Parameters
Basal parameter values for the wild-type (WT) cell cycle. All parameters that start with 'k' are rate constants (min-1) and all other parameters are dimensionless.
Basal parameter values for the wild-type stalked-cell division cycle. | |||
A. Rate constants, units = min-1 | |||
ks,CtrA-P1 = 0.0083, ks,CtrA-P2 = 0.073 |
(Domian et al., 1999; Grunenfelder et al., 2001; Holtzendorff et al., 2004) |
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kd,CtrA1 = 0.002 |
(Hung and Shapiro, 2002) |
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kd,CtrA2 = 0.15 |
(Domian et al., 1997) |
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ks,GcrA = 0.045 |
(Holtzendorff et al., 2004) |
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kd,GcrA = 0.022 |
(Collier et al., 2006; Holtzendorff et al., 2004) |
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ks,DnaA = 0.0165 |
(Zweiger and Shapiro, 1994) |
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kd,DnaA = 0.007 |
(Gorbatyuk and Marczynski, 2005) |
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ks,Fts = 0.063, kd,Fts = 0.035 |
(Martin et al., 2004; Sackett et al., 1998) |
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kzring,open = 0.8 |
(Judd et al., 2003) |
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kzring,closed1 = 0.0001, kzring,closed2 = 0.6 |
(Judd et al., 2003) |
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ks,DivK = 0.0054 |
(Grunenfelder et al., 2001) |
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kd,DivK = 0.002, kd,DivK~P = 0.002 |
(Jacobs et al., 2001) |
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ktrans,DivK = 0.5, ktrans,DivK~P = 0.0295 |
(Jacobs et al., 2001) |
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ks,I = 0.08, kd,I = 0.04 |
(Grunenfelder et al., 2001) |
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ks,CcrM = 0.072 |
(Grunenfelder et al., 2001) |
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kd,CcrM = 0.07 |
(Stephens et al., 1996) |
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km,cori = 0.4, km,ctrA = 0.4 |
(Stephens et al., 1996) |
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km,ccrM = 0.4, km,fts = 0.4 |
(Stephens et al., 1996) |
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ka,Ini = 0.01 |
(Quon et al., 1998) |
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kelong = 0.006 |
(Dingwall and Shapiro, 1989) |
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B. Binding constants and thresholds (dimensionless) | |||
Ji,CtrA-CtrA = 0.4 |
Ja,CtrA-CtrA = 0.45 |
Jd,CtrA-DivK~P = 0.55 |
Ji,GcrA-CtrA = 0.2 |
Ji,DnaA-GcrA = 0.5 |
Ja,DnaA-CtrA = 0.3 |
Ja,open = 0.01 |
Ja,closed = 0.1 |
JZring-Fts = 0.78 |
Jm,cori = 0.95 |
Jm,ctrA = 0.95 |
Jm,ccrM = 0.95 |
Jm,fts = 0.95 |
θCtrA = 0.2 |
θGcrA = 0.45 |
θDnaA = 0.6 |
θcori = 0.0002 |
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C. Gene positions on the chromosome (from http://ecocyc.org) | |||
*Pelong = 0.05 |
PccrM = 0.2 |
PctrA = 0.375 |
Pfts = 0.625 |
*Pelong is assumed as the end point of replication initiation and the starting point of chromosome elongation. | |||
D. Initial values of model variables, for a newborn, wild-type stalked cell | |||
[CtrA] = 0.11 |
[GcrA] = 0.78 |
[DnaA] = 0.6 |
[Fts] = 0.29 |
[Zring] = 1 |
[DivK] = 0.66 |
[DivK~P] = 0.34 |
[I] = 0.11 |
[CcrM] = 0.5 |
[hctrA] = 0 |
[hccrM] = 0 |
[hfts] = 0 |
[hcori] = 1 |
[Ini] = 0.0 |
[Elong] = 0.05 |
[DNA] = 1.05 |