reference reaction is</p></ul> | <ul><p>For phosphomevalonate kinase, the reference reaction is</p></ul> | ||
<ul><p>[[File:Eqn41.jpg]]</p></ul> | <ul><p>[[File:Eqn41.jpg]]</p></ul> | ||
<ul><p>The rate expression is defined as </p></ul> | <ul><p>The rate expression is defined as </p></ul> | ||
<ul><p>[[File:Eqn42.jpg]]</p></ul> | <ul><p>[[File:Eqn42.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 5. Parameters for phosphomevalonate kinase</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<ul><p>The rate expression is defined as </p></ul> | <ul><p>The rate expression is defined as </p></ul> | ||
<ul><p>[[File:Eqn44.jpg]]</p></ul> | <ul><p>[[File:Eqn44.jpg]]</p></ul> | ||
- | < | + | <div class="figurep"><ul><p>Table 6. Parameters of mevalonate pyrophosphate decarboxylase</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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</table></div> | </table></div> | ||
<ul><p>For isopentenyl diphosphate:dimethylallyl diphosphate isomerase, the reaction is</p></ul> | <ul><p>For isopentenyl diphosphate:dimethylallyl diphosphate isomerase, the reaction is</p></ul> | ||
- | |||
- | |||
<ul><p>[[File:Eqn46.jpg]]</p></ul> | <ul><p>[[File:Eqn46.jpg]]</p></ul> | ||
- | < | + | <ul><p>The rate expression is defined as</p></ul> |
+ | <ul><p>[[File:Eqn47.jpg]]</p></ul> | ||
+ | <div class="figurep"><ul><p>Table 7.</p></ul> | ||
<table> | <table> | ||
<tr> | <tr> | ||
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</table></div> | </table></div> | ||
<ul><p>For farnesyl diphosphate synthase, the first reaction is:</p></ul> | <ul><p>For farnesyl diphosphate synthase, the first reaction is:</p></ul> | ||
- | <ul><p>[[File: | + | <ul><p>[[File:Eqn48.jpg]]</p></ul> |
<ul><p>The rate expression is defined as</p></ul> | <ul><p>The rate expression is defined as</p></ul> | ||
- | <ul><p>[[File: | + | <ul><p>[[File:Eqn49.jpg]]</p></ul> |
<ul><p>The second reaction is</p></ul> | <ul><p>The second reaction is</p></ul> | ||
- | <ul><p>[[File: | + | <ul><p>[[File:Eqn50.jpg]]</p></ul> |
<ul><p>The rate expression is</p></ul> | <ul><p>The rate expression is</p></ul> | ||
- | <ul><p>[[File: | + | <ul><p>[[File:Eqn51.jpg]]</p></ul> |
- | < | + | <div class="figurep"><ul><p>Table 7. Parameters for the ERG20</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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</tr> | </tr> | ||
</table></div> | </table></div> | ||
- | < | + | <div class="figurep"><ul><p>Table 8. The turnover rate for each enzyme</p></ul> |
<table> | <table> | ||
<tr> | <tr> | ||
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<div class="context"> | <div class="context"> | ||
<h5>Result</h5> | <h5>Result</h5> | ||
- | <ul><p> Our Yao clustered the enzymes in a small space, so that the concentration of enzymes in YAO will be higher than in cytoplasm. We assume that the volume of YAO is 1/10000 of that of cell, and a cell often contains 20 YAOs. Thus the concentrations of enzymes in YAO should be 500 times of that in cytoplasm. However, the transported rate of enzymes with signal peptides should be considered. We let it range from 0.002 to 1, thus ratio of concentrations of enzymes between YAO and cytoplasm range from 0 to 500. We then plot the concentration of IPP, GPP and FPP as a function of time at different concentration of enzymes. We can see from the plot that the production of IPP, GPP and FPP in a certain period of time after the beginning of the reactions increase dramatically as the concentrations of enzymes increase.</p></ul> | + | <ul><p> Our Yao clustered the enzymes in a small space, so that the concentration of enzymes in YAO will be higher than in cytoplasm. We assume that the volume of YAO is 1/10000 of that of cell, and a cell often contains 20 YAOs. Thus the concentrations of enzymes in YAO should be 500 times of that in cytoplasm. However, the transported rate of enzymes with signal peptides should be considered. We let it range from 0.002 to 1, thus ratio of concentrations of enzymes between YAO and cytoplasm range from 0 to 500. </p></ul> |
