| name | GDP |
| name | GTP |
| name | Ste2 |
| daltons | 47849.8 |
| name | to-Gpa1 |
| name | default |
| name | default |
| name | to-alpha |
| name | default |
| name | default |
| name | Ste4 |
| daltons | 46581.2 |
| name | to-Gpa1 |
This binding site is in the default shape when Ste4 is not bound to Ste5. It goes into the obstructed shape when Ste4 binds Ste5, blocking or inhibiting binding to Gpa1.
| name | default |
| name | default |
| name | obstructed |
| name | to-Ste5 |
| name | default |
| name | default |
| name | obstructed |
| name | Ste5 |
| daltons | 102728 |
| name | to-Ste4 |
| name | default |
| name | default |
| name | to-Ste11 |
| name | default |
| name | default |
| name | to-Ste7 |
| name | default |
| name | default |
| name | to-Fus3 |
| name | default |
| name | default |
| name | Gpa1 |
| daltons | 54075.9 |
| name | to-Ste2 |
Affinity between Gpa1 and Ste2 is said to be increased by Gpa1's being bound to Ste4; the Ste4-bound shape brings about this increase in binding affinity.
| name | default |
| name | default |
| name | Ste4-bound |
| name | to-Ste4 |
The binding site between Gpa1 and Ste4 is affected both by binding of Gpa1 to pheromone-bound receptor and by binding of Gpa1 to GTP/GDP. These shape changes are assumed to affect only off-rates.
| name | default |
| name | default |
| name | Ste2-GTP-bound |
| name | Ste2-GDP-bound |
| name | GTP-bound |
| name | GDP-bound |
| name | to-GXP |
Rather than model nucleotide exchange by allosteric changes in binding and unbinding to GTP and GDP, this file models nuclotide exchange as a catalytic process, as it is apparently done in Ty's BioNetGen model.
| name | default |
| name | default |
| name | alpha |
| daltons | 13271.1 |
| name | to-Ste2 |
| name | default |
| name | default |
Competitive binding to Ste4 by Gpa1 and Ste5. Here, binding of Ste4 to Ste5 makes binding of Ste4 to Gpa1 impossible.
| name | the-Ste4 |
| name | the-Ste5 |
| name | the-Ste4 |
| name | to-Ste5 |
| name | the-Ste5 |
| name | to-Ste4 |
| name | the-Ste4 |
| name | to-Gpa1 |
| name | obstructed |
Competitive binding to Ste4 by Gpa1 and Ste5. Here, binding of Ste4 to Gpa1 makes binding of Ste4 to Ste5 impossible, but enhances binding of Gpa1 to Ste2.
| name | the-Gpa1 |
| name | the-Ste4 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | the-Ste4 |
| name | to-Gpa1 |
| name | the-Ste4 |
| name | to-Ste5 |
| name | obstructed |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | Ste4-bound |
Gpa1 dissociation from Ste4. This allosteric omni models the change of shape in Gpa1 that happens when Gpa1 is bound to GDP, in the case that Gpa1 IS bound to Ste2.
| name | the-Ste2 |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | Ste2-GDP-bound |
Gpa1 dissociation from Ste4. This allosteric omni models the change of shape in Gpa1 that happens when Gpa1 is bound to GTP, causing it to lose affinity for Ste4, in the case that Gpa1 IS bound to Ste2.
| name | the-Ste2 |
| name | the-Gpa1 |
| name | the-GTP |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GTP |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | Ste2-GTP-bound |
Gpa1 dissociation from Ste4. This allosteric omni models the change of shape in Gpa1 that happens when Gpa1 is bound to GTP, causing it to lose affinity for Ste4, in the case that Gpa1 is not bound to Ste2.
| name | the-Gpa1 |
| name | the-GTP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GTP |
| name | the-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | GTP-bound |
Gpa1 dissociation from Ste4. This allosteric omni models the change of shape in Gpa1 that happens when Gpa1 is bound to GDP, in the case that Gpa1 is not bound to Ste2.
