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| + | <!-- # TODO: #6 Fix table caption font--><!-- # TODO: #7 Fix citations links font size--><html lang="en">< head><meta charset=" utf- 8"/><meta content="width=device- width,initial- scale=1" name="viewport"/>< title> Model | iGEM Michigan</ title>< script src="https:// 2020.igem.org/ common/ MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></ script>< link href="https://2021.igem.org/ Template:Michigan/ css/contentCSS?action=raw&ctype=text/css" rel="stylesheet"/></ head>< body>< !-- # TODO: #6 Fix table caption font--><!-- # TODO: #7 Fix citations links font size--><nav class="navbar navbar-expand-xl fixed-top"><div class="container d-flex justify-content-between"><a class="navbar-brand d-lg-inline-block" href="https://2021.igem.org/ Team:Michigan">< span> iGEM </ span> Michigan</ a>< button aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation" class=" navbar-toggler" data-target="#navbarNav" data-toggle="collapse" type="button">< span class=" navbar-toggler-icon"></ span></ button>< div class="collapse navbar-collapse" id="navbarNav">< ul class="navbar-nav ml-auto">< li class="nav-item dropdown">< a aria-expanded="false" aria-haspopup="true" class=" nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarTeamDropdown" role="button"> Team</ a><div aria-labelledby="navbarTeamDropdown" class=" dropdown-menu">< a class="dropdown-item" href="https://2021.igem.org/Team:Michigan/Team"> Team</ a><a class="dropdown-item" href="https://2021. igem.org/Team:Michigan/Attributions"> Attributions< /a><a class="dropdown-item" href="https://2021.igem.org/ Team:Michigan/ Collaborations"> Collaborations</a></ div></ li>< li class=" nav-item dropdown">< a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarProjectDropdown" role="button"> Project</ a>< div aria-labelledby="navbarProjectDropdown" class="dropdown-menu"> <a class="dropdown-item" href="https://2021. igem. org/ Team:Michigan/Contribution"> Contribution< /a><a class="dropdown-item" href="https://2021.igem.org/ Team:Michigan/ Description"> Description</a><a class="dropdown-item" href="https://2021.igem.org/ Team:Michigan/ Modeling"> Modeling</a>< a class="dropdown-item" href="https:/ /2021.igem.org/Team:Michigan/Experiments"> Experiments</ a>< a class=" dropdown-item" href=" https://2021.igem.org/Team:Michigan/Engineering"> Engineering< /a>< a class="dropdown-item" href="https:/ /2021.igem.org/Team:Michigan/Notebook"> Notebook</ a> <a class="dropdown-item" href="https:/ /2021.igem.org/Team:Michigan/Results"> Results< /a><a class="dropdown-item" href="https:// 2021.igem.org/Team: Michigan/ Implementation"> Implementation</a ></div></li><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarPartsDropdown" role="button">Parts</a><div aria-labelledby="navbarPartsDropdown" class="dropdown-menu"><a class="dropdown-item" href="https:// 2021.igem.org/Team: Michigan/ Parts"> Parts</a ></div></li><li class="nav-item"><a class="nav-link" href="https:// 2021.igem.org/Team: Michigan/ Human_Practices"> Human Practices</a></li>< /ul>< /div><div class="d-flex" id="themeSwitchWrapper"><i class="far fa-sun"></i><div id="themeSwitch"><label class="switch" for="themeSwitchInput"><input id="themeSwitchInput" type="checkbox"/><span class="slider round"></span></label></div><i class="far fa-moon"></i></div></div></nav><header class="d-flex justify-content-center align-items-center"><div class="container"><h1>Model</h1><p class="lead pl-1">Computational Simulation of Encapsulin</p><hr class="my-4"/></div></header><main><div class="container"><div class="row"><div class="sidebar col-lg-3"><div class="nav" id="contents"><h5>Contents</h5><ul></ul></div></div><div class="content col-lg-9"><article><p>Computational modeling was a valuable tool in investigating the properties of encapsulin nanocompartments.</p><p>We used GROMACS, CHARMM and VMD software to simulate our encapuslin monomer. The encapsulin monomer is positioned in a box that is attached to a member of the yeast cell membrane using alpha-factor pheromone as a ligand. Under these simulated conditions, the encapsulin monomer is stable.