Mandelate Racemase: model and setup for simulation

The procedure that we follow for the setup and sampling of Mandelate Racemase system is not the same that the one we used in the preceeding chapters. A different QM/MM level with a different QM/MM partition, along with different solvation model and MD approach will be employed.

The same 2.0 Å resolution structure of the complex of Pseudomonas putida Mandelate Racemase enzyme (PDB code 1MNS [233]) has been used again as the starting point for the calculations. In this case we have used a modified version of the c28b2 CHARMM package of programs[53]. The waters from the X-ray structure have been kept, and the protonation of the non-titrable hydrogens have been added with the HBUILD facility of CHARMM.

With the exception of the active site the protonation state of titrable residues have been set at pH 7. The histidine residues are neutral with the hydrogen at $N_\epsilon$ or $N_\delta$ depending on the possibility of hydrogen bond formation. As for the active site the protonation of the relevant residues corresponds to the structure of reactant S. The mandelate substrate has been added matching the maximum number of atoms with the inhibitor (R)-$\alpha$-phenylglycidate found in the PDB structure. This process that may be too rough in some cases, in mandelate substrate is quite appropriate since the experimental results show that the binding of (R)-$\alpha$-phenylglycidate is very similar to the natural substrate.