Table 3 Chemical formulas, standard molal Gibbs energies and other properties for reference model proteins for compartments in yeast cellsa.
Location | Number | Length | Formula |
| Z |
| log |
|---|---|---|---|---|---|---|---|
actin | 22 | 469.41 | C2316.66H3636.43N632.31O721.64S10.01 | -18506 | -5.3 | -0.119 | -74.7 |
ambiguous | 123 | 572.02 | C2816.55H4465.61N759.39O870.87S17.91 | -22616 | -9.6 | -0.146 | NA |
bud | 57 | 462.56 | C2366.32H3668.44N614.02O681.16S20.19 | -16641 | 5.4 | -0.179 | -75.4 |
bud.neck | 11 | 905.26 | C4543.68H7203.75N1250.35O1443.95S26.67 | -38103 | -16.8 | -0.113 | -69.2 |
cell.periphery | 38 | 826.07 | C4178.75H6505.8N1098.18O1229.93S33.77 | -30641 | 1.7 | -0.164 | -79.4 |
cytoplasm | 746 | 436.12 | C2164.42H3440.33N590.61O659.94S12.66 | -17065 | -2.7 | -0.149 | -73.5 |
early.Golgi | 9 | 622.83 | C3198.27H5068.06N821.28O972.56S21.53 | -25441 | -19.7 | -0.193 | -78.0 |
endosome | 30 | 484.06 | C2441.34H3871.24N661.02O767.51S14.17 | -20265 | -12.1 | -0.133 | -75.8 |
ER | 197 | 245.57 | C1206.09H1897.94N314.1O365.15S8.58 | -9276 | -3.0 | -0.173 | -77.8 |
ER.to.Golgi | 5 | 595.02 | C2951.77H4601.25N790.99O907.31S18.89 | -22861 | -13.3 | -0.127 | NA |
Golgi | 14 | 481.43 | C2502.96H3880.54N651.84O740S13.63 | -18516 | -5.4 | -0.167 | -77.6 |
late.Golgi | 29 | 787.94 | C4015.6H6312.79N1044.15O1217.15S22.72 | -31255 | -24.7 | -0.174 | -77.4 |
lipid.particle | 17 | 501.83 | C2573.36H3985.56N672.88O751.67S17.52 | -18687 | -4.1 | -0.167 | -75.0 |
microtubule | 10 | 497.13 | C2509.19H3969.36N690O774.61S17.95 | -20031 | -4.0 | -0.125 | -75.0 |
mitochondrion | 426 | 402.95 | C1987.87H3166.52N542.82O596.6S13.18 | -15221 | 3.3 | -0.160 | -75.9 |
nuclear.periphery | 46 | 815.58 | C4111H6516.46N1092.04O1272.05S20.55 | -33146 | -11.5 | -0.159 | -77.0 |
nucleolus | 60 | 605.43 | C2990.75H4768.81N820.31O957.91S14.52 | -25444 | -10.4 | -0.121 | -75.6 |
nucleus | 453 | 339.30 | C1683.49H2686.85N472.89O517.13S8.7 | -13342 | 3.4 | -0.129 | -75.0 |
peroxisome | 18 | 422.30 | C2117.28H3334.08N568.6O641.97S13.56 | -16400 | -2.0 | -0.150 | -74.8 |
punctate.composite | 61 | 467.64 | C2320.38H3662.92N633.84O751.45S10.52 | -19985 | -22.3 | -0.102 | NA |
spindle.pole | 30 | 398.53 | C1996.48H3176.93N555.45O642.49S12.63 | -17251 | -13.5 | -0.100 | -79.5 |
vacuolar.membrane | 45 | 709.78 | C3532.93H5555.77N943.21O1075.43S23.29 | -27439 | -15.3 | -0.150 | -73.4 |
vacuole | 67 | 428.85 | C2078.86H3186.53N542.71O668.01S14.34 | -17065 | -18.1 | -0.093 | -73.2 |
- a. Chemical formulas of nonionized reference model proteins and standard molal Gibbs energy of formation from the elements (
in kcal mol-1, at 25°C and 1 bar) and net ionization state (Z) at pH = 7 of ionized reference model proteins were calculated using the amino acid compositions given in Additional File 2. Values of the nominal oxidation state of carbon (
) were calculated using Eqn. (6). The model log 
values for the compartments were obtained from the metastability limits of subcellular interactions listed in Table 4 (see text).