Team:Washington/Protocols/CompDesign

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=Using [[Team:Washington/Protocols/Software|FoldIt]] to Make CapD_CP a Better Hydrolase=
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As can be seen below Foldit uses an easily learned user interface and uses a score board to show the current player who is the best folder.  You can work alone or in teams, share puzzles, and test your ''protein design'' abilities against your friends.  Below we depict a small set of the MANY options that are available to you in the program [http://www.fold.it Foldit].
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'''[http://www.fold.it/ This accessible format has allowed over 100,000 users to help design proteins.<br/>Try Foldit Today]'''</div>
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[[Image:Washington 2011 270px-WashingtonPointMutation.png|270px|frameless|right]][[Image:Washington 2011 270px-WashingtonShake.png|270px|frameless|right]]
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REPACK, a.k.a. Shake:<br>Here we see a video of Foldit, showing one of our biotin puzzles "Hold Me Tightly". The protein is represented as a cartoon model, showing off its secondary structure as well as key amino acid groups. Steric clashes of the amino acid side chains show up as red balls and can also be observed in the video. These steric clashes can be removed with the Shake Function. The Shake function in Foldit performs coarse sampling of the amino acid conformations, looking for a global-minima.  
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REDESIGN, a.k.a. Mutate:<br>The function we see here is the Mutate function. This allows the user to sample many amino acids at a particular site, or the whole protein. Mutate looks for global-minima while sampling amino acids. As is seen here Alanine is mutated to Asparagine. The blue and white striped band indicates that a hydrogen bond has been formed, which is a favorable interaction between two polar residues.
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<p>To increase the decarbonylase of Aldehyde Decarbonylase (ADC), we made point mutations to the active site. We focused our attention on two types of mutations.</p>
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MINIMIZE, a.k.a. Wiggle:<br>Another nice feature of Foldit is the ability to select a sphere of amino acids around your ligand, and optimize these amino acids based off of a fine sampling of conformations. Here we see the amino acids surrounding the ligand being selected and having the Wiggle function performed on them. The Wiggle function in Foldit allows the user to fine tune the protein structure. Finding a local-minima for the amino acid conformations.
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First type of mutations is to increase hydrolysis by lowering the activation energy. To accomplish this, we created point mutations that can establish hydrogen bondings to a modeled transition state of our substrate. Second type of mutations concerns with the openness and polarity of the active site. To accomplish this, we mutated the active site into a more open and polar area so water molecules can enter and participate in hydrolysis easily.
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<p>To make these point mutation designs, we used a computer program named FoldIt to predict how changes in protein structure and composition will affect protein stability.  FoldIt provides a 3D representation of a protein's crystal structure that can be manipulated. Manipulation functions include point mutations, insertions, deletions, repacking of side chains (rotamer optimization), and backbone movement, which FoldIt then assesses for stability. This allows the user to quickly interact with a protein and easily predict how mutations will affect a protein.</p>
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[[Team:Washington/Protocols/Software|A more in depth explanation of FoldIt here.]]
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'''&larr; [[Team:Washington/Protocols|Back to Protocols]]'''
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Latest revision as of 23:47, 21 September 2011

Washington 2011 Uw foldit lofo.jpeg

As can be seen below Foldit uses an easily learned user interface and uses a score board to show the current player who is the best folder. You can work alone or in teams, share puzzles, and test your protein design abilities against your friends. Below we depict a small set of the MANY options that are available to you in the program Foldit.

REPACK, a.k.a. Shake:
Here we see a video of Foldit, showing one of our biotin puzzles "Hold Me Tightly". The protein is represented as a cartoon model, showing off its secondary structure as well as key amino acid groups. Steric clashes of the amino acid side chains show up as red balls and can also be observed in the video. These steric clashes can be removed with the Shake Function. The Shake function in Foldit performs coarse sampling of the amino acid conformations, looking for a global-minima.
REDESIGN, a.k.a. Mutate:
The function we see here is the Mutate function. This allows the user to sample many amino acids at a particular site, or the whole protein. Mutate looks for global-minima while sampling amino acids. As is seen here Alanine is mutated to Asparagine. The blue and white striped band indicates that a hydrogen bond has been formed, which is a favorable interaction between two polar residues.
MINIMIZE, a.k.a. Wiggle:
Another nice feature of Foldit is the ability to select a sphere of amino acids around your ligand, and optimize these amino acids based off of a fine sampling of conformations. Here we see the amino acids surrounding the ligand being selected and having the Wiggle function performed on them. The Wiggle function in Foldit allows the user to fine tune the protein structure. Finding a local-minima for the amino acid conformations.