Difference between revisions of "Team:IIT Madras/In-Silico"

 
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<h2>Prediction structure of a neutralising protein</h2>
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<h2>Predicting structure of a neutralising protein</h2>
 
<p> To achieve our goal of achieving an antimicrobial free environment, it was necessary to inactivate the antimicrobial peptide Alyteserin. When a protein interacts with another protein, its structure is altered. This prevents the protein from performing from it's usual function. This was what we set out to do-design a small peptide that would interact with Alyteserin favourably under specified conditions. We also tried to simulate the interaction between the two peptides using GROMACS, and the results will be discussed later on on this page. First let's analyse the structure of Alyteserin.
 
<p> To achieve our goal of achieving an antimicrobial free environment, it was necessary to inactivate the antimicrobial peptide Alyteserin. When a protein interacts with another protein, its structure is altered. This prevents the protein from performing from it's usual function. This was what we set out to do-design a small peptide that would interact with Alyteserin favourably under specified conditions. We also tried to simulate the interaction between the two peptides using GROMACS, and the results will be discussed later on on this page. First let's analyse the structure of Alyteserin.
  
 
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<img align="left" src = "https://static.igem.org/mediawiki/2015/9/9b/Alyteserin1.png">
 
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<img src = "https://static.igem.org/mediawiki/2015/2/24/Surface.png">
 
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<h2>Structural Features of Alyteserin and Naly</h2>
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&nbsp;<img height="350px" width="350px" src="https://static.igem.org/mediawiki/2015/7/7a/Alyteserin_structural_feature.png">
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<img height="350px" width="350px" src = "https://static.igem.org/mediawiki/2015/7/72/Naly_structural_feature.png">
  
 
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<h2>Interactions</h2>
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<div style="text-align:center"><img height="486px" width="633px" src = "https://static.igem.org/mediawiki/2015/a/ad/Aly_naly_interaction.png"></div>
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<h2>GROMACS Simulation</h2>
 
<div style="text-align:center"><img height="372px" width="650px" src = "https://static.igem.org/mediawiki/2015/0/05/Igem.gif"></div>
 
<div style="text-align:center"><img height="372px" width="650px" src = "https://static.igem.org/mediawiki/2015/0/05/Igem.gif"></div>
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<figcaption>Computer Simulation of the interactions between Alyteserin and NAly</figcaption>
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<figcaption>Molecular Dynamics Simulation of the interactions between Alyteserin(red) and NAly(green)</figcaption>
  
 
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Latest revision as of 14:48, 15 September 2015

Predicting structure of a neutralising protein

To achieve our goal of achieving an antimicrobial free environment, it was necessary to inactivate the antimicrobial peptide Alyteserin. When a protein interacts with another protein, its structure is altered. This prevents the protein from performing from it's usual function. This was what we set out to do-design a small peptide that would interact with Alyteserin favourably under specified conditions. We also tried to simulate the interaction between the two peptides using GROMACS, and the results will be discussed later on on this page. First let's analyse the structure of Alyteserin.

Structural Features of Alyteserin and Naly

 

Interactions



GROMACS Simulation

Molecular Dynamics Simulation of the interactions between Alyteserin(red) and NAly(green)