- | <ul><p> As the concentrations of products are increasing, need for ATP and NADPH also increase. The concentrations of NADPH and ATP will limit the produce of IPP, GPP and FPP. We then let the constant concentrations of NADPH and ATP range from 0 to maximum to see their affects on production. Our results show that concentrations of both ATP and NADPH do not have significant affects on production at the beginning of the reactions.</p></ul> | + | <ul><p> We then plot the concentration of IPP, GPP and FPP as a function of time at different concentration of enzymes. </p></ul> |
+ | <ul><div class="figurep"> | ||
+ | [[File:result_yao_factory_p1.jpg]] | ||
+ | <p>Figure 1. Production of IPP at different concentrations of enzymes.</p></div></ul> | ||
+ | <ul><div class="figurep"> | ||
+ | [[File:result_yao_factory_p2.jpg]] | ||
+ | <p>Figure 2. Production of GPP at different concentrations of enzymes.</p></div></ul> | ||
+ | <ul><div class="figurep"> | ||
+ | [[File:result_yao_factory_p3.jpg]] | ||
+ | <p>Figure 3. Production of FPP at different concentrations of enzymes.</p></div></ul> | ||
+ | <ul><p> We can see from the plot that the production of IPP, GPP and FPP in a certain period of time after the beginning of the reactions increase dramatically as the concentrations of enzymes increase.</p></ul> | ||
+ | <ul><p> As the concentrations of products are increasing, need for ATP and NADPH also increase. The concentrations of NADPH and ATP will limit the produce of IPP, GPP and FPP. We then let the constant concentrations of NADPH and ATP range from 0 to maximum to see their affects on production. </p></ul> | ||
+ | <ul><div class="figurep"> | ||
+ | [[File:result_yao_factory_p4.jpg]] | ||
+ | <p>Figure 4. Production of IPP at different concentrations of NADPH.</p></div></ul> | ||
+ | <ul><div class="figurep"> | ||
+ | [[File:result_yao_factory_p5.jpg]] | ||
+ | <p>Figure 5. Production of IPP at different concentrations of ATP.</p></div></ul> | ||
+ | <ul><p> Our results show that concentrations of both ATP and NADPH do not have significant affects on production at the beginning of the reactions.</p></ul> | ||
</div> | </div> | ||
<div class="context"> | <div class="context"> | ||
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<ul><p>[4]Middleton, B., The kinetic mechanism of 3-hydroxy-3-methylglutaryl-coenzyme A synthase from baker's yeast. Biochem J, 1972. 126(1): p. 35-47. </p></ul> | <ul><p>[4]Middleton, B., The kinetic mechanism of 3-hydroxy-3-methylglutaryl-coenzyme A synthase from baker's yeast. Biochem J, 1972. 126(1): p. 35-47. </p></ul> | ||
<ul><p>[5] Voynova, N.E., S.E. Rios, and H.M. Miziorko, Staphylococcus aureus mevalonate kinase: isolation and characterization of an enzyme of the isoprenoid biosynthetic pathway. J Bacteriol, 2004. 186(1): p. 61-7. </p></ul> | <ul><p>[5] Voynova, N.E., S.E. Rios, and H.M. Miziorko, Staphylococcus aureus mevalonate kinase: isolation and characterization of an enzyme of the isoprenoid biosynthetic pathway. J Bacteriol, 2004. 186(1): p. 61-7. </p></ul> | ||
- | <ul><p>[6] Scheer, Maurice. BRENDA. 2011. | + | <ul><p>[6] Scheer, Maurice. BRENDA. 2011. http://www.brenda-enzymes.org/</p></ul> |
</div> | </div> | ||
</div> | </div> | ||
{{:Team:Shenzhen/Temp/gallery.htm}} | {{:Team:Shenzhen/Temp/gallery.htm}} |
Latest revision as of 17:15, 26 September 2012