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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>. Web fonts from <a href="https://fonts.google.com">Google</a>.</p></div></footer><script src="https://2021.igem.org/Template:Michigan/content-bundleJS?action=raw&ctype=text/javascript"></script></body></html> | + | <!-- # 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/ Model"> Model</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>. Web fonts from <a href="https://fonts.google.com">Google</a>.</p></div></footer><script src="https://2021.igem.org/Template:Michigan/content-bundleJS?action=raw&ctype=text/javascript"></script></body></html> |
Model
Computational Simulation of Encapsulin
