Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases—Bornyl Diphosphate Synthase As a Representative Case

Abstract

Terpene synthases comprise a family of enzymes that convert acyclic oligo-isoprenyl diphosphates to terpene natural products with complex, polycyclic carbon backbones via the generation and protection of carbocation intermediates. To accommodate this chemistry, terpene synthase active sites generally are lined with alkyl and aromatic, i.e., nonpolar, sidechains. Predicting the correct, mechanistically relevant binding modes for entire terpene synthase reaction pathways remains an unsolved challenge. Here we describe a method for identifying such modes: , a series of protocols to predict the orientation of carbon skeletons of substrates and derived carbocations relative to the bound diphosphate group in terpene synthase active sites. Using this recipe for bornyl diphosphate synthase, we have predicted binding modesthat are consistent with all current experimental observations, including the results of isotope labeling experiments and known stereoselectivity. In addition, the predicted binding modes recapitulate key findings of a seminal study involving more computationally demanding QM/MM molecular dynamics methods on part of this pathway. This work illustrates the value of the approach as a starting point for more involved calculations and sets the stage for the rational engineering of this family of enzymes.

En route to terpene natural products utilizing supramolecular cyclase mimetics

“…1 Computational chemistry is increasingly utilized to learn more about the mechanisms involved in terpene cyclizations. [9][10][11][12][13][14] Such studies have provided insight into how cyclase enzymes exert control over the cyclization outcome, via specic interactions between active site moieties and carbocations. 9,11,14,15 The enzyme, however, not necessarily has to intervene throughout the whole cascade reaction; some steps can be driven by the intrinsic reactivity of the cationic intermediates.…”

Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity

“…Along with more efficient identification of new enzyme functions, continued structure-function studies will provide a deeper understanding of the functional diversity and molecular evolution of species-specific enzymes and pathways. Likewise, advanced quantum and molecular mechanics approaches for protein modeling and carbocation docking can utilize deeper structural insight to improve the precision of TPS functional prediction (Isegawa et al, 2014; Chow et al, 2015; Tian et al, 2016; O’Brien et al, 2018). Knowledge of terpenoid-metabolic genes, enzymes, and pathways will increasingly enable the investigation of terpenoid physiological functions in planta and under various environmental conditions.…”

Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry

“…Thus, there is often great uncertainty regarding the correct binding mode when commencing multi-scale simulation projects of terpene cyclases” (Major et al, 2014). To tackle this problem, O’Brien et al combined QM calculation and computational docking with Rosetta molecular modeling suite and reported the high-resolution all-atom models of epi-aristolochene synthase (TEAS) from Tobacco (O’Brien et al, 2016) and (+)-bornyl diphosphate synthase from Salvia officinalis (O’Brien et al, 2018).…”