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | GDP-bound |
G-protein dissociation. Binding between Ste4 and Gpa1 is modified by whether Gpa1 is bound to GTP or GDP. Binding between Ste4 and Gpa1 is also competitive with binding between Ste4 and Ste5.
| name | Gpa1 |
| name | Ste4 |
| value | 5.0e7 |
| value | 0.5 |
| name | GTP-bound |
| name | default |
| value | 5.0e7 |
| value | 500 |
| name | Ste2-GTP-bound |
| name | default |
| value | 5.0e7 |
| value | 50 |
| name | Ste2-GDP-bound |
| name | default |
| value | 5.0e7 |
| value | 0.05 |
| name | GTP-bound |
| name | obstructed |
| value | 1.0 |
| value | 1.0e10 |
| name | Ste2-GDP-bound |
| name | obstructed |
| value | 1.0 |
| value | 1.0e10 |
| name | Ste2-GTP-bound |
| name | obstructed |
| value | 1.0 |
| value | 1.0e10 |
| name | default |
| name | obstructed |
| value | 1.0 |
| value | 1.0e10 |
Gpa1-GTP binding. Binding and unbinding here is not the way that nuclotide exchange is accomplished. In this model, binding to either nucleotide is fast, but binding to GDP is faster, and unbinding from either is very slow.
| name | Gpa1 |
| name | GTP |
| value | 1.0e6 |
| value | 1.0e-10 |
Gpa1-GDP binding. Binding and unbinding here is not the way that nuclotide exchange is accomplished. In this model, binding to either nucleotide is fast, but binding to GDP is faster, and unbinding from either is very slow.
| name | Gpa1 |
| name | GDP |
| value | 1.0e7 |
| value | 1.0e-10 |
Competitive binding to Ste4 by Gpa1 and Ste5.
| name | Ste4 |
| name | Ste5 |
| value | 5.0e6 |
| value | 2.0 |
| name | obstructed |
| name | default |
| value | 1.0 |
| value | 1.0e10 |
Gpa1 binding to Ste2. Being complexed with Ste4 causes Gpa1 to bind more tightly to Ste2; here, this is achieved by reducing the off-rate.
| name | Gpa1 |
| name | Ste2 |
| value | 2.0e7 |
| value | 2.0e1 |
| name | Ste4-bound |
| name | default |
| value | 2.0e7 |
| value | 2.0 |
Pheromone-receptor binding.
| name | alpha |
| name | Ste2 |
| value | 2.65e5 |
| value | 1.3e-3 |
Gpa1 auto-catalysed hydrolysis of GTP. This model does not include Sst2.
| name | the-Gpa1 |
| name | the-GTP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GTP |
| name | phosphate |
| value | 5.0e-3 |
Gpa1 (no Ste4) nucleotide exchange
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| value | 6.17e-4 |
alpha-Ste2-Gpa1 (no Ste4) nucleotide exchange
| name | the-alpha |
| name | the-Ste2 |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-alpha |
| name | to-Ste2 |
| name | the-Ste2 |
| name | to-alpha |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| value | 1.5e3 |
Gpa1-Ste4 nucleotide exchange
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Ste4 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | the-Ste4 |
| name | to-Gpa1 |
| value | 6.17e-7 |
alpha-Ste2-Gpa1-Ste4 nucleotide exchange
| name | the-alpha |
| name | the-Ste2 |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Ste4 |
| name | the-alpha |
| name | to-Ste2 |
| name | the-Ste2 |
| name | to-alpha |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | the-Ste4 |
| name | to-Gpa1 |
| value | 1.5 |
| name | phosphate |
This population is unsupported. Intended to be a sufficiency.
| daltons | 5.0 |
| count | 3000 |
| name | GTP-singleton |
This population is unsupported. Intended to be a sufficiency.
