Team:University of Ottawa/Modeling/Parameters

<html>
<p><font size="3" face="Calibri">Values in µM, min, and mL unless specified.</font></p>
<div align="left">

<table width="529" border="2" cellspacing="0">
<tr valign="top"><td><font size="2" face="Cambria">Parameter</font></td>
  <td><font size="2" face="Cambria">Value</font></td>
  <td><font size="2" face="Cambria">Source</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Population 
  and culture</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>n</sub></font></td>
  <td><font size="3" face="Cambria">3.85e-3</font></td>

  <td align="center"><font size="3" face="Cambria">[1] observed division rate</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">N<sub>max</sub></font></td>
  <td><font size="3" face="Cambria">1e8</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">V</font></td>
  <td><font size="3" face="Cambria">1e-11</font></td>

  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dil</sub></font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>IP 
  binding to receptor</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>assoc</sub></font></td>

  <td><font size="3" face="Cambria">5e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dissoc</sub></font></td>
  <td><font size="3" face="Cambria">4.55e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Synthesis 
  of CRE1, YPD1, SKN7 species</b></font></td></tr>

<tr valign="top"><td><font size="3" face="Cambria">k<sub>s1</sub></font></td>
  <td><font size="3" face="Cambria">6.16e-5</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>s2</sub></font></td>
  <td><font size="3" face="Cambria">6.00e-4</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>

<tr valign="top"><td><font size="3" face="Cambria">k<sub>s3</sub></font></td>
  <td><font size="3" face="Cambria">2.46e-4</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dimer</sub></font></td>
  <td><font size="3" face="Cambria">20</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>

<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Phosphorylation/Dephosphorylation 
  reactions</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>p1</sub></font></td>
  <td><font size="3" face="Cambria">0.1</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>p2</sub></font></td>
  <td><font size="3" face="Cambria">1243</font></td>

  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>p3</sub></font></td>
  <td><font size="3" face="Cambria">56</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>p-3</sub></font></td>
  <td><font size="3" face="Cambria">4.8</font></td>

  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dp1</sub></font></td>
  <td><font size="3" face="Cambria">5.33e-2</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dp3</sub></font></td>
  <td><font size="3" face="Cambria">2.89e-3</font></td>

  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dp3</sub></font></td>
  <td><font size="3" face="Cambria">4.80e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Decay 
  constants</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>d1</sub></font></td>

  <td><font size="3" face="Cambria">5.33e-2</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>d2</sub></font></td>
  <td><font size="3" face="Cambria">2.89e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>d3</sub></font></td>

  <td><font size="3" face="Cambria">4.80e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dip</sub></font></td>
  <td><font size="3" face="Cambria">5e-4</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dgfp</sub></font></td>

  <td><font size="3" face="Cambria">5.77e-3</font></td>
  <td align="center"><font size="3" face="Cambria">[1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dtet</sub></font></td>
  <td><font size="3" face="Cambria">3.85e-3</font></td>
  <td align="center"><font size="3" face="Cambria">Cell division rate (assumed stable)</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>dckx</sub></font></td>

  <td><font size="3" face="Cambria">&lt;=3.85e-3</font></td>
  <td align="center"><font size="3" face="Cambria">Cell division rate, or lower if diffusion 
  is significant.</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Basal 
  expression</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>bgfp</sub>, 
  k<sub>btet</sub>, k<sub>bckx</sub></font></td>
  <td><font size="3" face="Cambria">6e-6</font></td>

  <td align="center"><font size="3" face="Cambria">adapted from [1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>tdim</sub></font></td>
  <td><font size="3" face="Cambria">1e3</font></td>
  <td align="center"><font size="3" face="Cambria">arbitrary</font></td></tr>
<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>Induced 
  expression</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>gfp</sub></font></td>

  <td><font size="3" face="Cambria">6e-3</font></td>
  <td align="center"><font size="3" face="Cambria">adapted from [1]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>tet</sub></font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">-</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>ckx</sub></font></td>

  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">-</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">K<sub>g,</sub> K<sub>t, </sub>
  K<sub>c</sub></font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>

  <td align="center"><font size="3" face="Cambria" align="center">-</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">α<sub>g, </sub>
  α<sub>t</sub> α<sub>c</sub> </font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>

  <td align="center"><font size="3" face="Cambria">-</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">K<sub>i</sub></font></td>
  <td><font size="3" face="Cambria">5e-6</font></td>
  <td align="center"><font size="3" face="Cambria">K<sub>ass</sub> = 2e11 M<sup>-1</sup> 
  [2], [3]</font></td></tr>

<tr valign="top"><td><font size="3" face="Cambria">β</font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">-</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>ipt4</sub></font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">-</font></td></tr>

<tr valign="top"><td><font size="2" face="Cambria"><b>IPT4 enzyme kinetics</b></font></td></tr>
  
<tr valign="top"><td><font size="3" face="Cambria">k<sub>sip</sub></font></td>
  <td align="center"><font size="3" face="Cambria">varied</font></td>
  <td align="center"><font size="3" face="Cambria">-</font></td></tr>

<tr valign="top"><td colspan="3"><font size="2" face="Cambria"><b>CKX 
  enzyme kinetics</b></font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">K<sub>m</sub></font></td>
  <td><font size="3" face="Cambria">40 µM</font></td>
  <td align="center"><font size="3" face="Cambria">[4]</font></td></tr>
<tr valign="top"><td><font size="3" face="Cambria">k<sub>cat</sub></font></td>
  <td><font size="3" face="Cambria">0.5-1000 s<sup>-1</sup></font></td>

  <td align="center"><font size="3" face="Cambria">[5], [6]</font></td></tr>
</table>
</html>

='''References'''=

# Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555.
# Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369.
#Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104.	
# Schmulling T, Werner T, Riefler M, Krupkova E, Bartrina y Manns I (2003) Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. J Plant Res 116:241-252
# Laskey, J.G., P. Patterson, et al. (2003). "Rate enhancement of cytokinin oxidase/dehydrogenase using 2,6-dichloroindophenol as an electron acceptor." Plant Growth Regulation 40: 189–196.
# Frebortova, J., M.W. Fraaije, et al. (2004). "Catalytic reaction of cytokinin dehydrogenase: preference for quinones as electron acceptors." Biochem. J. 380: 121–130. 



Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865.