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Table 2 Molecular amounts of initial species in the Ras/cAMP/PKA model

From: The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae

Molecular species

Copy number (molecules/cell)

Reference

Cyr1

200

[16]

Cdc25

300

[29]

Ira2

200

[16]

Pde1

1,400

[29]

PKA

2,500

[29]

PPA2

4,000

[29]

Pde2

6,500

[29]

Ras2-GDP

20,000

[29]

GDP

∗1.5 ×106

[23]

GTP

∗5.0 ×106

[23]

ATP

∗2.4 ×107

[23]

  1. The molecular amounts of the species initially occurring in the system are expressed as number of molecules per cell. The number of molecules for Ras2, Cdc25, PKA, Pde1, Pde2 and PPA2 were evaluated using the data presented in [29] (available online at http://yeastgfp.ucsf.edu/). The number of molecules for Ira2 and Cyr1 were estimated in [16] by comparing the fluorescence of yeast cells expressing fusion with eGFP (obtained by http://yeastgfp.ucsf.edu/) using Cdc25-eGFP as a standard (300 molecules/cell). The number of molecules for ATP, GTP and GDP were calculated by considering experimental data presented in [23] and assuming an internal free water volume of about 30 fL [16], obtained by considering an average cell volume of 45 fL [30, 31] and taking into account that part of this volume is occupied by the cell wall and internal structures. Therefore, assuming a concentration of 1mM, for ATP we obtained about 2.4×107 molecules/cell, while for GTP and GDP we estimated 5.0×106 and 1.5×106 molecules/cell, respectively, for yeast cells growing in minimal glucose medium [16]. Unless otherwise specified, the amounts of GDP, GTP and ATP—highlighted with an asterisk in the table—are kept constant during the execution of simulations.