Team:Virginia/Model
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
