This project is concerned with studying conformations, energetics and binding modes of enzymes in interaction with other ligands.
Enzymes are essential biomolecules responsible for catalysis of many biological reactions. They accelerate chemical reactions, and convert substrate into a product. To study efficiency of such conversion, we model enzymes (in wild-type form, and after introduction of mutations), and we elucidate and compare enzyme (and corresponding mutants) reaction mechanisms of biological catalysis. One of the enzymes of our interest is Arylmalonate decarboxylase from Bordetella bronchiseptica (AMDase), which catalyzes breaking of C-C bond and stereoselective decarboxylation of aryl and alkenyl malonic acids. It converts pro-chiral substrates into chiral product in either (R) or (S)-form.
Here, we will study stereoselectivity of this enzyme and its mutants, and the reasons for such selection by means of electron valence bond (EVB) approach. To have trustable results and reasonable statistics, we perform simulations of many replicas. For this reason, we ask for 200000 cpu hours per month.