This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and EU nationals.
Applicants should apply by completing the EASTBIO application form (downloadable from the EASTBIO website) and e-mail to EASTBIOapplications@dundee.ac.uk. Candidates should also include their academic transcripts and ensure that they ask their referees to send completed references to EASTBIOapplications@dundee.ac.uk. Applicants may wish to explain their motivation for joining the EASTBIO training programme.
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 the transcription machinery, including the capping enzymes, at the correct phase of transcription (2). However, the molecular details of how the CTD recruits, activates and regulates the capping enzymes-through the use of the CTD code-are currently 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 study 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 carry outlarge-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), as well as potentially in 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 play a key role in numerous cellular processes.
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). doi: 10.1016/j.bbagrm.2018.09.011
2.KM Harlen,LS Churchman. The codeandbeyond: transcription regulation bytheRNA polymerase II carboxy-terminal domain. Nature Reviews Molecular Cell Biology,18,263–273(2017). doi: 10.1038/nrm.2017.10
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). doi: 10.1093/nar/gkz613