| name | the-GTP |
| count | 10000000 |
| name | GDP-singleton |
This population is unsupported. Intended to be a sufficiency.
| name | the-GDP |
| count | 3000000 |
| name | alpha-singleton |
Alpha factor is added in a bolus at 2.0 sec.
| name | theAlpha |
| count | 0 |
| name | Ste5-singleton |
This 1900 is the wiki population; differing from my early number from Kirsten.
| name | the-Ste5 |
| count | 1900 |
| name | Ste2-singleton |
This 7100 is from the Wiki; my early numbers from Kirsten don't seem to include Ste2.
| name | the-Ste2 |
| count | 7100 |
| name | Ste4-singleton |
This 9000 is from the Wiki, differing from my early number from Kirsten.
| name | the-Ste4 |
| count | 9000 |
| name | Gpa1-singleton |
This 9000 is from the wiki, differing from my early number from Kirsten. In my earlier models, I've always started with Gpa1 loaded up with GDP; here, starting with all singleton molecules, to go along with what is being said in the Wiki.
| name | the-Gpa1 |
| count | 9000 |
This is the 'metabolic' reaction that makes GTP from GDP and phosphate.
| multiplicity | 1 |
| name | GDP-singleton |
| multiplicity | 1 |
| name | phosphate |
| multiplicity | 1 |
| name | GTP-singleton |
| value | 1.0e12 |
| liters | 5.0e-14 |
A spherical yeast of diameter 5 microns.
| name | four-one-total |
| name | the-Ste4 |
| name | the-Gpa1 |
| name | the-Ste4 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | four-one-GDP |
| name | the-Ste4 |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Ste4 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | four-one-GTP |
| name | the-Ste4 |
| name | the-Gpa1 |
| name | the-GTP |
| name | the-Ste4 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste4 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GTP |
| name | four-five |
| name | the-Ste4 |
| name | the-Ste5 |
| name | the-Ste4 |
| name | to-Ste5 |
| name | the-Ste5 |
| name | to-Ste4 |
| name | alpha-two |
| name | the-alpha |
| name | the-Ste2 |
| name | the-alpha |
| name | to-Ste2 |
| name | the-Ste2 |
| name | to-alpha |
| name | one-two |
| name | the-Gpa1 |
| name | the-Ste2 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | Gpa1-total |
| name | theGpa1 |
| name | Gpa1-GTP |
| name | the-Gpa1 |
| name | the-GTP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GTP |
| name | Gpa1-GDP |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| name | enabling-complex |
| name | the-alpha |
| name | the-Ste2 |
| name | the-Gpa1 |
| name | the-GDP |
| name | the-alpha |
| name | to-Ste2 |
| name | the-Ste2 |
| name | to-alpha |
| name | the-Ste2 |
| name | to-Gpa1 |
| name | the-Gpa1 |
| name | to-Ste2 |
| name | the-Gpa1 |
| name | to-GXP |
| name | the-GDP |
| dump-period | 0.01 |
| file-name | four.dmp |
| name | four-one-total |
| name | four-one-GDP |
| name | four-one-GTP |
| name | four-five |
| name | one-two |
| dump-period | 0.01 |
| file-name | alpha.dmp |
| name | alpha-two |
| name | enabling-complex |
| dump-period | 0.01 |
| file-name | gpa1.dmp |
| name | Gpa1-total |
| name | Gpa1-GTP |
| name | Gpa1-GDP |
| dump-period | 0.01 |
| file-name | phos.dmp |
| name | GTP-singleton |
| name | GDP-singleton |
| name | phosphate |
| dump-period | 0.01 |
| file-name | stats |
| name | species-count |
| name | reaction-count |
| name | reaction-event-count |
| time | 5.0 |
| name | alpha-singleton |
| count | 10000 |
| time | 29.0 |
| file-name | stateDump |
| time | 30.0 |