Difference between revisions of "Team:IIT Delhi/Write Model"
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mRNA is produced from DNA, and degraded spontaneously. Therefore, at any instant of time, the rate of change of mRNA can be written as - | mRNA is produced from DNA, and degraded spontaneously. Therefore, at any instant of time, the rate of change of mRNA can be written as - | ||
<br><br> | <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/4/45/T--IIT_Delhi--picture3.png"><br> | + | <img src = "https://static.igem.org/mediawiki/2017/4/45/T--IIT_Delhi--picture3.png" border="5"><br> |
<br> | <br> | ||
Note, that here, we have not written the reaction where mRNA is being converted to protein, since mRNA is not actually being consumed there or being produced. 1 molecule of mRNA simply produces 1 molecule of protein (assumption). <br> | Note, that here, we have not written the reaction where mRNA is being converted to protein, since mRNA is not actually being consumed there or being produced. 1 molecule of mRNA simply produces 1 molecule of protein (assumption). <br> | ||
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Now, we know that the DNA concentration remains constant and does not change over time. Therefore, the [DNA] term can be included in the constant itself, to give <br><br> | Now, we know that the DNA concentration remains constant and does not change over time. Therefore, the [DNA] term can be included in the constant itself, to give <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/3/3c/T--IIT_Delhi--picture4.png"><br> | + | <img src = "https://static.igem.org/mediawiki/2017/3/3c/T--IIT_Delhi--picture4.png" border="5"><br> |
<br> | <br> | ||
Now, the dynamics of the protein can be similarly written as <br><br> | Now, the dynamics of the protein can be similarly written as <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/7/77/T--IIT_Delhi--picture5.png"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/7/77/T--IIT_Delhi--picture5.png" border="5"><br><br> |
And that is it! We’ve just written down our first model, for a gene being expressed from a constitutive promoter. Now that we have our model, we can simulate these and find out the dynamics. <br> | And that is it! We’ve just written down our first model, for a gene being expressed from a constitutive promoter. Now that we have our model, we can simulate these and find out the dynamics. <br> | ||
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Thus, we write down the model on MATLAB here, and simulate it for a time period of 200 time units. The values of the constants used for alpha, gamma etc and the MATLAB code for the same can be found on the github library link given below. The plot obtained is as follows - <br><br> | Thus, we write down the model on MATLAB here, and simulate it for a time period of 200 time units. The values of the constants used for alpha, gamma etc and the MATLAB code for the same can be found on the github library link given below. The plot obtained is as follows - <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/8/80/T--IIT_Delhi--picture6.jpeg"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/8/80/T--IIT_Delhi--picture6.jpeg" border="5"><br><br> |
Changing the parameters for production and degradation rates can give different kinds of graphs, and can be explored by simply changing the values of alpha, gamma, K etc in the model and simulating the same. However, as we can see here, the mRNA and protein levels both rise to a certain fixed value. This is known as the steady state value. | Changing the parameters for production and degradation rates can give different kinds of graphs, and can be explored by simply changing the values of alpha, gamma, K etc in the model and simulating the same. However, as we can see here, the mRNA and protein levels both rise to a certain fixed value. This is known as the steady state value. | ||
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Therefore at steady state, | Therefore at steady state, | ||
<br><br> | <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/b/b6/T--IIT_Delhi--picture7.png"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/b/b6/T--IIT_Delhi--picture7.png" border="5"><br><br> |
Thus, <br><br> | Thus, <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/f/fc/T--IIT_Delhi--picture8.png"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/f/fc/T--IIT_Delhi--picture8.png" border="5"><br><br> |
Now, we can replace the value of [mRNA] in equation (2) with the value given above, to get - <br><br> | Now, we can replace the value of [mRNA] in equation (2) with the value given above, to get - <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/e/ea/T--IIT_Delhi--picture9.png"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/e/ea/T--IIT_Delhi--picture9.png" border="5"><br><br> |
We can now try to simulate and plot the graph for the protein levels, and compare the time series of the two models - <br><br> | We can now try to simulate and plot the graph for the protein levels, and compare the time series of the two models - <br><br> | ||
| − | <img src = "https://static.igem.org/mediawiki/2017/9/93/T--IIT_Delhi--picture10.png"><br><br> | + | <img src = "https://static.igem.org/mediawiki/2017/9/93/T--IIT_Delhi--picture10.png" border="5"><br><br> |
Therefore, we can see that by making the assumption that mRNA is already at steady state at the start of time, the protein levels begin to rise faster than the earlier model. However, the steady state value for protein remains the same. This is because we have only simplified the model by changing the time scale and assuming that at the given time scale, mRNA dynamics are at steady state. We have not changed the steady state per se. | Therefore, we can see that by making the assumption that mRNA is already at steady state at the start of time, the protein levels begin to rise faster than the earlier model. However, the steady state value for protein remains the same. This is because we have only simplified the model by changing the time scale and assuming that at the given time scale, mRNA dynamics are at steady state. We have not changed the steady state per se. | ||
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</h2> | </h2> | ||
</header> | </header> | ||
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| + | <h2 class="h2font">Model for<br> Regulated Gene Expression</h2> | ||
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| + | </p> | ||
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| + | Regulation of gene expression involves changing the expression of protein or RNA produced by a particular gene. Various mechanisms exist, for doing the same allowing for control at various stages of the expression of the gene. For instance, if the control/regulation is such that it does not allow transcription to happen, it is termed as transcriptional control. Similarly, translational, post translational and several other layers of control exist. <br> | ||
