Research Topics and Supervisors willing to supervise Chemistry
Part II students.
Professor R.G. Ratcliffe (Plant Sciences)
Development and application of methods for metabolic flux analysis in plants, including steady-state, stable isotope labelling experiments and genome-scale, constraints-based metabolic modelling. The most recent Part II student used steady-state 13C-labelling to analyse the impact of potassium stress on central metabolism in an Arabidopsis cell culture.
C.Y.M. Cheung, M.G. Poolman, D.A. Fell, R.G. Ratcliffe and L.J. Sweetlove (2014) A diel flux-balance model captures interactions between light and dark metabolism during day-night cycles in C3 and CAM leaves. Plant Physiology 165, 917-929.
S.K. Masakapalli, F.M. Bryant, N.J. Kruger and R.G. Ratcliffe (2014) The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation. The Plant Journal 78, 964-977.
N.J. Kruger and R.G. Ratcliffe (2015) Fluxes through plant metabolic networks: measurements, predictions, insights and challenges. Biochemical Journal 465, 27-38.
S. Shameer, K. Baghalian, C.Y.M Cheung, R.G. Ratcliffe, and L.J. Sweetlove (2018) Computational analysis of the productivity potential of CAM. Nature Plants 4, 165-171.
Professor Renier van der Hoorn
Chemical proteomics of novel chemical probes. The Plant Chemetics Laboratory at the Plant Science Department has a large collection of chemical probes that label different subproteomes in plants. In many cases, the labeled proteins have not yet been identified and the labeled residue in these labeled proteins is unknown. Importantly, most chemical probes label functionally relevant sites in enzymes and display their active state. MSc projects to validate novel probes usually involve: 1) test a set of new chemical probes on plant proteomes to detect optimal labelling; 2) purify labeled proteins and identify the labeled proteins and labelling sites by mass spectrometry; 3) confirm the labelling by labelling leaf extracts from mutant plants lacking the probe target or labelling a heterologously produced target protein. More experiments can include site-directed mutagenesis of the target protein; enzymatic assays to study the role of the (mutated) labelling site; and structure-function analysis of probe derivatives. The MSc student will learn how to work with proteins, interpret MS data, and work creatively to address unexpected research questions that arise during the project.
- Kovacs, J., and Van der Hoorn, R. A. L. (2016) Twelve ways to confirm targets of activity-based probes in plants. Bioorg. Med. Chem. 24, 3304-3311.
- Morimoto, K., and Van der Hoorn, R. A. L. (2016) The increasing impact of activity-based protein profiling in plant science. Plant Cell Physiol. 57, 446-461.
- Stiti, N., Chandrasekar, B., Strubl, L., Mohammed, S., Bartels, D., and Van der Hoorn, R. A. L. (2016) Nicotinamide cofactors suppress active-site labeling of aldehyde dehydrogenases. ACS Chem. Biol. 11, 1578-1586.
- Chandrasekar, B., Colby, T., Emon, A. E. K., Jiang, J., Hong, T. N., Villamor, J. G., Harzen, A., Overkleeft, H. S., and Van der Hoorn, R. A. L. (2014) Broad range glycosidase activity profiling. Mol. Cell. Proteomics. 13, 2787-2800.
- Gu, C., Shannon, A., Colby, T., Wang, Z., Shabab, M., Kumari, S., Villamor, J. G., McLaughlin, C. J., Weerapana, E., Kaiser, M., Cravatt, B. F., and Van der Hoorn, R. A. L. (2013) Chemical proteomics with sulfonyl fluoride probes reveals selective labeling of functional tyrosines in glutatione transferases. Chem. & Biol. 20, 541-548.
- Lu, H., Wang, Z., Shabab, M., Oeljeklaus, J., Verhelst, S. H., Kaschani, F., Kaiser, M., Bogyo, M., and Van der Hoorn, R. A. L. (2013) A substrate-inspired probe monitors translocation, activation and subcellular targetting of bacterial type III effector protease AvrPphB. Chem. & Biol. 20, 168-176.
- Wang, Z., Gu, C., Colby, T., Shindo, T., Balamurugan, R., Waldmann, H., Kaiser, M., and Van der Hoorn, R. A. L. (2008) Beta-lactone probes identify a papain-like peptide ligase in Arabidopsis thaliana. Nat. Chem. Biol. 4, 557-563.