Adds a new exoenzyme to the simulation and links it to a specific organism.
Usage
add_exoenzyme(
object,
organism,
id,
mets,
stoich,
production.rate = 0.01,
name = NULL,
D = 10,
lambda = 0.4,
Kcat = 10000,
Km = 100,
init.conc = 0
)Arguments
- object
S4-object of type growthSimulation
- organism
Character indicating the name of the organism, to which the exoenzyme production is linked
- id
Character defining the ID used for the specific exoenzyme
- mets
Character vector with the compound IDs that participate in reaction catalyzed by the exoenzyme.
- stoich
Numeric vector of the same length and order as `mets` specifying the stoichiometries of compounds. First entry (the substrate's coefficient) should be -1.
- production.rate
Numeric indicating the production rate of the enzyme by the organism. Unit: nmol enzyme catalytic centers per gDW cells per hr. Default: 0.01
- name
Character with an optional name for the enzyme.
- D
Diffusion coefficient of the enzyme. Unit \(\mu\)m^2/s. Default: 10
- lambda
Numeric indicating the decay rate of the enzyme. Unit: per hour. Default: 0.4 . The enzyme's half life can be calculated by ln(2)/lambda
- Kcat
Numeric for enzyme's turnover rate. Unit: 1/s . Default: 10000
- Km
Numeric for Menten-Michaelis Km value. Unit: mM . Default: 100
- init.conc
Numeric indicating the initial concentration of the enzyme in the growth environment. Unit: nM . Default: 0
Details
Exoenzymes can differ markedly in their kinetic parameters. The defaults provided here do not represent a typical enzymes, but are chosen based on data from inveratases (EC 3.2.1.26) from Zymomonas mobilis. Kcat (~10000 s^-1) and Km (100 mM) were obtained from https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.26&Suchword=&reference=&UniProtAcc=&organism