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SimEvolEnzCons (version 2.0.0)

Simulation of Evolution of Enzyme Under Constraints

Description

Simulate the evolution of enzyme concentrations under selection for increased flux in a metabolic pathway, with cellular constraints. Create graphics for the simulation results. Compute evolutionary equilibrium and Range of Neutral Variations of enzyme concentrations. This package is part of "Coton, C., Talbot, G., Le Louarn, M., Dillmann, C., de Vienne, D. (2021) ". Version 2.0.0 and more takes account of regulation groups, and is part of a second article "Coton, C., Dillmann, C., de Vienne, D. (in progress)".

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Version

Install

install.packages('SimEvolEnzCons')

Monthly Downloads

42

Version

2.0.0

License

GPL (>= 3)

Maintainer

Charlotte Coton

Last Published

October 28th, 2021

Functions in SimEvolEnzCons (2.0.0)

RNV.compute.elements

Compute RNV and associated elements for all enzymes (Deprecated)
RNV.mean.suitability

Compare RNV mean in simulation with predicted RNV at equilibrium
RNV.graph.double.at.eq

Graph of e and RNV in relation to A at equilibrium
RNV.mean.simul

Mean of RNV size in simulation
RNV.for.simul

Compute RNV for simulation
RNV.delta.all.enz

Delta at RNV for all enzymes
activities

Activity computation
SimEvolEnzCons

SimEvolEnzCons: Simulation of Enzyme Evolution Under Constraints
RNV.size.at.equilibr

Plot and linear model of RNV size at equilibrium
RNV.ranking.order.factor

Name and value of RNV-ranking-order factor
compute.delta

Computation of mutation actual effect
coef_sel.continue

Selection coefficient computation
class_group

Classify enzymes in regulation groups
droites

Line of relative enzyme concentrations (co-regulations cases)
compute.B.from.beta

Global co-regulation coefficient computation
compute.beta.from.B

Co-regulation coefficient computation
alpha_ij

Redistribution coefficient computation
mut.kin

Mutation of kinetic parameters
extract.tabEtot

Table of concentrations
name.correl

Help to name parameter 'correl'
flux.shape.for.all.points

Flux shape computing for all points
is.correl.authorized

Verification of constraint name
mut.E.direct

Direct mutation of enzyme concentrations
flux.shape.from.one.point

Flux shape computing from one point
apparent.activities.Aq

Apparent activity computation
mut.E.indirect

Indirect mutation of enzyme concentrations
data_sim

Simulation results for each constraint
search_group

Search the regulation group for an enzyme
range_tau

Bounds of tau
simul.evol.graph.methods

Graphic methods for simulations of enzyme evolution
coef_sel.discrete

Selection coefficient computation
graph.simul.triangle.diagram.e

Triangular diagram of relative concentrations for simulations of enzyme evolution
group_types

Which types are the different regulation groups?
solv.2dg.polynom

Real solutions of quadratic equation
sol_eqeff

Expression of null response coefficient
flux.dome.graphics

Plot of the flux dome
is.B.accurate

Verification of B accuracy
is.beta.accurate

Verification of beta matrix accuracy
predict_eff_allE0

Prediction of effective equilibrium for all possible initial relative concentrations
flux

Flux computation
coef_rep

Response coefficient computation
mut.E.old

Old method for mutation of enzyme concentrations
simul.evol.enz.multiple

Multiple simulations of enzyme evolution
flux.shape.from.one.point.graphics

Plots of flux shape computing from one point
graph.simul.conc.end

Graphics of simulation ends
simul.evol.enz.one

Simulation of enzyme evolution
simul.next.resident

Time step simulation (next resident values)
sumbis

Sum of vector elements
predict_grp

Prediction of equilibrium with regulation groups
odd.discrete.sel.coef

Equation of null coefficient selection
predict_th

Prediction of theoretical equilibrium
predict_eff

Prediction of effective equilibrium
range_delta

Bounds of delta_i