Canavan Task 8 - Molecular Dynamics Simulations
From Bioinformatikpedia
Protocol
Further information can be found in the protocol.
Choosing Mutants
We decided to use A305E and K213E for the MD analysis. In <xr id="CD_MD_mutants"/>.
<figtable id="CD_MD_mutants">
| Mutation | Comment | Visualisation |
| A305E | A305 is located at the end of the 13th beta sheet at the C-terminus of the protein. In figure <xr nolink id="a305e_crowded"/> the mutated residue glutamic acid is shown in red. The space at this position is rather crowded, so that alanine as a small residue fits very well in this position. Glutamic acid instead, hardly finds space and overlaps with neighboring residues. There is a slight difference in orientation for the carboxyl group between the pymol and scwrl output. Although this group is rotated in the scwrl output, there will still be steric clashes with neighboring residues. |
<figure id="a305e_crowded"></figure> |
| K213E | K213 is located on the loop connecting the N-, and C-terminal of the enzyme. It is on the surface of the protein, far away from the binding site or the dimer interaction site. Change of colour (sorry, schlechte Absprache im Team ;-)): In <xr nolink id="k213e_pymol"/>, the mutated residue K213E as computed by PyMol is presented in blue and the reference structure and residue in green. The mutated residue Glutamic Acid is able to form an HBond with the neighbouring helix. <xr nolink id="k213e_scwrl"/> shows the mutated residue in as computed by scwrl. | <figure id="k213e_pymol"></figure> |
</figtable>
