Research

Terpene synthases (TPSs) are enzymes responsible for the generation of the first structural diversity found among terpenoids¹, the most abundant group of natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates² (see figure below). Terpenes are abundant in plants, bacteria, and fungi, and also form the basis of all life through sterols, carotenoids, and other very basic metabolites². The biochemistry of terpene synthases has been the subject of a lot of research. However, today the major the challenge is to translate a strong in-silico model and table top biochemistry in to enzyme product prediction².

Several studies have explored the biochemistry of terpene synthases and have delved into the regulation, diversity, and functional evolution of terpene synthases, shedding light on their importance in biological systems^{1, 2}. Studies have also explored techniques such as directed evolution to modify terpene synthases for non-natural applications, potentially expanding their industrial utility. However, so far prediction of the product formed by the TPS has been very difficult due to the nature of the chemical reaction involving a carbocation formation, hydrogen and methyl group shifts, ring closure, and finally either hydrogen abstraction or hydroxylation².

Modelling and other techniques are gradually being implemented to further understand the biochemistry of terpene synthases, and to explore the reaction mechanism of a terpene synthase^{1, 2}. Comprehensive knowledge is required for these predictions, and with ModBioTerp we propose to provide a strong basis for a fundamental enzymatic understanding of TPSs.

Canonical Terpene synthases comprise of one, two, or three structural domains, a, b, and g (figure below, g domain not shown) and biosynthesise both general and specialized metabolites^{1, 2}. In ModBioTerp we will focus on canonical TPSs that all generate carbocations and involve hard to predict. The physical structure of the three different domains is to some extent established and explain the first ionization event. This knowledge is based on crystal structures, and the first crystal structures of TPSs have been established many years ago^{1, 2}. These crystal structures and others from our own research will form the basis for ModBioTerp, and we will provide fundamental insight into the enzyme mechanisms from modelling to predictions of products and also understand this in terms of their evolution.

Figure 1. A ribbon diagram of Limonene synthase co-crystallized with FLPP. The a-domain is green b-domain in orange, FLPP is red, and Mn²⁺ ions are purple. TO the right is shown the chemical reaction catalyzed by the enzyme, showing the initial carbocation formation followed by rotation and a cyclization. Adopted from Hyatt et al., PNAS, 2007, 104 (13) 5360-5365

References:

1: Ringel et al, 2022, Green Chem, 22, 6033-46; Raz et al, 2020, JACS 142, 21562-74; Schrepfer et al, 2020, Comp Struct Biotech J 18, 1819-29; Escorcia et al, 2018, Comput Chem 39, 1215–25; Schrepfer et al, 2016, PNAS 113, E958-E967

2: Rudolf & Chang, 2020, Nat Prod Rep 37, 425-63; Chen et al, 2016, PNAS, 113, 12132-7; Jia et al., 2022 PNAS 119, :e2100361119; Driller et al, Nat Comm 9, 3971; Brück et al, 2014, ChemCatChem, 6, 1142-65