QM/MM methods have been applied to different systems to probe the relationship between structure and reactivity in enzyme/substrate systems. QM/MM methods allow for the in depth study of a localised region of an enzyme without sacrificing the effects of the enzyme environment and bulk solvent. We validate the use of this method by reproducing results observed in experiment.
A reaction path for the hydrolysis mechanism of carboxypeptidase A has been computed using the QM/MM method. It is found that the deprotonation of the nucleophilic water molecule and addition of the hydroxide to the scissile carbonyl bond occurs in a single step with a barrier height of 14.7 kcal/mol. We also perform QM/MM molecular dynamics simulations on the Michaelis complex. The results from these studies highlight possible weaknesses of the SCCDFTB method.
The QM/MM method is used to compute vibrational frequencies of localised regions in large systems. In enzymes, this allows for the probing of the interactions that could be responsible for enzyme recognition as well as those which are essential for the mechanism of reaction. The method was validated by performing tests on a molecule of acetone in water and an oxaloacetate molecule bound in the active site of citrate synthase. Both these studies yielded promising results with good comparisons to experiment. This method was then applied for the study of an acyl-enzyme intermediate between the substrate, aztreonam and a class C β-lactamase enzyme. We were able to probe the conformational multiplicity of the acyl group in the oxyanion hole. Results from this study agree well with experiment and reveals the possible factors which play a role in the aztreonam molecule being a poor substrate for β-lactamases.