Team:Aberdeen Scotland/hillinput

Repression of a Promoter

During repression of a promoter a repressor protein, X, binds to a DNA site of the promoter, D. The product of this binding process is [XD]. [XD] can also fall apart into [X] and [D] again:

 

(I)

where k_on describes the collisions of X and D that occur per time per protein at a given concentration and k_off determines the strength of the chemical binding X and D. In form of a differential equation, the rate of change of [XD] is described by

 

(II)

At steady state the concentration [XD] does not change.

 

(II.1)

 

(II.2)

 

(II.3)

 

(II.4)

Equation (II.4) is called the chemical equilibrium constant equation, where Kd is the dissociation or equilibrium constant. Kd has units of concentration. Therefore, transcription of a gene only happens whenever the repressor is not bound. That is when D is free. The total concentration of the DNA sites [DT] can be written with the help of the conservation law:

 

or

(III)

Substituting (III) in (II.4) we find

 

(IV)

 

(IV.1)

 

(IV.2)

 

(IV.3)

 

(IV.4)

 

(IV.5)

 

(IV.6)

As a result, the probability describing that the site D is free is dependent on [X]. The promoter activity, p, is defined by

 

or

(V)

where β is the maximal transcription rate of the promoter. If then [X] = K_d and the promoter activity is reduced by 50%. This [X] needed to repress the promoter activity by a half is called the repression coefficient.

Activation of a Promoter

In the case of an activation of a promoter, an activator protein, X, binds to its DNA site of the promoter and increases the rate of transcription of the promoter. Similarly to the repression of the promoter the promoter activity, p, in the case of activation can be derived as

 

(VI)

Michaelis –Menten Equation for a Repressor Protein

To turn a repressor system from Off state to On state, we need an input signal (for example a molecule called inducer,S) such that the repressor protein, X, binds off the promoter side DNA. The inducer forms a complex with X varying X’s affinity to D. The total amount of concentration of the repressor, [X_T], can be considered as a product of the repressor protein forming a complex with the inducer, [XS] and the repressor protein in its free form [X], whereby free does not differ between bound to the promoter’s DNA site or not.

 

or or

(VII)

Writing the mass-action kinetic equation for the S binding with the X leaves us with

 

(II.X)

In steady state