Team:UANL Mty-Mexico/Modelling/Parameters
From 2011.igem.org
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- | + | <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 & 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](https://static.igem.org/mediawiki/igem.org/3/38/Notebook-3.jpg)
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:
- https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
- 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.
- 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.
- Ackers, GK, et al., (1982), Quantitative model for gene regulation by A phage repressor, Proc. NatL Acad. Sci. USA, Vol. 79, pp. 1129-1133.
- Srividhya and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44
- 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.