Molecular dynamics study of the binding of phenylalanine stereoisomers to thermolysin

The stereospecificity in binding of phenylalanine as inhibitor in the active site of the thermolysin, has been investigated by means of molecular dynamics simulations using free energy integration techniques. The difference in the free energy of binding was found to be 2.0 ± 1.8 kJ/mol in favour of the D-form. This agrees with the experimental value, 2.8 kJ/mol. The result was obtained using a standard empirical force field (that of GROMOS). A different force field with 30% bigger charges (more like ab initio charges) was also tried. This resulted in less fluctuations and a more precise binding, but in a free energy. difference that was clearly larger than the experimental one. The phenylalanine backbone is located close to the zinc atom and the ring stays in the hydrophobic pocket in both the cases. The two stereoisomers differ mainly in the orientation of the backbone plane with respect to the active site and the rotational state of the dihedral around the C---CO^β bond.