Team:UANL Mty-Mexico/Modelling/Parameters

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     <div id="leftColumn">
     <div id="leftColumn">
     <div id="ColorHeader">
     <div id="ColorHeader">
-
             Modelling
+
             Modelling: Parameters
     </div>
     </div>
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<div class="br2"></div><div class="br2"></div><div class="br2"></div>             
<div class="br2"></div><div class="br2"></div><div class="br2"></div>             
       </div>
       </div>
-
   
 
<div class="br"></div>
<div class="br"></div>
<div class="br"></div>
<div class="br"></div>
<div class="br"></div>             
<div class="br"></div>             
-
 
+
 
 +
<span class="subtitle"><a name="Transcription"></a>
 +
Maximum transcription rates </span>
 +
<p><br></p>
 +
<center>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr class="yellow">
 +
      <td valign="top">
 +
        <p>Gene</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Maximum Transcription Rate (molecules min<sup>.1</sup>)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Source</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>Red Photoreceptor</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>1.879194631</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>ompR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.857740586</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>mnt</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>14.58333333</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>tetR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>6.363636364</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>cI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.6</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>lacI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>3.723404255</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>cI434</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>6.278026906</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>lasI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>1.20E-01</p>
 +
        <p><br></p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>B</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>lasR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>2.88E-01</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>B</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>GFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.533596838</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>SBFP2</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.833333333</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>CFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.511811024</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>YFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.511811024</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>RFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>5.809128631</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
  </tbody>
 +
</table>
 +
</center>
 +
<p><b></b><br></p>
 +
<span class="subtitle"><a name="Translation"></a>
 +
Maximum Translation Rate</span>
 +
<p><br></p>
 +
<center>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr class="yellow">
 +
      <td valign="top">
 +
        <p>Protein</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Maximum Translation Rate (molecules min.1)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Source</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>Red Photoreceptor</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>3.22147651</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>OmpR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>10.041841</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>Mnt</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>25</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>TetR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>10.90909091</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>cI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.6</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>LacI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>6.382978723</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>cI434</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>10.76233184</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>LasI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.60E-01</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>B</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>LasR</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.60E-01</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>B</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>GFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.486166008</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>SBFP2</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>10</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>CFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.448818898</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>YFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.448818898</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>RFP</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>9.958506224</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
  </tbody>
 +
</table>
 +
</center>
 +
<p><b></b><br></p>
 +
<span class="subtitle"><a name="Dissociation"></a>
 +
Dissociation Constants and Phosphorylation Rates</span>
 +
<p><br></p>
 +
 
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr class="yellow">
 +
      <td colspan="7" valign="top">
 +
        <p>Transcription factors/DNA-binding molecules</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>Protein</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>Dissociation constant (nM)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Hill coefficient</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Source</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>CcaR-Phosphate</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>N/A</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>OmpR-pompC</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>31.4</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>Mnt</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>50</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>1</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>TetR</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>0.179</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>3</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>LacI</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>800</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>2</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>cI434</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>40</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>2</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td rowspan="2" valign="top">
 +
        <p>cI</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>O2 Binding (No cooperativity)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>77.60592</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>O2 Binding (With cooperativity)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>1.7599E-08</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td rowspan="2" valign="top">
 +
        <p>2</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A,D</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>O3 Binding (No cooperativity)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>77.60592</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>O3 Binding (With cooperativity)</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>2.3542E-07</p>
 +
        <p><br></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>A,D</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top">
 +
        <p>LasI-3-oxo-C12-HSL &amp; LasR</p>
 +
      </td>
 +
      <td colspan="4" valign="top">
 +
        <p>0.011</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>1</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
  </tbody>
 +
</table>
 +
<p><br></p>
 +
 
 +
<div id="header-project-column">
 +
<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
 +
          <a name="Light"></a>Light-induced systems
 +
<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
 +
      </div>
 +
<div class="br"></div>
 +
<div class="br"></div>
 +
<div class="br"></div>
 +
 
 +
 
 +
<p>The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:</p>
 +
<p>IMAGEN</p>
 +
<p>OmpR-P dephosphorylation rate (from Qin, L, et al., 2001, reference F): 17 min when red light is present / 56 min when far-red light is present.</p>
 +
 
