(Start of Modeling Section) |
(Populated Subsections) |
||
Line 42: | Line 42: | ||
</span></p> | </span></p> | ||
− | <span class="ptitle">Protecting Group | + | <span class="ptitle">Protecting Group</span><br><br> |
− | + | <span class="stitle">Selection - Modeling Considerations</span><br><br> | |
<span class="ptitle">Leucine Synthetase Selection</span><br><br> | <span class="ptitle">Leucine Synthetase Selection</span><br><br> | ||
− | + | <span class="stitle">Synthetase File: 4aq7</span><br><br> | |
<span class="ptitle">Residue Selection</span><br><br> | <span class="ptitle">Residue Selection</span><br><br> | ||
+ | <span class="stitle">Literature</span><br><br> | ||
+ | <span class="stitle">Autodock Vina and Ligplot</span><br><br> | ||
+ | <span class="stitle">Final Selections</span><br><br> | ||
− | |||
<span class="ptitle">MUT</span><br><br> | <span class="ptitle">MUT</span><br><br> | ||
+ | <span class="stitle">Purpose</span><br><br> | ||
+ | <span class="stitle">Components</span><br><br> | ||
+ | <span class="stitle">Output</span><br><br> | ||
+ | <span class="stitle">Source</span><br><br> | ||
<span class="ptitle">Pepsin Modeling</span><br><br> | <span class="ptitle">Pepsin Modeling</span><br><br> | ||
− | + | <span class="stitle">Purpose</span><br><br> | |
+ | <span class="stitle">Results</span><br><br> | ||
+ | <span class="stitle">Conclusions</span><br><br> | ||
Revision as of 20:37, 16 October 2016
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 GroupSelection - Modeling Considerations
Leucine Synthetase Selection
Synthetase File: 4aq7
Residue Selection
Literature
Autodock Vina and Ligplot
Final Selections
MUT
Purpose
Components
Output
Source
Pepsin Modeling
Purpose
Results
Conclusions