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Merge pull request #33 from DenisTitovLab/update_GAPDH_params
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Update GAPDH kinetic params
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@Denis-Titov
Denis-Titov committed Apr 11, 2024
2 parents bcff33c + 013ee9a commit 85c3a47
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Showing 4 changed files with 53 additions and 54 deletions.
1 change: 0 additions & 1 deletion .vscode/settings.json
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@@ -1,3 +1,2 @@
{
"julia.environmentPath": "/Users/Denis/.julia/dev/Glycolysis"
}
2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "Glycolysis"
uuid = "1acb6d80-f93a-4117-912f-ae4c0dd090a6"
authors = ["Denis-Titov <titov@berkeley.edu> and contributors"]
version = "0.7.0"
version = "0.7.1"

[deps]
LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
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2 changes: 1 addition & 1 deletion src/enzyme_rates.jl
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Expand Up @@ -153,7 +153,7 @@ function rate_GAPDH(metabs, params)
metabs.NADH / params.GAPDH_K_i_NADH * (
1 +
metabs.GAP / params.GAPDH_K_GAP * (1 + metabs.Phosphate / params.GAPDH_K_i_Phosphate) +
metabs.BPG / (params.GAPDH_α_i_BPG * params.GAPDH_K_BPG)
params.GAPDH_β_i_BPG * metabs.BPG / params.GAPDH_K_BPG
)

Rate = (
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102 changes: 51 additions & 51 deletions src/model_parameters.jl
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Expand Up @@ -2,7 +2,7 @@ using LabelledArrays, Measurements

#=
This file contains all the parameters needed to run Glycolysis.jl including
kinetic constants, thermodynamic constants, enzyme concentrations, initial
kinetic constants, thermodynamic constants, enzyme concentrations, initial
conditions for ODE simulations (i.e., estimates of intracellular concentration of metabolites),
and various constants for unit convertions.
Expand All @@ -21,7 +21,7 @@ water_fraction_cell_volume = 0.66
cytosol_fraction_cell_volume = 0.66

"""
Correction for cytosolic volume and its water content to better estimate concentration of
Correction for cytosolic volume and its water content to better estimate concentration of
cytosolic molecules from total cellular concentration and vice versa
"""
cell_volume_correction = water_fraction_cell_volume * cytosol_fraction_cell_volume
Expand Down Expand Up @@ -163,19 +163,19 @@ MW - g / mole /1000
###########################################################################################

"""
Mean ± SEM of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params_w_uncertainty)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
Mean ± SEM of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params_w_uncertainty)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
"""
glycolysis_params_w_uncertainty = LVector(
GLUT_Km_Glucose = 20e-3 ± 4e-3,
Expand Down Expand Up @@ -231,19 +231,19 @@ glycolysis_params_w_uncertainty = LVector(
TPI_Vmax = 6600.0 ± 800.0,
TPI_Keq = 0.0045 ± 0.0024,
TPI_MW = 26669.0 / 1000,
GAPDH_L = 1.6 ± 0.3,
GAPDH_L = 2.9 ± 1.7,
GAPDH_K_GAP = 1.7e-6 ± 0.1e-6,
GAPDH_K_a_NAD = 83e-6 ± 5e-6,
GAPDH_K_i_NAD = 180e-6 ± 20e-6,
GAPDH_K_a_Phosphate = 1.9e-3 ± 0.1e-3,
GAPDH_K_i_Phosphate = 10e-3 ± 4e-3,
GAPDH_K_BPG = 0.78e-6 ± 0.1e-6,
GAPDH_K_a_NADH = 7.8e-6 ± 1.2e-6,
GAPDH_K_i_NADH = 1.8e-6 ± 0.3e-6,
GAPDH_α_i_BPG = 4.5 ± 0.7,
GAPDH_K_a_NAD = 78e-6 ± 9e-6,
GAPDH_K_i_NAD = 130e-6 ± 34e-6,
GAPDH_K_a_Phosphate = 1.5e-3 ± 0.4e-3,
GAPDH_K_i_Phosphate = 5.5e-3 ± 3.8e-3,
GAPDH_K_BPG = 0.82e-6 ± 0.14e-6,
GAPDH_K_a_NADH = 12e-6 ± 7e-6,
GAPDH_K_i_NADH = 2.5e-6 ± 1.1e-6,
GAPDH_β_i_BPG = 0.22 ± 0.04,
GAPDH_Conc = (cell_protein_density / cell_volume_correction) * (5.6e-3 ± 0.5e-3),
GAPDH_Vmax = 130 ± 20,
GAPDH_Keq = 16 ± 5,
GAPDH_Keq = 15 ± 6,
GAPDH_MW = 36053.0 / 1000,
PGK_K_BPG = 3e-6 ± 0.7e-6,
PGK_K_ADP = 42e-6 ± 10e-6,
Expand Down Expand Up @@ -326,35 +326,35 @@ glycolysis_params_w_uncertainty = LVector(
)

"""
LArray containing mean of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
LArray containing mean of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
"""
glycolysis_params = Measurements.value.(glycolysis_params_w_uncertainty)

"""
SEM of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params_uncertainty)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
SEM of kinetic and thermodynamic parameters for enzyme rate equations.
Use `propertynames(glycolysis_params_uncertainty)` for list of all parameters given
as "EnzymeGeneName_ParameterName".
Parameters have the following units:
K - M
β - unitless
Vmax - µmol/min per mg protein or U per mg
Keq - depends on reaction stoichiometry
Conc - mg protein/ul of cytosolic volume (converted from mg protein/mg proteome)
Conc⋅Vmax - M/min
Keq - either unitless or concentration
MW - g / mole /1000
"""
glycolysis_params_uncertainty = Measurements.uncertainty.(glycolysis_params_w_uncertainty)

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Registration pull request created: JuliaRegistries/General/104675

Tip: Release Notes

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"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.7.1 -m "<description of version>" 85c3a477d120a1bef742fc10fc672d3376d69cc6
git push origin v0.7.1

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