QM/MM free energy simulations of the reaction catalyzed by (4S)-limonene synthase involving linalyl diphosphate (LPP) substrate
J. Yao, F. Chen, and H. Guo.  2018.  Molecular Simulation, 44: 1158 1167.

Abstract:
A large number of terpenoid natural products are known to exist in nature. Terpene synthases are pivotal enzymes for the biosynthesis of diverse terpenoid skelotons. Monoterpene synthases are one type of terpene synthases responsible for the production of several hundreds of natural monoterpenes based on a very limited pool of substrates. Therefore, understanding detailed catalytic mechanisms of those enzymes are important for understanding the product specificity of terpene synthases. In this study, we present a detailed mechanistic description of the biosynthesis of the (4S)-α-terpinyl carbocation from (3S)-linalyl diphosphate (LPP) catalysed by (4S)-limonene synthase (LS) using two-dimensional QM/MM free energy (2D-PMF) simulations. Our estimated free energy barrier is in a reasonable agreement with the corresponding experimental kinetic data. We also perform the one-dimensional QM/MM free energy (1D-PMF) simulations and show that His579 can act as a general base to deprotonate (4S)-α-terpinyl carbocation and to generate the limonene product.