Difference between revisions of "Team:Virginia/Model"

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                <span class="ptitle">Overview</span><br><br>
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<p><span class="p">We modeled our system in silico to select a sterically feasible protecting group and to optimize a mutant leucyl-tRNA synthetase for complementarity of its catalytic site to protected leucine, and of its editing site to leucine. To select a protecting group, the team used protein-ligand docking software to compare binding affinities of several protected leucine/synthetase complexes. To perform mutagenesis on leucyl-tRNA synthetase, an integrated software script was written in the Linux shell, with inputs including a protein to mutate, a ligand, a list of residues of interest, and binding pocket location. The script runs mutagenesis, assesses mutant protein stability, then performs ligand docking. The program then ranks the outputs, acting as a streamlined mutagenesis optimization algorithm. We confirmed, using CSM software suites and iGEMDOCK, that AMP and AMS yield energetically comparable binding affinities. Lastly, we performed Michaelis-Menten modeling for the enzyme pepsin to gauge activity in nonspecific cleavage enzymes.
 
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                <span class="ptitle">Protecting Group Selection</span><br><br>
  
  
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                <span class="ptitle">Leucine Synthetase Selection</span><br><br>
  
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                <span class="ptitle">Residue Selection</span><br><br>
  
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                <span class="ptitle">MUT</span><br><br>
  
  
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                <span class="ptitle">Pepsin Modeling</span><br><br>
  
  

Revision as of 20:07, 16 October 2016

← Project Design Experiments →
Overview

We modeled our system in silico to select a sterically feasible protecting group and to optimize a mutant leucyl-tRNA synthetase for complementarity of its catalytic site to protected leucine, and of its editing site to leucine. To select a protecting group, the team used protein-ligand docking software to compare binding affinities of several protected leucine/synthetase complexes. To perform mutagenesis on leucyl-tRNA synthetase, an integrated software script was written in the Linux shell, with inputs including a protein to mutate, a ligand, a list of residues of interest, and binding pocket location. The script runs mutagenesis, assesses mutant protein stability, then performs ligand docking. The program then ranks the outputs, acting as a streamlined mutagenesis optimization algorithm. We confirmed, using CSM software suites and iGEMDOCK, that AMP and AMS yield energetically comparable binding affinities. Lastly, we performed Michaelis-Menten modeling for the enzyme pepsin to gauge activity in nonspecific cleavage enzymes.

Protecting Group Selection

Leucine Synthetase Selection

Residue Selection

MUT

Pepsin Modeling