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Amory, Ross (2025) Computational analysis of the taxadiene synthase reaction pathway. PhD thesis, University of Nottingham.

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Abstract

The taxadiene synthase reaction pathway defines a complex carbocation cascade that offers multiple stable intermediates that, in turn, can lead to multiple relevant products in chemistry. Because of the promiscuity of the terpene chemistry, simple modifications to the natural taxadiene synthase protein can completely modify the potential energy landscape, leading to alternate major product distributions.

This research uses a variety of computational techniques including homology modelling, molecular dynamics, quantum mechanics, and hybrid quantum mechanics/molecular mechanics to better understand how terpene synthases control the distribution of the resultant products.

In this work, we present the first complete and active structure of the wildtype taxadiene synthase protein. Using this structure, we study the effect of truncating the protein, which is known experimentally to deactivate the enzyme. We also performed simulations of some of the key intermediates in the taxadiene synthase reaction pathway to investigate how the protein controls the conformation of each of the intermediates.

We also generated a mutant protein (V584M) of taxadiene, which is known to produce verticillene rather than taxadiene. Using this mutant protein, we studied the effect that the mutation had on the structure of the protein. We also performed simulations similar to those performed in the wildtype protein on key intermediates on the reaction pathway. This was to understand how the mutations interacted with the carbocation cascade.

Item Type:	Thesis (University of Nottingham only) (PhD)
Supervisors:	Hayes, C. J. Hirst, J. D.
Keywords:	QM/MM, MD, Taxadiene Synthase, Umbrella Sampling, DFT Benchmark, Mutation Study
Subjects:	Q Science > QD Chemistry > QD 71 Analytical chemistry
Faculties/Schools:	UK Campuses > Faculty of Science > School of Chemistry
Item ID:	80721
Depositing User:	Amory, Ross
Date Deposited:	24 Jul 2025 04:40
Last Modified:	24 Jul 2025 04:40
URI:	https://eprints.nottingham.ac.uk/id/eprint/80721

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