Difference between revisions of "Team:CCU Taiwan/Binding"

 
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Medal"><li class="list" id="home3">Medals</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/Medal"><li class="list" id="home3">Medals</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/Judge"><li class="list" id="home4">For Judges</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/Judge"><li class="list" id="home4">For Judges</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Achievements"><li class="list" id="home5">Achievements</li></a>
 
                         </ul>
 
                         </ul>
 
                     </li>
 
                     </li>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Entrepreneurship"><li class="list" id="human_practice3">Entrepreneurship</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/Entrepreneurship"><li class="list" id="human_practice3">Entrepreneurship</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/engaging_experts"><li class="list" id="human_practice4">Engaging Experts</li></a>
 
<a href="https://2018.igem.org/Team:CCU_Taiwan/engaging_experts"><li class="list" id="human_practice4">Engaging Experts</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Intergrate"><li class="list" id="human_practice5">Intergrated HP</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Integrate"><li class="list" id="human_practice5">Integrated HP</li></a>
 
                         </ul>
 
                         </ul>
 
                     </li>
 
                     </li>
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     </header>
 
     </header>
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<div class="indicator">
  
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<div class="pointerModeling" id="1"><a href="#ca1">Free radicals</a></div>
 +
<div class="pointerModeling" id="2"><a href="#ca2">Dimer formation</a></div>
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</div>
  
 
<div class="backgroundModeling">
 
<div class="backgroundModeling">
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<p class="first">Gibbs free energy</p>
 
<p class="first">Gibbs free energy</p>
 
<br>
 
<br>
−
\(ax^2 + bx + c = 0\)
+
<p class="description">&emsp;&emsp;Literature shows that coniferyl alcohol (monolignol G) forms resonance structure after creating a free radical, these resonance structures would form dimers (β-5, β-O-4, β-β). <br>
−
<p class="description">&emsp;&emsp;In our experiment, coniferyl alcohol (monolignols G) would become resonance structure after create a free radical, and two specific resonance structures would form a dimer (β-5, β-O-4, β-β). <br>
+
&emsp;&emsp;The reactions starts from the catalytic of the enzyme and the addition of water. We first assumed that our conditions may be different as the literature, so we decided to confirm the feasibility of the reaction through Gibbs free energy calculation.<br>
−
It is changed into a dimer by the action of the enzyme and the addition of water. Because the method we used may not be the same as the literature, we decided to confirm the feasibility of the reaction through Gibbs free energy calculation.<br>
+
 
(Calculation method using Spartan 16)
 
(Calculation method using Spartan 16)
 
</p><br><br>
 
</p><br><br>
−
<p class="second">(1) From monomeric alcohol to carrying free radicals</p>
+
<p class="second" id="ca1">(1) From monomeric alcohol to carrying free radicals</p>
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<p class="description">Figure 1. Reaction diagram (Initial figure is from Reference [1])</p>
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      <div id="Bind1" class="polaroid" style="display:inline-block">
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<p class="description">Figure 2. Monolignol alcohol as the free energy benchmark (1 hartree ≈ 2625.5 kJ/mole), Resonance(left) is Figure 1. left resonance, Resonance(middle) is Figure 1. middle resonance, Resonance(right) is Figure 1. right resonance<br></p>
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                  <img id="twopics"src="https://static.igem.org/mediawiki/2018/f/f2/T--CCU_Taiwan--model1.png">
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<p class="description">In Figure 2, we found that the free energy of the process of creating free radicals is positive, so it is not spontaneous, so we need to make the reaction happen using enzymes and hydrogen peroxide.</p><br><br>
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                  <img id="twopics" src="https://static.igem.org/mediawiki/2018/8/8e/T--CCU_Taiwan--CCUmodel232.png">
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<p class="second">(2) Free radical state to dimer formation</p>
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                  <div class="container">
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<p class="description">Figure 3. The green indicator is β-O-4; the blue indicator is β-β; the red indicator is β-5 (Initial figure is from Reference [1])</p>
+
                    <p>Figure 1: (Left) Three resonance forms(Wang, Y. et al. 2013), (Right) Reaction diagram (Vanholme, R. et al. 2010)</p>
−
<p class="description">Figure 4. β-β free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-β formation (1  hartree ≈ 2625.5 kJ/mole)</p>
+
                  </div>
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<p class="description">Figure 5. β-5 free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-5 formation (1 hartree ≈ 2625.5 kJ/mole)</p>
+
                </div>     
−
<p class="description">Figure 6. β-O-4 free energy change, (a) is two resonance monolignols, (b) is two resonance monolignol bonding, (c) is formed by β-O-4, and water is added to the reaction at 2 to 3 (1 hartree ≈ 2625.5 kJ/mole)</p>
+
<br><br>
−
<p class="description">Boltzmann distribution is a probability distribution that gives the probability that a system will be in a certain state as a function of that state’s energy and the temperature of the system. [wiki]</p>
+
      <div id="Bind2" class="polaroid" style="display:inline-block">
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<p class="description">From Boltzmann distribution we knew<br>
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                  <img id="twopics3" src="https://static.igem.org/mediawiki/2018/6/6c/T--CCU_Taiwan--CCUmodel213212.png">
−
P_i=e^((-ε_i)/(k_B T))/(∑_(j=1)^N▒e^((-ε_j)/(k_B T)) )<br>
+
                  <div class="container">
−
</p>
+
                    <p>Figure 2: Monolignol as the free energy benchmark (1 hartree ≈ 2625.5 kJ/mole)</p>
−
<p class="description">If the system at constant pressure<br>
+
                  </div>
−
1. We can use enthalpy (H) as the energy of state (ε).
+
                </div>
 +
 
