SimEvolEnzCons (version 2.0.0)

mut.E.old: Old method for mutation of enzyme concentrations

Description

Computes the mutant value of enzyme concentrations with the old method (see Lion et al. 2004).

Usage

mut.E.old(E_fun,i_fun,nu_fun,correl_fun,beta_fun=NULL,typ_E=1)

Arguments

E_fun

Numeric vector of enzyme concentrations (resident)

i_fun

Numeric value corresponding to number of the enzyme targeted by the mutation

nu_fun

Numeric value of canonical mutation effect

correl_fun

Character string indicating the abbreviation of the constraint applied on the system

beta_fun

Matrix of co-regulation coefficients

typ_E

Numeric for mutation method. Authorized values: 1 or 2. Default is 1.

Value

Numeric vector corresponding to mutant value of enzyme concentrations

Details

This mutation method is named old, because it was used the first one used for evolution simulation. Some improvements has been made since.

The main difference with mutation function mut.E.direct is the method to compute mutant values under competition constraint. In this function mut.E.old, canonical effect \(\nu\) is redistributed only on enzymes different from the target one, whereas in mut.E.direct, mutation canonical effect is redistributed between all enzymes, including the target one.

Moreover, computation method in mut.E.direct is simplified.

Last, this old method includes two model of mutations: additive and multiplicative.

• Additive method (typ_E=1): mutant concentration is the sum of the resident one plus size of mutation \(\nu\)

• Multiplicative method (typ_E=2): mutant concentration is the product of the resident one and \(1+\nu\)

Default is method 1.

In mut.E.direct, only method 1 is kept.

References

Lion, S., F. Gabriel, B. Bost, J. Fi<U+00E9>vet, C. Dillmann, and D. De Vienne, 2004. An extension to the metabolic control theory taking into account correlations between enzyme concentrations. European Journal of Biochemistry 271:4375<U+2013>4391.

See Also

See function mut.E.direct for a direct computation method of mutation.

Examples

# NOT RUN {
E <- c(30,30,30)
beta <- matrix(c(1,10,5,0.1,1,0.5,0.2,2,1),nrow=3)
correl <- "RegPos"
mu <- 1 #canonical size of mutation
i <- 3 #enzyme directly targeted by mutation

mut.E.old(E,i,mu,correl,beta)

# }