Difference between revisions of "Team:Aalto-Helsinki/Modeling cellulose"

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<h1 style="text-align:center">Under construction</h1>
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<h1>Introduction</h1>
  
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<p>Our goal in the project is to produce propane from cellulose. For modeling team this means that both <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_propane">propane pathway</a> and cellulose pathway should be modeled.</p>
  
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<h2>Introduction</h2>
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<p>Our cellulose pathway is pretty simple, consisting only of a few genes cutting the cellulose into cellobiose and then to glucose. The challenge of this model lies instead in the properties of enzymes or rather, our limited knowledge of those. The members of our team spent many frustrating days trying to find the information we would need to model the pathway and were finally forced to give up.</p>
  
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<p>Why should we model this? Why not?</p>
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<p style="color:gray">--pic of cellulose pathway?--</p>
  
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<h2>Our thoughts</h2>
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<h1>Our thoughts</h1>
  
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<p>Should we tell about what we have thought about modeling? If we don't actually model this then just some thoughts?</p>
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<p>If it were possible to get the needed values, our model of cellulose pathway would have been based on <a href="https://fd-files-production.s3.amazonaws.com/107565/eH3BiZBtiRaOYETFPiaJtg?X-Amz-Expires=300&X-Amz-Date=20150805T080338Z&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIA2QBI5WP5HA3ZEA/20150805/us-east-1/s3/aws4_request&X-Amz-SignedHeaders=host&X-Amz-Signature=cbcd8addf8cc88e5553889036933f06b0353ddb4d1bbb2c6f25062cd8a424a90">this paper.</a></p>
  
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<p>Langmuir isotherm models adsorbtion (do we want to put equation here or a link to wikipedia?), and the rate equations are as follows. Inhibition of glucose and cellobiose is taken into account. \( R_s\) is substrate reactivity, \(K_{iG2}\) is inhibition constant of cellobiose, \(K_{iG}\) is inhibition constant for glucose. Cellulose to cellobiose:
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\[r_1 = \frac{k_{1r}[\beta\text{-glucosidase(bound)}]R_s [\text{cellulose}]}{1+\frac{[\text{cellobiose}]}{K_{iG2}} + \frac{[\text{glucose}]}{K_{iG}}}\]  Cellobiose to glucose:
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\[r_3 = \frac{k_{3r}[\beta\text{-glucosidase}][\text{cellobiose}]}{K_{3M}\left( 1+\frac{[\text{glucose}]}{K_{3iG}}\right) + [\text{cellobiose}]}\]</p>
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<p>This model could have been implemented into Copasi with following reactions where the rate equations are above.  \begin{align}
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\text{cellulose} &\rightarrow \text{cellulose} + \text{cellobiose} \\
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\text{cellulose} &\rightarrow 2\cdot\text{cellobiose} \\
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\text{cellobiose} &\rightarrow 2\cdot\text{glucose}
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\end{align} It should be implemented so, that cellulose to two cellobioses -reaction would occur about XXXX (what was the length of cellulose chain?) times less frequently than cellulose to cellulose and cellobiose. This is to model the fact that cellulose is cut slowly away without having to implement the reaction with all the specific cellulose lengths. </p>
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<p>Even if we would have gotten all the constants of our cellulose pathway the model would have not been perfect. We would have been forced to guess the amount of enzymes produced, as well as how much of them would travel outside of cell to cellulose. One thing was also what is the impact of the chemical environment of the extracellular space on the function of the enzymes. Finally, how much the cell benefits of the produced glucose or how much of it it can use and to what effect. </p>
  
 
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Revision as of 08:39, 5 August 2015

Introduction

Our goal in the project is to produce propane from cellulose. For modeling team this means that both propane pathway and cellulose pathway should be modeled.

Our cellulose pathway is pretty simple, consisting only of a few genes cutting the cellulose into cellobiose and then to glucose. The challenge of this model lies instead in the properties of enzymes or rather, our limited knowledge of those. The members of our team spent many frustrating days trying to find the information we would need to model the pathway and were finally forced to give up.

--pic of cellulose pathway?--

Our thoughts

If it were possible to get the needed values, our model of cellulose pathway would have been based on this paper.

Langmuir isotherm models adsorbtion (do we want to put equation here or a link to wikipedia?), and the rate equations are as follows. Inhibition of glucose and cellobiose is taken into account. \( R_s\) is substrate reactivity, \(K_{iG2}\) is inhibition constant of cellobiose, \(K_{iG}\) is inhibition constant for glucose. Cellulose to cellobiose: \[r_1 = \frac{k_{1r}[\beta\text{-glucosidase(bound)}]R_s [\text{cellulose}]}{1+\frac{[\text{cellobiose}]}{K_{iG2}} + \frac{[\text{glucose}]}{K_{iG}}}\] Cellobiose to glucose: \[r_3 = \frac{k_{3r}[\beta\text{-glucosidase}][\text{cellobiose}]}{K_{3M}\left( 1+\frac{[\text{glucose}]}{K_{3iG}}\right) + [\text{cellobiose}]}\]

This model could have been implemented into Copasi with following reactions where the rate equations are above. \begin{align} \text{cellulose} &\rightarrow \text{cellulose} + \text{cellobiose} \\ \text{cellulose} &\rightarrow 2\cdot\text{cellobiose} \\ \text{cellobiose} &\rightarrow 2\cdot\text{glucose} \end{align} It should be implemented so, that cellulose to two cellobioses -reaction would occur about XXXX (what was the length of cellulose chain?) times less frequently than cellulose to cellulose and cellobiose. This is to model the fact that cellulose is cut slowly away without having to implement the reaction with all the specific cellulose lengths.

Even if we would have gotten all the constants of our cellulose pathway the model would have not been perfect. We would have been forced to guess the amount of enzymes produced, as well as how much of them would travel outside of cell to cellulose. One thing was also what is the impact of the chemical environment of the extracellular space on the function of the enzymes. Finally, how much the cell benefits of the produced glucose or how much of it it can use and to what effect.