 +
<br><br>
 +
<p class="description">&emsp;&emsp;In Figure 2. , we found that the free energy of this process is positive, which means it's not spontaneous. Thus, we think the way to make the reactions spontaneous is to use enzymes such as laccase and peroxidase.</p><br><br>
 +
<p class="second" id="ca2">(2) Free radical state of dimer formation</p><br>
 +
      <div id="Bind3" class="polaroid" style="display:inline-block">
 +
                  <img src="https://static.igem.org/mediawiki/2018/5/58/T--CCU_Taiwan--model2.png" width="100%">
 +
                  <div class="container">
 +
                    <p>Figure 3: The green indicator is β-O-4; the blue indicator is β-β; the red indicator is β-5 (Barceló, A. R. et al. 2004)</p>
 +
                  </div>
 +
                </div>
 +
      <div id="Bind4" class="polaroid" style="display:inline-block">
 +
                  <img src="https://static.igem.org/mediawiki/2018/2/2d/T--CCU_Taiwan--model4.png" width="100%">
 +
                  <div class="container">
 +
                    <p>Figure 4: β-β free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-β formation (1  hartree ≈ 2625.5 kJ/mole)</p>
 +
                  </div>
 +
                </div><br><br><br>
 +
 
 +
      <div id="Bind5" class="polaroid">
 +
                  <img id="twopics" src="https://static.igem.org/mediawiki/2018/f/f5/T--CCU_Taiwan--model5.png">
 +
                  <img  id="twopics" src="https://static.igem.org/mediawiki/2018/d/da/T--CCU_Taiwan--model6.png">
 +
                  <div class="container">
 +
                    <p>Figure 5: β-5 free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-5 formation (1 hartree ≈ 2625.5 kJ/mole)</p>
 +
                  </div>
 +
                </div><br>
 +
<br>
 +
      <div id="Bind6" class="polaroid" style="display:inline-block">
 +
                  <img  id="twopics" src="https://static.igem.org/mediawiki/2018/e/ef/T--CCU_Taiwan--model7.png">
 +
                  <img  id="twopics" src="https://static.igem.org/mediawiki/2018/0/04/T--CCU_Taiwan--model8.png">
 +
                  <div class="container">
 +
                    <p>Figure 6: β-O-4 free energy change, (a) is two resonance monolignols, (b) is two resonance monolignol bonding, (c) is formed by β-O-4, and water is added to the reaction at 2 to 3 (1 hartree ≈ 2625.5 kJ/mole)</p>
 +
                  </div>
 +
                </div><br><br>
 +
<p class="description">&emsp;&emsp;Through these simulations, it's obvious that these reactions are thermodynamically spontaneous at room temperature with catalysts, and it's also feasible to synthesize these bonds by using our enzymes.</p>
 +
 
 +
 
 +
 
 +
      <div id="Bind7" class="polaroid" style="display:inline-block">
 +
                  <img src="https://static.igem.org/mediawiki/2018/c/c8/T--CCU_Taiwan--model_table1.png" width="100%">
 +
                  <div class="container">
 +
                    <p>Figure 7: Calculation data-coniferyl alcohol to resonance form</p>
 +
                  </div>
 +
                </div>
 +
      <div id="Bind8" class="polaroid" style="display:inline-block">
 +
                  <img src="https://static.igem.org/mediawiki/2018/a/a5/T--CCU_Taiwan--model_table2.png" width="100%">
 +
                  <div class="container">
 +
                    <p>Figure 8: Calculation data-resonance form to dimer</p>
 +
                  </div>
 +
                </div><br><br>
 +
 