 +
<span class="subtitle"><a name="Quorum"></a>Quorum Sensing
 +
</span>
 +
 
 +
<p>For simplicity just the parameters of the LasI/LasR quorum sensing system are shown, because they are supposed to be equivalent according to the used general Quorum Sensing model.</p>
 +
<p><br></p>
 +
<center>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr class="yellow">
 +
      <td colspan="3" valign="bottom">
 +
        <p>Quorum sensing</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Parameter</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>Constant</p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>Source</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Transcription of lasI</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>1.20E-01 molecules min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Translation of lasI</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>9.60E-01 molecules min<sup>.1</sup> </p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Degradation of lasI mRNA</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>3.60E-01 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Degradation of LasI </p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>3.00E-03 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Transcription of lasR</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>2.88E-01 molecules min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Translation of lasR</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>9.60E-01 molecules min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Degradation of lasR mRNA</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>3.60E-01 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Degradation of LasR</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>1.20E-02 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Enzymatic activity LasI</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>27 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Autoinductor diffusibility</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>2.40E+01 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Binding between LasR/3-oxo-C12-HSL</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>6.00E-03 molecules min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Dissociation of  LasR/3-oxo-C12-HSL</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>1.80E-01 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Dimerization LasR/3-oxo-C12-HSL</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>1.80E-03 molecules min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="bottom">
 +
        <p>Dissociation of the dimer</p>
 +
      </td>
 +
      <td valign="bottom">
 +
        <p>6.00E-01 min<sup>.1</sup></p>
 +
      </td>
 +
      <td valign="top">
 +
        <p>C</p>
 +
      </td>
 +
    </tr>
 +
  </tbody>
 +
</table>
 +
</center>
 +
<p><br></p>
 +
<span class="subtitle"><a name="Degradation"></a>
 +
Degradation rates </span>
 +
 
 +
<p>Following the recommendations of team Peking 2009, we set all mRNAs half-lives to 4.4 min and, supposing that all regulatory and reporter gene would have an LVG tag attached, all protein half-lives were set to 40 min, with the exception of phosphorylated OmpR, whose case is exposed on the last sections.</p>
 +
<p>Considering a cell division rate of 30 min, then, the degradation rates for mRNA are: 1/4.4 + 1/30 min, and the protein degradation rates are: 1/40 + 1/30 min.</p>
 +
<p><br></p>
 +
    <div id="header-project-column">
 +
<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
 +
          <a name="References"></a>References
 +
<div class="br2"></div><div class="br2"></div><div class="br2"></div>           
 +
      </div>
 +
<div class="br"></div>
 +
<div class="br"></div>
 +
<div class="br"></div>
 +
<ol>
 +
  <li><a href="https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a></li>
 +
  <li>Schuster M, Urbanowski L, Greenberg EP (2004) Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. <i>Proc Natl Acad Sci USA</i> <b>101</b>:15833–15839. </li>
 +
  <li>Goryachev AB,  Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. <i>Biosystems</i> <b>83</b>:178-87.</li>
 +
  <li>Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. <i>Proc Natl Acad Sci USA</i> <b>79</b>:1129-1133.</li>
 +
  <li>Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. <i>BMC Microbiology</i> <b>4</b>:44.</li>
 +
  <li>Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in <i>Escherichia coli</i>.  <i>Proc Natl Acad Sci USA</i><b> 98</b>:908-913.</li>
 +
</ol>
 +
<p><br></p>
     </div>
     </div>
      
      
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+
     <a href="#top" title="Go back to top"><img src="https://static.igem.org/mediawiki/igem.org/0/09/OurSymbol.png" width="200" height="160" alt="OurSymbol"></a>
      
      
  <div class="br"></div>
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     <div id="botonera">
     <div id="botonera">
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     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/The_Code">The Code</a></div>
+
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Transcription">Transcription</a></div>
-
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism">Mechanism</a></div>
+
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Translation">Translation</a></div>
-
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Circuit">Genetic Circuit</a></div>
+
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Dissociation">Dissociation</a></div>
-
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Applications">Applications</a></div>
+
     <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Light">Light induction</a></div>
 +
    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Quorum">Quorum Sensing</a></div>
 +
    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#Degradation">Degradation rates</a></div>
 +
    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters#References">References</a></div>
 +
 