</p><div class="image"><img alt="Free Encapsulin Monomer" src="https:// static.igem.org/ mediawiki/ 2021/f/f8/T--Michigan--img--modeling1.gif" style="width: 80%"/> <p>Figure 1: Free Encapsulin Monomer</ p>< /div>< div class="image"><img alt="Encapsulin Monomer Bound to Yeast Plasma Membrane with Alpha Factor Tag" src="https:// static.igem.org/ mediawiki/ 2021/d/d5/T--Michigan--img--modeling2.gif" style="width: 80%"/> <p>Figure 2: Encapsulin Monomer Bound to Yeast Plasma Membrane with Alpha Factor Tag</ p></ div><p>Due to computational constraints, it was not feasible to simulate the entire protein with alpha-factor pheromones attached to each monomer. Nevertheless, we made the following observations based on the simulated scenarios:</p><ul><li> The N-term of the pheromone is required to be free for binding< /li> <li>Only the C-term of the encapsulin is available for linkage</li><li>This precludes the fusing of the free C-term of the ligand and the C-term of the encapsulin</li><li>This has implications for primer design and linker positioning when adding the alpha factor sequence</li></ul></article></div></div></div></main><footer><div class="container"><p>Built using the iGEM Wiki Starter Pack by BITS Goa.</p><p>Code released under the MIT license.</p><p>Based on <a href="https:// getbootstrap. com">Bootstrap</ a> and themes <a href="https:/ /bootswatch.com/flatly/"> Flatly</a> and < a href="https:/ /bootswatch.com/darkly/"> Darkly< /a> from <a href="https:// bootswatch. com/">Bootswatch</a>. </ p><p>Icons from <a href="flaticon.com">Flaticon</a>. Images from <a href="https:/ /unsplash.com"> Unsplash</a> . 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| − | <h3>★ ALERT! </h3> | + | |
| − | <p>This page is used by the judges to evaluate your team for the <a href="https://2021.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2021.igem.org/Judging/Awards"> award listed below</a>. </p> | + | |
| − | < p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2021.igem.org/ Judging/Pages_for_Awards"> Instructions for Pages for awards< /a> .</ p> | + | |
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| − | <h1> Modeling</h1>
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| − | <p>Mathematical models and computer simulations provide a great way to describe the function and operation of Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. </p>
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| − | <p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p> | + | |
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| − | <h3> Gold Medal Criterion #3</h3> | + | |
| − | <p> | + | |
| − | Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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| − | Please see the <a href="https://2021.igem.org/ Judging/ Medals"> 2021 Medals Page</a> for more information. | + | |
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| − | <h3>Best Model Special Prize</h3> | + | |
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| − | <p>Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior before or in conjunction with experiments in the wetlab. | + | |
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| − | To compete for the <a href="https://2021.igem.org/ Judging/ Awards"> Best Model prize</a> , please describe your work on this page and also fill out the description on the <a href="https://2021.igem.org/ Judging/ Judging_Form"> judging form</a> . | + | |
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| − | <h3> Inspiration </h3> | + | |
| − | <p>You can look at what other teams did to get some inspiration! <br /> | + | |
| − | Here are a few examples:</p>
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| − | <li><a href="https:// 2018.igem.org/Team: GreatBay_China/ Model"> 2018 GreatBay China</a></li> | + | |
| − | <li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li> | + | |
| − | <li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li> | + | |
| − | < li><a href="https:// 2019.igem.org/ Team:Exeter/ Model"> 2019 Exeter</ li> | + | |
| − | <li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li> | + | |
| − | <li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li> | + | |
| − | < li><a href="https:// 2020. igem. org/ Team: Leiden/ Model"> 2020 Leiden</a></ li> | + | |
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Model
Computational Simulation of Encapsulin
