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Project properties |
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| Title | Prediction and testing of protein dimerization using structural modeling and in vitro validation. |
| Group | Plant Physiology, Laboratory of |
| Project type | thesis |
| Credits | 30-39 ECTs |
| Supervisor(s) | Kilian Duijts, Dr. Aalt-Jan van Dijk, Prof. Dr. Christa Testerink |
| Examiner(s) | Prof. Dr. Christa Testerink |
| Contact info | kilian.duijts@wur.nl, christa.testerink@wur.nl AND thesis.PPH@wur.nl |
| Begin date | 2022/01/02 |
| End date | 2025/10/01 |
| Description | Soil salinity is an increasing problem for agriculture worldwide. To understand how plants deal with this stress we study the development of their root systems under salinity stress. In this thesis you will be studying the dimerization affinity of two potential regulators of root development under salt stress.
In previous experiments we have identified a salt induced transcription factor (SIT1) that is involved in lateral root development during salt stress, and in consequent Y2H and BIFC experiments SIT1 has been shown to interact with other TF in this family, some of which are also involved in stress responses. In this thesis you will use bioinformatic structural protein modelling tools to predict what residues facilitate this interaction. Next you will use molecular cloning techniques to do site directed mutagenesis on these residues and transient gene expression to test their interaction in vivo. Further reading: Evans, Richard, et al. Protein Complex Prediction with AlphaFold-Multimer. 2021, doi:10.1101/2021.10.04.463034. Grefen, Christopher, and Michael R. Blatt. “A 2in1 Cloning System Enables Ratiometric Bimolecular Fluorescence Complementation (RBiFC).†BioTechniques, vol. 53, no. 5, 2012, doi:10.2144/000113941. Lee, Han Woo, et al. “The Conserved Proline Residue in the LOB Domain of LBD18 Is Critical for DNA-Binding and Biological Function.†Molecular Plant, vol. 6, no. 5, Cell Press, Sept. 2013, pp. 1722–25, doi:10.1093/mp/sst037. Pandey, Shashank K., and Jungmook Kim. “Coiled-Coil Motif in LBD16 and LBD18 Transcription Factors Are Critical for Dimerization and Biological Function in Arabidopsis.†Plant Signaling & Behavior, vol. 13, no. 1, NLM (Medline), Jan. 2018, p. e1411450, doi:10.1080/15592324.2017.1411450. See more from our group on rootsinsalt.com If you are interested in this project please contact the supervisor via email with a copy to thesis.PPH@wur.nl with: 1. Your motivation for choosing this project 2. For which purpose (BSc or MSc thesis, research practice, etc) 3. Your BSc/MSc program 4. When you would like to start Please be aware that if you do not provide the required information above it may cause a delay in our reply. |
| Used skills | Structural protein modelling, cloning, BIFC, protein-protein interaction assays, (confocal) microscopy, N. benthamiana agrobacterium infiltration, protoplasting |
| Requirements | (Advanced) Bioinformatics and molecular biology/plant biotech experience |