Difference between revisions of "Team:ECUST/Model"

 
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              Hydrogen production
 
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       <h1 id="tables">Introduction</h1>
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       <h1 id="tables">Overview</h1>
 
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   <p><i>Rhodobacter sphaeroides 2.4.1(R. sphaeroides 2.4.1)</i> is the representative and most studied bacteria of phototrophic bacteria which can produce H<sub>2</sub> continuously in light. Some external factors of <i>R. sphaeroides 2.4.1</i> could influence the H<sub>2</sub> yield. These factors are culture medium, pH, temperature, illumination intensity and aerobic/anaerobic condition. All of important, internal factors containing ATP, reducing power, activity of uptake hydrogenase and nitrogenase decide hydrogen production. Photosynthetic system provides enough ATP for nitrogenase, and uptake hydrogenases consume the H<sub>2</sub>. [1]</p><br>
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   <p>The purpose of this modeling is to predict the improvement of hydrogen production of <i>Rhodobacter sphaeroids 2.4.1</i> after modifications of photobioreactor and <i>Rhodobacter sphaeroids 2.4.1</i>.</p><br>
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   <p>In Photosynthetic system of purple bacteria, both the light driven and respiratory electron transfers serve the sole purpose of generating a proton-motive force across their inner membrane (Fig. 1)。Almost all the useful work derived from absorbed sunlight is delivered to the cell in form of the ATP/ADP-couple in purple bacteria (Fig. 2). [2]</p><br>
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  <p>Our modelling is divided into three parts: <b>Model of Reactor</b>, <b>Föster theory</b>, <b>Hydrogen production</b>. it includes the whole process from photon absorption in photobioreactor to hydrogen production from <i>Rhodobacter spaeroids 2.4.1</i>.</p><br><br>
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      <h1 id="tables">Part One: Model of Reactor</h1>
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         <img src="https://static.igem.org/mediawiki/2017/f/f5/ATP.png " height:300px;>
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         <img src="https://static.igem.org/mediawiki/2017/e/ee/940201059.png" height:300px;>
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        <p style="color: black;">Fig 1. Formation of proton motive force</p>
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         <p>In this part we will predict how much photons fluorescent proteins in the photobioreactor can absorb .<br><br>
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        <p style="color: black;">Fig 2. Cartoon representation of bacterial ATP synthase</p>
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<p><font size="5"><i> To learn more about this，<a href="https://2017.igem.org/Team:ECUST/Part/Reactor">please click here.</font></a></i></p><br><br>
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    <p>The presence of hydrogenase has been found to be a common feature of the photosynthetic bacteria. In vitro studies show the hydrogenase of photosynthetic bacteria to be capable of both hydrogen production and consumption. However, since hydrogen production is attributed mainly to nitrogenase, hydrogen-producing activity of hydrogenase is negligible (if any). Studies seem to verify this assumption for R.capsulatus at least by showing that the hydrogen producing activity of hydrogenase is less than 10% of the hydrogen consuming activity and that the maximum activity for hydrogenase occurs at conditions favorable for H<sub>2</sub> uptake only. [3]So Hydrogen production is associated mainly or completely with the action of nitrogenase. This enzyme catalyzes hydrogen production in the absence of molecular nitrogen[4]:</p><br>
 
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    <p>However, nitrogenase needs sufficient amount of reducing power and energy in the form of ATP to produce H<sub>2</sub>, and the most significant role of photosynthetic system is to generate ATP. So the conversion efficiency of light is a limit to produce H<sub>2</sub>.</p><br><br>
 
  
  
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       <h1 id="tables">Modelling</h1>
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       <h1 id="tables">Part Two: Föster theory</h1>
 
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     <p>We have already obtained the protons(Nhv) absorbed by sYFP2, and energy can be transferred into reaction center through FRET to excite bacterial chlorophyll P. Then the electrons are transferred to proton quinone through charge separation.</p><br>
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    <p>The electron entering the proton quinone Q causes the quinone to become QH<sub>2</sub>. With the Catalysis of Rieske/Cyt b (RB) complexes，translocate protons across the bioenergetic membrane, thus storing a portion of the potential energy from the two electron / two proton oxidation reaction in the electrochemical proton gradient, or proton motive force (pmf) The pmf in turn drives the synthesis of ATP at the FO-F1-ATP synthase [2].</p><br>
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        <p>This section proves that energy of photons absorbed by fluorescent proteins can be transmitted to RC complex by Föster resonance energy transfer. By building a fusion protein model of H subunit in RC complex and fluorescent protein, we can predict the distance between the donor and the receptor and calculate the energy transfer efficiency by Föster theory.<br><br>
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<p><font size="5"><i> To learn more about this，<a href="https://2017.igem.org/Team:ECUST/Part/Theory">please click here.</font></a></i></p><br><br>
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  Q/QH<sub>2</sub>: the oxidized and reduced forms of the native quinone <br>
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  C(ox)/C(r): oxidized and reduced downstream electron carriers<br>
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  H+(P)/H+(n): aqueous protons on the positively and negatively charged sides of the energy transducing membrane.<br>
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    <p>Many studies shows ATP can be synthetized per four H+ through FO-F1-ATP synthase [2].</p>
 
