Team:TU-Eindhoven/ProteinSelection

From 2013.igem.org

Molecular Dynamics

To refine the selection the accessibility of the various exchangable hydrogen atoms of the Lysines and Arginines was taken into account. Hereto Molecular Dynamics simulations of the proteins in water were carried out. Gromacs was used to run the sequence of simulations. For every protein a in vacuo energy minimization was carried out to stabilize the protein. Subsequently an energy minimization in water with ions (0.15 M KCl) was executed to stabilize the whole system. Further stabilization was done by running a NVT and NPT simulation with position restraints followed by a NPT simulation without the restraints. Then the final run, of which the data was used for further analysis, was carried out.

For the analysis of the data the g_dist utility provided with Gromacs was used in combination with self-made Matlab scripts. Using g_dist the number of water molecules within a 5 nm radius of certain characteristic groups was calculated for each protein. This value was divided by the runtime of the simulation, resulting in an indication of the accessibility of the characteristic group by water molecules. The results are shown in the table below, numbers should be interpreted as an index value.