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}); | }); | ||
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− | + | // The function actually applying the offset | |
− | + | function offsetAnchor() { | |
− | + | if (location.hash.length !== 0) { | |
− | + | window.scrollTo(window.scrollX, window.scrollY - 90); | |
− | }) | + | } |
+ | } | ||
+ | |||
+ | // Captures click events of all <a> elements with href starting with # | ||
+ | $(document).on('click', 'a[href^="#"]', function(event) { | ||
+ | // Click events are captured before hashchanges. Timeout | ||
+ | // causes offsetAnchor to be called after the page jump. | ||
+ | window.setTimeout(function() { | ||
+ | offsetAnchor(); | ||
+ | }, 0); | ||
+ | }); | ||
+ | |||
+ | // Set the offset when entering page with hash present in the url | ||
+ | window.setTimeout(offsetAnchor, 0); | ||
+ | |||
+ | $(document).scroll(function () { // remove "$" | ||
+ | var y = $(this).scrollTop(); | ||
+ | if (y > 300) { | ||
+ | $('.indicator').fadeIn(); | ||
+ | } | ||
+ | else { | ||
+ | $('.indicator').fadeOut(); | ||
+ | } | ||
+ | }); | ||
</script> | </script> | ||
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'https://2018.igem.org/Team:CCU_Taiwan';"> <img src="https://static.igem.org/mediawiki/2018/0/08/T--CCU_Taiwan--home_button.png"></img></div> | 'https://2018.igem.org/Team:CCU_Taiwan';"> <img src="https://static.igem.org/mediawiki/2018/0/08/T--CCU_Taiwan--home_button.png"></img></div> | ||
− | <li class="title" style="cursor:pointer;" id="Home"><img class="img_title" src="https://static.igem.org/mediawiki/2018/2/24/T--CCU_Taiwan--aboutus.png"></img><a>About Us</a | + | <li class="title" style="cursor:pointer;" id="Home"><img class="img_title" src="https://static.igem.org/mediawiki/2018/2/24/T--CCU_Taiwan--aboutus.png"></img><a>About Us</a> |
<ul class="sub" id="sub_home" style="cursor:default;"> | <ul class="sub" id="sub_home" style="cursor:default;"> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Team"><li class="list" id="home1">Team</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Team"><li class="list" id="home1">Team</li></a> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Attributions"><li class="list" id="home2">Attributions</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Attributions"><li class="list" id="home2">Attributions</li></a> | ||
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/Medal"><li class="list" id=" | + | <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=" | + | <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/Achievements"><li class="list" id="home5">Achievements</li></a> | ||
</ul> | </ul> | ||
</li> | </li> | ||
− | <li class="title" style="cursor:pointer;" id="Project"><img class="img_title" src="https://static.igem.org/mediawiki/2018/6/6f/T--CCU_Taiwan--project.png"></img><a>Project</a | + | <li class="title" style="cursor:pointer;" id="Project"><img class="img_title" src="https://static.igem.org/mediawiki/2018/6/6f/T--CCU_Taiwan--project.png"></img><a>Project</a> |
<ul class="sub" id="sub_project" style="cursor:default;"> | <ul class="sub" id="sub_project" style="cursor:default;"> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Description"><li class="list" id="project1">Description</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Description"><li class="list" id="project1">Description</li></a> | ||
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Results"><li class="list" id="project3">Results</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Results"><li class="list" id="project3">Results</li></a> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Demonstrate"><li class="list" id="project4">Demonstration</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Demonstrate"><li class="list" id="project4">Demonstration</li></a> | ||
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/InterLab "><li class="list" id="project5">InterLab</li></a> | + | <a href="https://2018.igem.org/Team:CCU_Taiwan/InterLab"><li class="list" id="project5">InterLab</li></a> |
</ul> | </ul> | ||
</li> | </li> | ||
− | <li class="title" style="cursor:pointer;" id="Parts"><img class="img_title" src="https://static.igem.org/mediawiki/2018/1/17/T--CCU_Taiwan--part.png"></img><a>Parts</a | + | <li class="title" style="cursor:pointer;" id="Parts"><img class="img_title" src="https://static.igem.org/mediawiki/2018/1/17/T--CCU_Taiwan--part.png"></img><a>Parts</a> |
<ul class="sub" id="sub_parts" style="cursor:default;"> | <ul class="sub" id="sub_parts" style="cursor:default;"> | ||
+ | <a href="https://2018.igem.org/Team:CCU_Taiwan/Parts"><li class="list" id="parts1">Overview</li></a> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Basic_Part"><li class="list" id="parts1">Basic Part</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Basic_Part"><li class="list" id="parts1">Basic Part</li></a> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Composite_Part"><li class="list" id="parts2">Composite Part</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Composite_Part"><li class="list" id="parts2">Composite Part</li></a> | ||
− | |||
</ul> | </ul> | ||
</li> | </li> | ||
