Dynamics of macromolecular complexes through computational modelling and structural mass spectrometry

Student thesis: Doctoral ThesisDoctor of Philosophy


For a large part its history, structural biology has relied on X-ray crystallography as the primary means of accessing the atomic structures of proteins and other molecules. 140,000 crystal structures currently populate the Protein Data Bank, each representing a single snapshot of the cellular landscape. To what extent are these conformations representative of each protein’s biochemical capabilities? What percentage of the proteome’s conformational space has been mapped? While these questions remain far too large and impossible for any one PhD student to answer, this thesis demonstrates several ways in which the conformational dynamics of proteins and complexes can be tackled through combining computational modelling with the powerful analytical capabilities of mass spectrometry (MS). 
The structural characterisation of large dynamic molecules remains one of the major challenges in biology due to the lack of techniques capable of capturing their motions. In Chapter 2 of this thesis, we model the conformational dynamics of large flexible Immunoglobulin G (IgG) antibodies using a workflow integrating ion mobility (IM)-MS, modelling and molecular dynamics simulations. This workflow provides the means of leveraging experimental IM-MS measurements with atomistic models. Next, the use of hydrogen deuterium exchange (HDX)-MS for protein characterisation has gained traction over the recent years due to its ability to capture dynamic aspects of protein behaviour. Advances in HDX-capable instrumentation has been paralleled by developments into software that facilitates its analysis. Chapter 3 documents the development of Deuteros, a software designed for rapid statistical analysis and visualisation of HDX-MS data, including recent upgrades to its code and analytical facilities. Finally, in Chapter 4, the structural dynamics of a large multi-subunit enzyme known as the Constitutive Photomorphogenesis 9 Signalosome (CSN) is examined using the synergy of structural MS and cryo-electron microscopy density maps. Integration of these techniques provided a method of exposing the multifaceted dimensions of the CSN and revealed its stepwise activation cascade. The work comprising Chapters 2, 3 and 4 have each been published in Angewandte Chemie, Bioinformatics and Nature Communications respectively. Overall, the research presented in this thesis has not only contributed important biological insights into the conformational dynamics of IgG and the CSN but has also demonstrated the utility of using integrative approaches for the characterisation of dynamic macromolecules.
Date of Award1 Dec 2019
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorArgyris Politis (Supervisor)

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