Enantioselectivity in Candida antarctica lipase B: A molecular dynamics study

A major problem in predicting the enantioselectivity of an enzyme toward su bstrate molecules is that even high selectivity toward one substrate enanti omer over the other corresponds to a very small difference in free energy. However, total free energies in enzyme-substrate systems are very large and fluctuate significantly because of general protein motion. Candida antarct ica lipase B (CALB), a serine hydrolase, displays enantioselectivity toward secondary alcohols. Here, we present a modeling study where the aim has be en to develop a molecular dynamics-based methodology for the prediction of enantioselectivity in CALB. The substrates modeled (seven in total) were 3- methyl-2-butanol with various aliphatic carboxylic acids and also 2-butanol , as well as 3,3-dimethyl-2-butanol with octanoic acid. The tetrahedral rea ction intermediate was used as a model of the transition state. Investigati ve analyses were performed on ensembles of nonminimized structures and focu sed on the potential energies of a number of subsets within the modeled sys tems to determine which specific regions are important for the prediction o f enantioselectivity. One category of subset was based on atoms that make u p the core structural elements of the transition state. We considered that a more favorable energetic conformation of such a subset should relate to a greater likelihood for catalysis to occur, thus reflecting higher selectiv ity. The results of this study conveyed that the use of this type of subset was viable for the analysis of structural ensembles and yielded good predi ctions of enantioselectivity.