Unravelling the mysteries of retinoid signalling
Dr E Pohl
Prof J Endicott
No more applications being accepted
Funded PhD Project (European/UK Students Only)
Retinoids, such as all-trans-retinoic acid (ATRA), are a class of endogenous molecules derived from Vitamin A. These compounds control a wide range of cellular processes in chordates, including differentiation, proliferation and apoptosis, by binding one or more of related transcriptional receptors in the cell nucleus. Natural retinoids have limited use due to their inherent instability. Based on a large number of synthetic retinoids that we have designed and synthesized in the past the aim of this project is to develop a tool box of custom-made synthetic retinoids that are specific for one of the receptors with the fluorescent properties required for either medical chemistry or cell biology applications. These chemical probes will be characterized by biophysical and structural methods and applied to cancer research.
Retinoid acid (RA) and its natural and synthetic derivatives control a wide range of cellular processes in chordates, including differentiation, proliferation, apoptosis and homeostasis, by regulating transcriptional control in the cell nucleus. Retinoids are high affinity ligands for a family of nuclear receptor proteins - retinoic acid receptors (RARs) and retinoid X receptors (RXRs). Once bound to these receptors, dimerization allows the formation heterodimers that are able to bind their target DNA sequences. To reach the nucleus, the highly lipophilic retinoids are bound to a carrier protein, the Cellular Retinoic Acid Binding Protein (CRABPII). The overall goal of this project is to develop an entire tool box of synthetic specific retinoids that are specific for application ranging from drug discovery to fluorescent probes in cell biology.
Work Package 1: Biophysical and biochemical characterization
In this WP the student will characterize the specificity of binding of all compounds to CRABPII and the three RAR isoforms.. The interactions of CRAPBII with the ligand binding domains of all RARs as well as with Cyclin D will be investigated using the FRET assays developed in the group of Prof. J. Endicot (NCRI, NCL).
WP 2: Structural Characterisation
In order to unravel the molecular basis of compounds that exhibit specific binding properties or elicit unexpected biological activities the student will determine the X-ray co-crystal structures of selected compounds with their target proteins. While it is expected that all biologically active compounds bind CRAPBII, the binding pockets of the three RAR proteins differ significantly. Highresolution crystal structures will inform future design of novel compounds and serve as a starting point for high-level molecular dynamics simulations.
WP 3: Exploring protein-protein interactions
In order to investigate the mechanisms by which retinoids elicit the specific biological response the student will utilize those compounds that stabilize CRABPII-RAR complexes for further biophysical and cell biological and biophysical characterization. straightforward FRET assays could lead to structural characterization by either MX or cryCryoEM.
Training & Skills
• Molecular biology, protein expression in recombinant systems
• Protein purification and quality control
• Biophysical techniques to investigate proteinligand and protein-protein interactions
• Crystallisation, X-ray crystallography
• Diffraction data collection at our partner synchrotrons
• fluorescence microscopy
• HTP assay development
Dr Ehmke Pohl
[Email Address Removed]
+44 (0) 191 33 43619
How to Apply
To apply for this project please visit the Durham University application portal to be found at: https://www.dur.ac.uk/study/pg/apply/
Please select the course code F1A201 for a PhD in Molecular Sciences for Medicine and indicate the reference MoSMed20-09 in the ‘Field of Study’ section of the application form.
Should you have any queries regarding the application process at Durham University please contact the Durham MoSMed CDT Manager, Emma Worden at: [Email Address Removed]