add_exoenzyme: Add an exoenzyme to organism and simulation

In Waschina/Eutropia: Agent-based modelling of microbial communities in time and continuous µ-meter-scale space

Add an exoenzyme to organism and simulation

Description

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 μm^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

Waschina/Eutropia documentation built on Jan. 4, 2023, 12:42 p.m.