 +
                <p class="second">Reference</p>
 +
                <p class="description">Barceló, A. R., Ros, L. G., Gabaldón, C., López-Serrano, M., Pomar, F., Carrión, J. S., & Pedreño, M. A. (2004). Basic peroxidases: the gateway for lignin evolution? . Phytochemistry Reviews. (2004), 3(1-2), 61-78
 +
<br>
 +
<br>
 +
Vanholme, R., Demedts, B., Morreel, K., Ralph, J., & Boerjan, W. (2010). Lignin biosynthesis and structure.(2010) Plant physiology, 153(3), 895-905.
 +
<br>
 +
<br>
 +
Wang, Y., Chantreau, M., Sibout, R., & Hawkins, S. (2013). Plant cell wall lignification and monolignol metabolism. Frontiers in plant science, 4, 220
 
</p>
 
</p>
−
<p class="description">2.  We needed to multiply the number of different arrangement.</p>
+
<br>
−
<p class="description">(From thermodynamic, (H - TS) = Gibbs free energy)</p>
+
<br>
−
<p class="description">so Boltzmann distribution become</p>
+
<br>
−
<p class="description">Used this form equation, we estimated that the probability of state is smaller if Gibbs free energy is larger.<br>
+
<br>
−
Finally, we used this information to estimated that<br>three kinds dimer occurrence probabilities are β-5 > β-β >β-O-4  .
+
 
−
</p><br><br>
+
 
       </div>
 
       </div>
 
</div>
 
</div>

Latest revision as of 08:48, 1 December 2018

BINDING MODEL



Gibbs free energy


  Literature shows that coniferyl alcohol (monolignol G) forms resonance structure after creating a free radical, these resonance structures would form dimers (β-5, β-O-4, β-β).
  The reactions starts from the catalytic of the enzyme and the addition of water. We first assumed that our conditions may be different as the literature, so we decided to confirm the feasibility of the reaction through Gibbs free energy calculation.
(Calculation method using Spartan 16)



(1) From monomeric alcohol to carrying free radicals

Figure 1: (Left) Three resonance forms(Wang, Y. et al. 2013), (Right) Reaction diagram (Vanholme, R. et al. 2010)



Figure 2: Monolignol as the free energy benchmark (1 hartree ≈ 2625.5 kJ/mole)



  In Figure 2. , we found that the free energy of this process is positive, which means it's not spontaneous. Thus, we think the way to make the reactions spontaneous is to use enzymes such as laccase and peroxidase.



(2) Free radical state of dimer formation


Figure 3: The green indicator is β-O-4; the blue indicator is β-β; the red indicator is β-5 (Barceló, A. R. et al. 2004)

Figure 4: β-β free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-β formation (1 hartree ≈ 2625.5 kJ/mole)




Figure 5: β-5 free energy changes, (a) is the two resonant monolignols, (b) is the two resonant monolignol bonds, (c) is β-5 formation (1 hartree ≈ 2625.5 kJ/mole)



Figure 6: β-O-4 free energy change, (a) is two resonance monolignols, (b) is two resonance monolignol bonding, (c) is formed by β-O-4, and water is added to the reaction at 2 to 3 (1 hartree ≈ 2625.5 kJ/mole)



  Through these simulations, it's obvious that these reactions are thermodynamically spontaneous at room temperature with catalysts, and it's also feasible to synthesize these bonds by using our enzymes.

Figure 7: Calculation data-coniferyl alcohol to resonance form

Figure 8: Calculation data-resonance form to dimer



Reference

Barceló, A. R., Ros, L. G., Gabaldón, C., López-Serrano, M., Pomar, F., Carrión, J. S., & Pedreño, M. A. (2004). Basic peroxidases: the gateway for lignin evolution? . Phytochemistry Reviews. (2004), 3(1-2), 61-78

Vanholme, R., Demedts, B., Morreel, K., Ralph, J., & Boerjan, W. (2010). Lignin biosynthesis and structure.(2010) Plant physiology, 153(3), 895-905.

Wang, Y., Chantreau, M., Sibout, R., & Hawkins, S. (2013). Plant cell wall lignification and monolignol metabolism. Frontiers in plant science, 4, 220