This project is offered as part of the University of Dundee 4-year MRC DTP Programme “Quantitative and Interdisciplinary approaches to biomedical science”. This PhD programme brings together leading experts from the School of Life Sciences (SLS), the School of Medicine (SoM) and the School of Science and Engineering (SSE) to train the next generation of scientists at the forefront of international science. The outstanding biomedical research at the University of Dundee was recognised by its very high rankings in REF 2014, with Dundee rated as the top University for Biological Sciences in the UK. A wide range of projects are available within this programme crossing exceptional strengths in four key areas: Infection and Disease; Responses to Cellular Stresses; Development, Stem Cells and Neurobiology; and Big Data and Translation. All students on this programme will receive training in computational biology, mathematical biology and statistics to equip with the quantitative skills in tackling complex biological questions. In the 1st year, students will carry out 3 rotation projects prior to selection of the final PhD project.
Molecular simulation methods will be utilized to reveal theprecise molecular details of the proteins that control regulated gene expression. mRNA capping is a key process required for efficient gene expression and regulation in all eukaryotic organisms. The cap structure prevents degradation by exonucleases and acts as a platform to recruit the initiation factors required for splicing, nuclear export and translation (1). Adding more complexity, the process is tightly coupled to transcription through the recruitment to the site of transcription by the RNA polymerase II C-terminal Domain (CTD), which is the largest subunit of Pol II composed of multiple heptad repeats. The CTD is structurally disordered and dynamically phosphorylated to form a highly complex phosphorylation “CTD code” used to recruit and regulate thetranscription machinery, including the capping enzymes, at the correct phase of transcription (2). Currently, the molecular details of how the CTD recruits, activates and regulates the capping enzymes-through the use of the CTD code-are largely unknown. To address these questions the project will employ the computational biology/biophysics methods. Over the past decade, molecular dynamics (MD) simulation has grown into a robust tool for describing dynamics of proteins at atomic resolution, often revealing missing features that purely experimental techniques could not provide. For example, in our recent studies extensive MD simulations uncovered the long-range allosteric networks and mechanism of allosteric regulation of RNMT, one of the enzymes involved in the capping process (3).
In this PhD project, the student will master the state-of-the-art biomolecular modelling and simulation tools and run large-scale calculations on the high-performance computing facilities. Predictions made on the basis of computational work will be tested experimentally in the lab of Professor Victoria Cowling (School of Life Sciences). Since the capping enzymes are currently considered as promising drug targets against cancer and parasitic diseases, there isa potential link to the drug discovery studies. While the project focuses on the capping enzymes and CTD, it will offer insights into the broader areas of the protein-protein interactions and post-translational modifications, which both play a key role innumerous cellular processes.
Recent work from the lab can be found in the following references:
1.A Galloway,VH Cowling. mRNA cap regulation in mammalian cell function and fate. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1862, 270-279 (2019).
2.KM Harlen,LS Churchman. The code and beyond: transcription regulation bytheRNA polymerase II carboxy-terminal domain. Nature Reviews Molecular Cell Biology,18,263–273(2017).
3.JA Bueren-Calabuig, MG Bage, VH Cowling, AV Pisliakov. Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations. Nucleic Acids Research, 47, 8675–8692 (2019); D Varshney, AP Petit, JA Bueren-Calabuig, C Jansen, DA Fletcher, M Peggie, S Weidlich, P Scullion, AV Pisliakov, VH Cowling. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Research.44, 10423-36 (2016).