Team:Paris/Modeling/Programs
From 2008.igem.org
(→Finding Parameters) |
|||
Line 1: | Line 1: | ||
- | {{Paris/ | + | {{:Team:Paris/MenuBackup}} |
- | + | ||
- | + | ||
- | + | ||
==Complexations Caracterisation== | ==Complexations Caracterisation== |
Latest revision as of 07:06, 30 October 2008
Go back to the normal Wiki
Contents |
Complexations Caracterisation
The first hypothesis is that a complexation reaction is fully determined by the following :
and that the rates k_{+} et k_{-} stay constant under all conditions. Then, the second hypothesis is that these equations are (kinetically speaking) elementary :
Then, since we guess that the only datas we will have are the quantities of A and B introduced (A_{i} and B_{i}), the only equations we will deal with is the following, entirely determining the concentration C_{eq} at steady-state (at least if we take the smallest real root of the equation, it is useless to demonstrate the unicity, or even the existence, of such a solution) :
Equilibrium of a Complex
Know, if we imagine a given amount of A_{i} and B_{i}, that are calculated as their equilibrium without taking acount of their complexation (but, for instance, of other interactions, productions and disappearance), and that the produced complex C disappears along time with a degradation rate γ, we get :
so that the equilibrium gives :
with
Hill Functions
The previous system of complexation applied in particular to the association of the Promoters (P) and its Transcription Factor (TF).
Because the promoters on a "low copy plasmid" exists in the cell in ten exemplaries, in contrary to a protein, which, as long as it is produced (even weakly) exists in thousands of exemplaries, we assume can the quantities of TF and P are different by several orders of magnitude. Then, with the previous notations, if A, B and C stands respectively for TF, P and the complex TF><P, we will get
that we can easily solve with :
Depending to the order n (also called cooperativity, because it correponds to the possibilities of the transcription factor to binds in a group on the promoter), this function is a sigmoïd, known as the Hill function. The parameter K , called activation constant, is often replaced in the previous expression by the following notation
It simplifies the manipulations of the expression ; we can notice that K represents now the amount of TF needed to bind half of the total P in the cell.
Induction by a small molecule
Introduction
In certain steps of our system, and in our caracterisation plan, we use the diffusion of a small molecule (SM), that binds to a transcription factor.
We make the hypothesis of a simple, passive diffusion, that leads at the steady-state at equal amount of the small molecule, inside and outside the cells. The resulting equations are the following coupling :
where
- permeability is the membrane permeability multiplied by the average external surface of a cell (in min^{-1})
- N is the average cell population
- V_{int} is the average volume of a cell (in L) ; V_{ext} is the volume of the culture medium outer the cells (in L)
The situation
The involvement of the previous process is, in our systems,under these conditions :
- Prot is a protein, produce by a promoter
- expr_prom is the given expression of this promoter (production rate of Prot)
- γ is the degradation/dilution rate of the proteins and complexes in the cell (especially due to cell division, we made so far the hypothesis that it is the same for all the proteins)
- SM_{int} binds to Prot, with a cooperativity n and a dissociation constant K_{d}, to form the complex Compl
- The cell culture is in a chemostat : the cell population is N; The renewal rate (flow of the medium, divided by the volume of the chemostat, in min^{-1}) is rnw; The Volume of a cell is V_{int}; and of the outer medium is V_{ext} ( = Volume(chemostat) - N * V_{int})
Induction for the caracterisations
In these experimental conditions, we assume that the external concentration of SM remains constant. So, at steady-state,
Then, considering the previous complexations equations, and by the equilibrium of Prot ( expr(prom) denotes protein production rate ), we have at steady states
and by the definition of the dissociation constant
that leads to the following expression of the complexes and proteins :
These equations will be used to estimate K_{d} and n, and then to estimate the relative amount of bound or free protein in the cell, for a given amount of SM.
Finding Parameters
|}