Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

Abstract

Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases. Here, we investigate to what extent metabolic pathways can be reconstructed just from knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β-caryophyllene, α-humulene, and β-farnesene. We also introduce a graph database to integrate simulation results with experimental biological evidence for selected predicted sesquiterpenes biosynthesis.

Optimization of factors influencing enzyme activity and product selectivity and the role of proton transfer in the catalytic mechanism of patchoulol synthase

“…The biosynthetic pathway for the conversion of farnesyl pyrophosphate (FPP) by PTS is not yet fully understood, but it is known that the reaction mechanism involves ring closures, hydride shifts and rearrangements . The presence of several aspartate‐rich regions with the sequence DDXXD around the active center is characteristic for sesquiterpene synthases and coordinates magnesium ions, which enable the binding of E , E ‐FPP molecules .…”

Representing catalytic mechanisms with rule composition

“…The framework has a well established foundation rooted in category theory, 5,6,12 as well as numerous chemical applications. [13][14][15][16][17][18] A molecule is treated as a typed graph, where a typed node represents an atom with a charge while a typed edge represents a bond of a given order. A collection of molecules is then represented by a disconnected typed graph, referred to as a mixture, where each connected component is a molecule.…”