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     <p>ATP synthetized will be provided for nitrogenase to produce H<sub>2</sub>, Given that the turnover of nitrogenase is 6.4s-1. [1] It still has potential to use more electrons and ATP to synthetize hydrogen.</p>
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      <h1 id="tables">Part Three: Hydrogen production</h1>
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  <p>We can finally estimate the excess H<sub>2</sub> produced through sYFP2.</p><br>
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        <p>This part mainly introduces the pathway of hydrogen production and calculates how much hydrogen will be produced. <br><br>
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<p><font size="5"><i> To learn more about this，<a href="https://2017.igem.org/Team:ECUST/Part/Hydrogen">please click here.</font></a></i></p><br><br>
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       <h1 id="tables">Reference</h1>
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       <h1 id="tables">Discussion</h1>
 
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    <p>We solved the following questions through modeling:</p>
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  1. Hallenbeck P C, Yakunin A F, Gennaro G. Electron Transport as a Limiting Factor in Biological Hydrogen Production[M]// BioHydrogen. Springer US, 1998:99-104. <br>
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     <p style="font-size: 8px;">
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  2. Sener, M. K. & Schulten, K. in The Purple Phototrophic Bacteria (eds Hunter, C. N. et al.) 475-493(Springer, 2009).<br>
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      1.We simulated increase of the photons absorbed by internal cells with light-emitting agitator. <br>
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  3. Koku H, İnci Eroğlu, Gündüz U, et al. Aspects of the metabolism of hydrogen production by <i>Rhodobacter sphaeroides</i>[J]. International Journal of Hydrogen Energy, 2002, 27(11):1315-1329.<br>
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      2.We proved the feasibility of FRET by homology modeling as well as calculating its efficiency.<br>
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  4. Frank B. Simpson The hydrogen reactions of nitrogenase.<br>
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      3.We calculated the theoretical increase in the amount of hydrogen production, give us greater confidence to complete the experiment.<br>
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    </p>
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    <p> Firstly, in <a href="https://2017.igem.org/Team:ECUST/Part/Reactor">model of reactor</a> , based on the simulated light intensity distribution, we figured out that the number of photons absorbed by fluorescent protein per second was 5.2×10 <sup>19</sup> and the energy of these photons was 20.1 joule. What’s more, in <a href="https://2017.igem.org/Team:ECUST/Part/Theory">Förster theory</a> , after predicting the distance(67.9 &Aring;) between energy donor(fluorescent protein) and energy acceptor(bacteriochlorophyll dimer in reaction center), we figured out that the efficiency of energy transfer from the fluorescent protein to reaction was 28.3%. Finally, in <a href="https://2017.igem.org/Team:ECUST/Part/Hydrogen">hydrogen production</a> , we further studied the charge separation, the electron transport chains and ATP synthesis of <i>Rhodobacter sphaeroides</i> as well as their relationship with hydrogen production. The theoretical increase in the amount of hydrogen production can be calculated as 0.12ml/s at last. </p>
  
  

Latest revision as of 03:59, 2 November 2017


Overview

The purpose of this modeling is to predict the improvement of hydrogen production of Rhodobacter sphaeroids 2.4.1 after modifications of photobioreactor and Rhodobacter sphaeroids 2.4.1.


Our modelling is divided into three parts: Model of Reactor, Föster theory, Hydrogen production. it includes the whole process from photon absorption in photobioreactor to hydrogen production from Rhodobacter spaeroids 2.4.1.



Part One: Model of Reactor

In this part we will predict how much photons fluorescent proteins in the photobioreactor can absorb .

To learn more about this，please click here.



Part Two: Föster theory

This section proves that energy of photons absorbed by fluorescent proteins can be transmitted to RC complex by Föster resonance energy transfer. By building a fusion protein model of H subunit in RC complex and fluorescent protein, we can predict the distance between the donor and the receptor and calculate the energy transfer efficiency by Föster theory.

To learn more about this，please click here.



Part Three: Hydrogen production

This part mainly introduces the pathway of hydrogen production and calculates how much hydrogen will be produced.

To learn more about this，please click here.



Discussion

We solved the following questions through modeling:

1.We simulated increase of the photons absorbed by internal cells with light-emitting agitator.
2.We proved the feasibility of FRET by homology modeling as well as calculating its efficiency.
3.We calculated the theoretical increase in the amount of hydrogen production, give us greater confidence to complete the experiment.



Firstly, in model of reactor , based on the simulated light intensity distribution, we figured out that the number of photons absorbed by fluorescent protein per second was 5.2×10 19 and the energy of these photons was 20.1 joule. What’s more, in Förster theory , after predicting the distance(67.9 Å) between energy donor(fluorescent protein) and energy acceptor(bacteriochlorophyll dimer in reaction center), we figured out that the efficiency of energy transfer from the fluorescent protein to reaction was 28.3%. Finally, in hydrogen production , we further studied the charge separation, the electron transport chains and ATP synthesis of Rhodobacter sphaeroides as well as their relationship with hydrogen production. The theoretical increase in the amount of hydrogen production can be calculated as 0.12ml/s at last.