Mechanistic understanding and inhibitor design strategies for non-mevalonate pathway TPP-dependent enzymes
Lead Research Organisation:
University of Leeds
Department Name: Sch of Molecular & Cellular Biology
Abstract
In this 4-year BBSRC iCASE PhD studentship between the University of Leeds and Syngenta PLC, the student will investigate the structure, function and mechanism of plant enzymes important to the agriscience industry. The project, which is co-supervised in the Astbury Centre for Structural Molecular Biology, University of Leeds by Profs Alex Breeze and Frank Sobott, builds on previous collaboration between Syngenta and the University of Leeds to further elucidate the mechanistic biology and modes of inhibition of
non-mevalonate pathway TPP-dependent enzymes including 1-deoxy-D-xylulose-5-phosphate synthase (DXS). The outcome will be an enhanced understanding of potential inhibitor design strategies and mechanisms, that in turn may lead to the development of improved herbicidal agents targeting this pathway.
Despite belonging to a generally well-understood class of enzymes, mechanistic understanding of DXS and its inhibition is still relatively limited, at least in part because structure determination, particularly of substrate-, catalytic intermediate-, product- or inhibitor-bound forms by X-ray crystallography has proved to be quite challenging. The student will use cutting-edge ultra-high field methyl NMR and hydrogen-deuterium
exchange mass spectrometry (HDX-MS) to build on our earlier work. Specifically, we will
transfer our methyl NMR approach based on the E. coli DXS system to orthologue(s) from
plant species that will be more relevant model systems for herbicidal inhibitor
development. In addition to NMR, we will use structural MS (HDX-MS, fast photochemical
oxidation of proteins (FPOP)-MS and ion-mobility spectrometry- (IMS)-MS to map the binding sites and modes of interaction of substrates, catalytic / transition state intermediates and inhibitors. Molecular modelling based on existing PDB structures and AlphaFold2 structural models will be used as a basis for incorporating our experimentally-derived restraints.
non-mevalonate pathway TPP-dependent enzymes including 1-deoxy-D-xylulose-5-phosphate synthase (DXS). The outcome will be an enhanced understanding of potential inhibitor design strategies and mechanisms, that in turn may lead to the development of improved herbicidal agents targeting this pathway.
Despite belonging to a generally well-understood class of enzymes, mechanistic understanding of DXS and its inhibition is still relatively limited, at least in part because structure determination, particularly of substrate-, catalytic intermediate-, product- or inhibitor-bound forms by X-ray crystallography has proved to be quite challenging. The student will use cutting-edge ultra-high field methyl NMR and hydrogen-deuterium
exchange mass spectrometry (HDX-MS) to build on our earlier work. Specifically, we will
transfer our methyl NMR approach based on the E. coli DXS system to orthologue(s) from
plant species that will be more relevant model systems for herbicidal inhibitor
development. In addition to NMR, we will use structural MS (HDX-MS, fast photochemical
oxidation of proteins (FPOP)-MS and ion-mobility spectrometry- (IMS)-MS to map the binding sites and modes of interaction of substrates, catalytic / transition state intermediates and inhibitors. Molecular modelling based on existing PDB structures and AlphaFold2 structural models will be used as a basis for incorporating our experimentally-derived restraints.
People |
ORCID iD |
| Alexander Breeze (Primary Supervisor) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/T007222/1 | 01/10/2020 | 30/09/2028 | |||
| 2878051 | Studentship | BB/T007222/1 | 01/10/2023 | 30/09/2027 |