− | <li class="title" style="cursor:pointer;" id="Modeling"><img class="img_title" src="https://static.igem.org/mediawiki/2018/0/09/T--CCU_Taiwan--model.png"></img><a>Modeling</a | + | <li class="title" style="cursor:pointer;" id="Modeling"><img class="img_title" src="https://static.igem.org/mediawiki/2018/0/09/T--CCU_Taiwan--model.png"></img><a>Modeling</a> |
<ul class="sub" id="sub_modeling" style="cursor:default;"> | <ul class="sub" id="sub_modeling" style="cursor:default;"> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Model"><li class="list" id="model1">Overview</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Model"><li class="list" id="model1">Overview</li></a> | ||
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/Binding"><li class="list" id="model2">Binding</li></a> | + | <a href="https://2018.igem.org/Team:CCU_Taiwan/Binding"><li class="list" id="model2">Binding Model</li></a> |
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/Polymer"><li class="list" id="model3">Polymer</li></a> | + | <a href="https://2018.igem.org/Team:CCU_Taiwan/Polymer"><li class="list" id="model3">Polymer Model</li></a> |
</ul> | </ul> | ||
</li> | </li> | ||
− | <li class="title" style="cursor:pointer;" id="Drylab"><img class="img_title" src="https://static.igem.org/mediawiki/2018/f/fc/T--CCU_Taiwan--Dry_lab.png"></img><a>Product</a | + | <li class="title" style="cursor:pointer;" id="Drylab"><img class="img_title" src="https://static.igem.org/mediawiki/2018/f/fc/T--CCU_Taiwan--Dry_lab.png"></img><a>Product</a> |
<ul class="sub" id="sub_drylab" style="cursor:default;"> | <ul class="sub" id="sub_drylab" style="cursor:default;"> | ||
<a href="https://2018.igem.org/Team:CCU_Taiwan/Our_Plan"><li class="list" id="drylab1">Analysis</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Our_Plan"><li class="list" id="drylab1">Analysis</li></a> | ||
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</ul> | </ul> | ||
</li> | </li> | ||
− | <li class="title" style="cursor:pointer;" id="Human_Practice"><img class="img_title" src="https://static.igem.org/mediawiki/2018/9/96/T--CCU_Taiwan--humanpractice.png"></img><a>HP</a | + | <li class="title" style="cursor:pointer;" id="Human_Practice"><img class="img_title" src="https://static.igem.org/mediawiki/2018/9/96/T--CCU_Taiwan--humanpractice.png"></img><a>HP</a> |
<ul class="sub" id="sub_human_practice" style="cursor:default;"> | <ul class="sub" id="sub_human_practice" style="cursor:default;"> | ||
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/Human_Practices"><li class="list" id="human_practice1"> | + | <a href="https://2018.igem.org/Team:CCU_Taiwan/Human_Practices"><li class="list" id="human_practice1">Human Practice</li></a> |
<a href="https://2018.igem.org/Team:CCU_Taiwan/Public_Engagement"><li class="list" id="human_practice2">Public Engagement</li></a> | <a href="https://2018.igem.org/Team:CCU_Taiwan/Public_Engagement"><li class="list" id="human_practice2">Public Engagement</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/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> | ||
− | <a href="https://2018.igem.org/Team:CCU_Taiwan/ | + | <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> | ||
+ | <div class="indicator"> | ||
+ | |||
+ | <div class="pointerModeling" id="1"><a href="#ca1">Free radicals</a></div> | ||
+ | <div class="pointerModeling" id="2"><a href="#ca2">Dimer formation</a></div> | ||
+ | </div> | ||
<div class="backgroundModeling"> | <div class="backgroundModeling"> | ||
− | <div class=" | + | <div class="photoBinding"><h1 class="bigtitle">BINDING MODEL<h1></div> |
<div class="content"> | <div class="content"> | ||
− | + | <br><br> | |
− | <p class="description">   | + | <p class="first">Gibbs free energy</p> |
− | + | <br> | |
− | (Calculation method using Spartan 16 | + | <p class="description">  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> | + |   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> |
− | <p class="second">(1) From monomeric alcohol to carrying free radicals</p> | + | (Calculation method using Spartan 16) |
− | + | </p><br><br> | |
− | + | <p class="second" id="ca1">(1) From monomeric alcohol to carrying free radicals</p> | |
− | <p class="description">In Figure 2, we found that the free energy of | + | <div id="Bind1" class="polaroid" style="display:inline-block"> |
− | <p class="second">(2) Free radical state | + | <img id="twopics"src="https://static.igem.org/mediawiki/2018/f/f2/T--CCU_Taiwan--model1.png"> |
− | + | <img id="twopics" src="https://static.igem.org/mediawiki/2018/8/8e/T--CCU_Taiwan--CCUmodel232.png"> | |
− | + | <div class="container"> | |
− | + | <p>Figure 1: (Left) Three resonance forms(Wang, Y. et al. 2013), (Right) Reaction diagram (Vanholme, R. et al. 2010)</p> | |
− | + | </div> | |
− | + | </div> | |
− | + | <br><br> | |
− | + | <div id="Bind2" class="polaroid" style="display:inline-block"> | |
− | + | <img id="twopics3" src="https://static.igem.org/mediawiki/2018/6/6c/T--CCU_Taiwan--CCUmodel213212.png"> | |
− | </ | + | <div class="container"> |
− | + | <p>Figure 2: Monolignol as the free energy benchmark (1 hartree ≈ 2625.5 kJ/mole)</p> | |
− | + | </div> | |
− | + | </div> | |
− | + | ||
− | + | <br><br> | |
+ | <p class="description">  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">  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> | ||
+ | <br> | ||
+ | <br> | ||
+ | <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