Pettitt, Alice Jane;
(2024)
Biophysical characterisation of ORF6 from SARS-CoV-2.
Doctoral thesis (Ph.D), UCL (University College London).
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Abstract
Open reading frame 6 (ORF6) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in suppressing the immune response in coronavirus disease 2019 (COVID-19). Notably, the C-terminal region of ORF6 (ORF6-CTR; residues 41-61) is predicted to be intrinsically disordered, contains a single proline residue that may undergo cis/trans isomerisation, and is recognised as the biologically relevant region of ORF6. While molecular dynamics (MD) simulations have the potential to fully characterise disordered proteins, including proline cis and trans subensembles, they are hindered by the slow timescales of isomerisation and force field inaccuracies. Nuclear magnetic resonance spectroscopy (NMR) can provide insights into ensemble-averaged observables for both the cis and trans proline states; however, achieving a complete atomic characterisation of these subensembles remains challenging. Given the lack of structural data available for ORF6, I employed a combination of all-atom MD simulations with enhanced sampling (metadynamics), NMR, and small-angle X-ray scattering (SAXS) to characterise ORF6. After introducing the biological background and methodological theory in Chapters 1 and 2, respectively, and outlining the materials and methods in Chapter 3, I present the results from my detailed characterisation of ORF6-CTR and its cis and trans proline subensembles in Chapter 4. My findings suggest that the AMBER03ws force field provides the best agreement with experimental data, and both the cis-proline and trans-proline ORF6-CTR conformations are highly dynamic. Finally, in Chapter 5, I explore full-length ORF6 and its interactions with biological binding partners. The work presented in this thesis advances our understanding of the structural and dynamic properties of ORF6. Furthermore, I demonstrate that integrating multi-scale computations with experimental methods provides valuable insights into highly dynamic states that cannot be reliably characterised by either approach in isolation.
| Type: | Thesis (Doctoral) |
|---|---|
| Qualification: | Ph.D |
| Title: | Biophysical characterisation of ORF6 from SARS-CoV-2 |
| Open access status: | An open access version is available from UCL Discovery |
| Language: | English |
| Additional information: | Copyright © The Author 2024. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request. |
| Keywords: | Biophysics, Disordered proteins, Metadynamics, NMR spectroscopy, Proline isomerisation |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10200133 |
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