Team:Freiburg Bioware/Modeling/Structure Modeling

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<h1>Structure Modeling</h1>
<h1>Structure Modeling</h1>
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<h3>Virus Assembly</h3>
<h3>Virus Assembly</h3>
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The capsid assembly follows the scheme shown on the right. After
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transcription of plasmids coding for capsid proteins they assemble in
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groups of five.<br>
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Subsequently 15 of those pentamers are arranged in an icosahedral
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symmety and form the complex virus capsid where each pentamer
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corresponds to one corner with a pore complex in the center. <br>
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<br>
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Structure modeling was used to simulate and visualize the capsid
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assembly based on X-ray crytallography data. For this purpose
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cryo-frozen virus crystals were analysed with Laue diffraction and
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three dimensional structure was recontructed (Xie et al. 2002; Xie et
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al. 2003).<br>
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Based on the published data set we simulated the capsid formation in
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PyMOD (Schrödinger 2010). The whole 3D-structure was decomposed into
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single proteins. Each assembly step was rendered individually finally
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put together to animations consisting of up to 100 images depending on
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the perspective.<br>
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<br>
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To see the resulting animation just click on the overview image on the
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right! <br>
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Revision as of 11:45, 27 October 2010

Structure Modeling


Virus Assembly



The capsid assembly follows the scheme shown on the right. After transcription of plasmids coding for capsid proteins they assemble in groups of five.
Subsequently 15 of those pentamers are arranged in an icosahedral symmety and form the complex virus capsid where each pentamer corresponds to one corner with a pore complex in the center.

Structure modeling was used to simulate and visualize the capsid assembly based on X-ray crytallography data. For this purpose cryo-frozen virus crystals were analysed with Laue diffraction and three dimensional structure was recontructed (Xie et al. 2002; Xie et al. 2003).
Based on the published data set we simulated the capsid formation in PyMOD (Schrödinger 2010). The whole 3D-structure was decomposed into single proteins. Each assembly step was rendered individually finally put together to animations consisting of up to 100 images depending on the perspective.

To see the resulting animation just click on the overview image on the right!


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