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| + | The simplest and most commonly employed mode of regulation is the transcriptional control by repressor proteins. These are protein molecules that can bind to specific “operator” sites in the promoter region, and stop the promoter to recruit RNA polymerase successfully, thereby inhibiting transcription. Common examples of such systems are LacI, TetR and cI, which can inhibit transcription from the pLac, pTet and pCI promoter respectively. This mode of control is also commonly referred to as repression, and should not be confused with inhibition, which is a separate control mechanism.<br> | ||
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| + | Here, let us try to model what regulated gene expression looks like, by looking at a typical example of transcriptional activation. Consider the following case - <br><br> | ||
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| + | <img src = "https://static.igem.org/mediawiki/2017/6/65/T--IIT_Delhi--picture11.png" border="5"><br><br> | ||
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| + | We have a protein X, that can exist in two states, the native (inactive) state X, and an active form X*. The molecule X* can bind to the promoter (say P), and promote transcription of the gene by helping the promoter to recruit RNA polymerase. | ||
| + | <br><br> | ||
| + | Lets look at another case, where we have transcriptional repression -<br><br> | ||
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| + | <img src = "https://static.igem.org/mediawiki/2017/2/2b/T--IIT_Delhi--picture12.png" border="5"><br><br> | ||
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| + | Here we are given 2 proteins, A and B. The protein A is produced and degraded, and is a transcriptional repressor for the gene B. A has its own production and degradation rates, described by alpha and gamma, and B also has its own production and degradation rates, given by beta and gamma respectively. Further, DA and Do represent the two states that the DNA region of the promoter PB can have. DA represents the state where A is bound to the operator, and Do represents the state where A is unbound. | ||
| + | <br> | ||
| + | The system can be represented by a set of reactions as follows –<br><br> | ||
| + | <img src = "https://static.igem.org/mediawiki/2017/9/92/T--IIT_Delhi--picture13.png" border="5"><br><br> | ||
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| + | Based on these reactions, we can write the mass action model for the system. This can be represented by the following differential equations –<br><br> | ||
| + | <img src = "https://static.igem.org/mediawiki/2017/9/92/T--IIT_Delhi--picture14.png" border="5"><br><br> | ||
| + | |||
| + | Further, we have a 5th equation in the model, which is based on the conservation of DNA. Since all of the DNA of the promoter can either be bound by transcription factor A (DA state) or be unbound (Do state), therefore, the total DNA (DT), at any time, can be represented as –<br><br> | ||
| + | <img src = "https://static.igem.org/mediawiki/2017/9/92/T--IIT_Delhi--picture15.png" border="5"><br><br> | ||
| + | |||
| + | Thus, the model of the system, based on mass action kinetics and conservation relations can be represented by –<br><br> | ||
| + | <img src = "https://static.igem.org/mediawiki/2017/9/92/T--IIT_Delhi--picture16.png" border="5"><br><br> | ||
| + | </h2> | ||
| + | </header> | ||
Revision as of 14:43, 1 November 2017
Model for
Unregulated Gene Expression
A model for this simple system shown above can then be written, keeping the assumptions in mind. To start with, we can consider the two variables that are of importance to us in determining the level of gene expression. These are the mRNA and protein levels (since the DNA levels in a cell are assumed to be constant, they are not of interest).
Therefore, let us write the differential equation for mRNA first -
mRNA is produced from DNA, and degraded spontaneously. Therefore, at any instant of time, the rate of change of mRNA can be written as -
Note, that here, we have not written the reaction where mRNA is being converted to protein, since mRNA is not actually being consumed there or being produced. 1 molecule of mRNA simply produces 1 molecule of protein (assumption).
Further, it has to be noted that the [DNA] and [mRNA] terms appear in the equation since in writing the model, we assume that mass action kinetics are valid, ie, the rate of the reaction is equal to the rate constant times the concentration of the reactant, raised to a power equal to the number of molecules of the reactant.
Now, we know that the DNA concentration remains constant and does not change over time. Therefore, the [DNA] term can be included in the constant itself, to give
Now, the dynamics of the protein can be similarly written as
And that is it! We’ve just written down our first model, for a gene being expressed from a constitutive promoter. Now that we have our model, we can simulate these and find out the dynamics.
Simulation basically means solving the differential equations to get the variation of the component (mRNA, protein) with time. This can be done by hand for the equations above. However, as models get more complex, implicit equations appear, which are much more difficult to solve by hand. Thus, it is essential to get the hang of modelling software such as MATLAB or R, which solve differential equations and simulate the model for a specified period of time.
Thus, we write down the model on MATLAB here, and simulate it for a time period of 200 time units. The values of the constants used for alpha, gamma etc and the MATLAB code for the same can be found on the github library link given below. The plot obtained is as follows -
Changing the parameters for production and degradation rates can give different kinds of graphs, and can be explored by simply changing the values of alpha, gamma, K etc in the model and simulating the same. However, as we can see here, the mRNA and protein levels both rise to a certain fixed value. This is known as the steady state value.
However, we can make a further simplification in this model. Generally, the mRNA dynamics are faster than the protein dynamics. This means that mRNA levels approach their steady state value faster than proteins do. Therefore, we can say make the assumption and further simplification that before the protein dynamics start to come into play, the date of change of mRNA is zero. This is known as the “quasi steady state assumption”.
Therefore at steady state,
Thus,
Now, we can replace the value of [mRNA] in equation (2) with the value given above, to get -
We can now try to simulate and plot the graph for the protein levels, and compare the time series of the two models -
Therefore, we can see that by making the assumption that mRNA is already at steady state at the start of time, the protein levels begin to rise faster than the earlier model. However, the steady state value for protein remains the same. This is because we have only simplified the model by changing the time scale and assuming that at the given time scale, mRNA dynamics are at steady state. We have not changed the steady state per se.
Model for
Regulated Gene Expression
