Team:UANL Mty-Mexico/Modelling/Parameters

From 2011.igem.org

(Difference between revisions)
Line 121: Line 121:
<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>             
-
    
+
   <p><b>Parameters</b></p>
 +
<p><b>Maximum transcription rates </b></p>
 +
<p><br></p>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr>
 +
      <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>
 +
<p><b></b><br></p>
 +
<p><b>Maximum Translation Rate</b></p>
 +
<p><br></p>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr>
 +
      <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>
 +
<p><b></b><br></p>
 +
<p><b>Dissociation Constants and Phosphorylation Rates</b></p>
 +
<p><br></p>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr>
 +
      <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>
 +
<p><b>Light-induced systems:</b></p>
 +
<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>
 +
<p><b>Quorum Sensing</b></p>
 +
<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>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tbody>
 +
    <tr>
 +
      <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>
 +
<p><br></p>
 +
<p><b>Degradation rates</b></p>
 +
<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><b>References:</b></p>
 +
<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, et al., (2004), Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR, Proc. NatL Acad. Sci. USA, Vol. 101, pp. 15833–15839. </li>
 +
  <li>Goryachev, AB, et al., (2005),  Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems, pp. 178-87.</li>
 +
  <li>Ackers, GK, et al., (1982), Quantitative model for gene regulation by A phage repressor, Proc. NatL Acad. Sci. USA, Vol. 79, pp. 1129-1133.</li>
 +
  <li>Srividhya and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44</li>
 +
  <li>Qin, L, et al., (2001), The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli, PNAS, Vol. 98, No. 3, pp. 908-913.</li>
 +
</ol>
 +
<p><br></p>
     </div>
     </div>
      
      

Revision as of 20:54, 28 September 2011

banner-main iGEM-logo
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, et al., (2004), Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR, Proc. NatL Acad. Sci. USA, Vol. 101, pp. 15833–15839.
  3. Goryachev, AB, et al., (2005), Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems, pp. 178-87.
  4. Ackers, GK, et al., (1982), Quantitative model for gene regulation by A phage repressor, Proc. NatL Acad. Sci. USA, Vol. 79, pp. 1129-1133.
  5. Srividhya and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44
  6. Qin, L, et al., (2001), The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli, PNAS, Vol. 98, No. 3, pp. 908-913.


OurSymbol

Team: UANL_Mty-Mexico

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