    
    
     </div>
     </div>

Latest revision as of 17:18, 13 February 2012

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Team: UANL_Mty-Mexico
Team: UANL_Mty-Mexico
Modelling: Parameters
Parameters
Maximum transcription rates


Gene

Maximum Transcription Rate (molecules min.1)

Source

Red Photoreceptor

1.879194631

A

ompR

5.857740586

A

mnt

14.58333333

A

tetR

6.363636364

A

cI

5.6

A

lacI

3.723404255

A

cI434

6.278026906

A

lasI

1.20E-01

B

lasR

2.88E-01

B

GFP

5.533596838

A

SBFP2

5.833333333

A

CFP

5.511811024

A

YFP

5.511811024

A

RFP

5.809128631

A


Maximum Translation Rate


Protein

Maximum Translation Rate (molecules min.1)

Source

Red Photoreceptor

3.22147651

A

OmpR

10.041841

A

Mnt

25

A

TetR

10.90909091

A

cI

9.6

A

LacI

6.382978723

A

cI434

10.76233184

A

LasI

9.60E-01

B

LasR

9.60E-01

B

GFP

9.486166008

A

SBFP2

10

A

CFP

9.448818898

A

YFP

9.448818898

A

RFP

9.958506224

A


Dissociation Constants and Phosphorylation Rates


Transcription factors/DNA-binding molecules

Protein

Dissociation constant (nM)

Hill coefficient

Source

CcaR-Phosphate

N/A


A

OmpR-pompC

31.4


A

Mnt

50

1

A

TetR

0.179

3

A

LacI

800

2

A

cI434

40

2

A

cI

O2 Binding (No cooperativity)

77.60592

O2 Binding (With cooperativity)

1.7599E-08

2

A,D

O3 Binding (No cooperativity)

77.60592

O3 Binding (With cooperativity)

2.3542E-07

A,D

LasI-3-oxo-C12-HSL & LasR

0.011

1

C


Light-induced systems

The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:

IMAGEN

OmpR-P dephosphorylation rate (from Qin, L, et al., 2001, reference F): 17 min when red light is present / 56 min when far-red light is present.

Quorum Sensing

For simplicity just the parameters of the LasI/LasR quorum sensing system are shown, because they are supposed to be equivalent according to the used general Quorum Sensing model.


Quorum sensing

Parameter

Constant

Source

Transcription of lasI

1.20E-01 molecules min.1

C

Translation of lasI

9.60E-01 molecules min.1

C

Degradation of lasI mRNA

3.60E-01 min.1

C

Degradation of LasI

3.00E-03 min.1

C

Transcription of lasR

2.88E-01 molecules min.1

C

Translation of lasR

9.60E-01 molecules min.1

C

Degradation of lasR mRNA

3.60E-01 min.1

C

Degradation of LasR

1.20E-02 min.1

C

Enzymatic activity LasI

27 min.1

C

Autoinductor diffusibility

2.40E+01 min.1

C

Binding between LasR/3-oxo-C12-HSL

6.00E-03 molecules min.1

C

Dissociation of LasR/3-oxo-C12-HSL

1.80E-01 min.1

C

Dimerization LasR/3-oxo-C12-HSL

1.80E-03 molecules min.1

C

Dissociation of the dimer

6.00E-01 min.1

C


Degradation rates

Following the recommendations of team Peking 2009, we set all mRNAs half-lives to 4.4 min and, supposing that all regulatory and reporter gene would have an LVG tag attached, all protein half-lives were set to 40 min, with the exception of phosphorylated OmpR, whose case is exposed on the last sections.

Considering a cell division rate of 30 min, then, the degradation rates for mRNA are: 1/4.4 + 1/30 min, and the protein degradation rates are: 1/40 + 1/30 min.


References
  1. https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
  2. Schuster M, Urbanowski L, Greenberg EP (2004) Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. Proc Natl Acad Sci USA 101:15833–15839.
  3. Goryachev AB, Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems 83:178-87.
  4. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. Proc Natl Acad Sci USA 79:1129-1133.
  5. Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiology 4:44.
  6. Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli. Proc Natl Acad Sci USA 98:908-913.


OurSymbol

Team: UANL_Mty-Mexico

Retrieved from "http://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters"