Difference between revisions of "Team:NAIT Edmonton/Modeling"

 
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<h2>We find that in science, it is hard to fully grasp a real life concept when it is shown to us only in two dimensions. We live in a three dimensional world! Why are we learning how things work only in 2D? We visualized our project with 3D models and made animations so that anyone of the general public could watch the videos, understand and get excited about the science behind our project.</h2>
 
<h2>We find that in science, it is hard to fully grasp a real life concept when it is shown to us only in two dimensions. We live in a three dimensional world! Why are we learning how things work only in 2D? We visualized our project with 3D models and made animations so that anyone of the general public could watch the videos, understand and get excited about the science behind our project.</h2>
  
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<center><h2>If a picture is worth a thousand words, a video is worth a million. Take a gander through our our 3D models and animations! </h2> </center>
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<center><h2>If a picture is worth a thousand words, a video is worth a million. Take a gander through our 3D models and animations! </h2> </center>
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<center><img src="https://static.igem.org/mediawiki/2015/0/00/NAIT_Apoferritin.jpg"></center><br>
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<h2>Above is a typical textbook representation of the protein, apoferritin. From this 2D representation, personally we find it difficult to gauge the actual structure and shape of the protein. Since the shape of the protein is essential to its function, why do we limit ourselves to such a primitive 2D drawing? </h2>
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<h2>Below is an interactive 3D model of apoferritin. Through 3D technology, you can gain a better appreciation of the shape, contours and therefore function of the protein. </h2><br>
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<center><object width="640" height="480" data="https://sketchfab.com/models/b46ac7c5a7a34ddcabb3cd091e100f4f/embed" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" onmousewheel=""></object></center>
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<center><h1>How Does SDS PAGE Work?</h1></center>
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<h3>SDS PAGE is a technique used to separate proteins by their molecular weight. Within a sample, there are multiple different types of protein. If we wanted to study a specific one, we would have to separate the different types first and isolate our desired protein. </h3> <br>
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<center><img src="https://static.igem.org/mediawiki/2015/7/74/NAIT_ProteinSample.png" width="500px"><font style="12px">Figure 1, A rendered visualization of what a protein sample may look like through SEM</font></center> <br><br>
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<center><object width="100%" height="250px" data="http://sketchfab.com/models/1a59a35728ac4323aabc905c8363c619/embed" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" onmousewheel=""></object></center>
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<p><font style="12px">Source: apoferritin: complex with SDS, RCSB Protein Data Bank</font></p>
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<h3>As a quick overview, proteins are first denatured and linearized by SDS after being suspended in a protein sample loading buffer. Additionally, the SDS coats proteins with a negative charge. Immediately after denaturation, proteins are loaded into the wells of a polyacrylamide gel and an electric current is passed through it. The negatively charged proteins are pulled through the gel and migrate towards the electrode. The model you see here is an example of a binding site for SDS in mammalian apoferritin. SDS binds to multiple sites such as these and along with a heat treatment, plays a role in linearizing the proteins. Often, heat treatment is skipped all together and proteins are completely denatured using only the detergent, SDS.</h3> <br>
  
 
    
 
    
 
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<center><object width="999" height="562" data="http://www.youtube.com/embed/cLNwq9Ci9fk" frameborder="0" allowfullscreen></object></center>
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<font style="12px">Figure 2, An Autodesk Maya render of a protein linearizing and denaturing in the presence of SDS </font> <br><br>
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<h3>Polyacrylamide gel acts like a mesh that strains and separates proteins based on size or molecular weight. Larger, bulkier proteins have a difficult time twisting and turning through the pores while smaller proteins slip through quite easily. Therefore, smaller proteins travel further down the gel within the specific time that the current is on while larger proteins stay closer to the top of the gel. </h3>
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Latest revision as of 18:20, 2 November 2015

Team NAIT 2015

Modeling

We find that in science, it is hard to fully grasp a real life concept when it is shown to us only in two dimensions. We live in a three dimensional world! Why are we learning how things work only in 2D? We visualized our project with 3D models and made animations so that anyone of the general public could watch the videos, understand and get excited about the science behind our project.

If a picture is worth a thousand words, a video is worth a million. Take a gander through our 3D models and animations!


Above is a typical textbook representation of the protein, apoferritin. From this 2D representation, personally we find it difficult to gauge the actual structure and shape of the protein. Since the shape of the protein is essential to its function, why do we limit ourselves to such a primitive 2D drawing?

Below is an interactive 3D model of apoferritin. Through 3D technology, you can gain a better appreciation of the shape, contours and therefore function of the protein.





How Does SDS PAGE Work?


SDS PAGE is a technique used to separate proteins by their molecular weight. Within a sample, there are multiple different types of protein. If we wanted to study a specific one, we would have to separate the different types first and isolate our desired protein.


Figure 1, A rendered visualization of what a protein sample may look like through SEM


Source: apoferritin: complex with SDS, RCSB Protein Data Bank

As a quick overview, proteins are first denatured and linearized by SDS after being suspended in a protein sample loading buffer. Additionally, the SDS coats proteins with a negative charge. Immediately after denaturation, proteins are loaded into the wells of a polyacrylamide gel and an electric current is passed through it. The negatively charged proteins are pulled through the gel and migrate towards the electrode. The model you see here is an example of a binding site for SDS in mammalian apoferritin. SDS binds to multiple sites such as these and along with a heat treatment, plays a role in linearizing the proteins. Often, heat treatment is skipped all together and proteins are completely denatured using only the detergent, SDS.


Figure 2, An Autodesk Maya render of a protein linearizing and denaturing in the presence of SDS

Polyacrylamide gel acts like a mesh that strains and separates proteins based on size or molecular weight. Larger, bulkier proteins have a difficult time twisting and turning through the pores while smaller proteins slip through quite easily. Therefore, smaller proteins travel further down the gel within the specific time that the current is on while larger proteins stay closer to the top of the gel.