Investigating the role of lipids for membrane protein complexes using native mass spectrometry and molecular dynamics simulations

The work described in this thesis is a combination native mass spectrometry experiments, molecular dynamics simulations and scientific software development. It consists of three results chapters which each chapter describing a distinct project with a focus on one of the aspects above. In chapter 3, I employed molecular dynamics simulations in a collaborative project on using surface-induced dissociation to probe the effect of lipid binding on the stability of oligomerisation interfaces. My simulations offer a rationale of lipid bind- ing to different locations to explain these stability differences. In addition, I contributed to experiments to probe the molecular features of these interfaces through site-directed mutagenesis to weaken these interfaces. Chapter 4 describes my investigation on lipid binding to a bacterial potassium channel, MthK. Native mass spectrometry and molecular dynamics simulations are used to characterise lipid binding after initial experiments indicated endogenous lipids being bound to MthK. Cardiolipin has been revealed to bind specifically to MthK. These results are compared to the eukaryotic homologues through further simula- tions. A part of this chapter outlines different approaches to obtain the in vivo stoichiometry. Among these approaches I employed SoLVe-MS, which leads to very complex mass spectra. The analysis of these spectra sparked the development of the program described in chapter 5. In the final results chapter, a web-based program for the analysis of native mass spectra, NaViA, is described. This program allows one to analyse native mass spectra through a visual user interface directly in a web browser. In addition, it offers auxiliary tools to facilitate the analysis as well as the ability to save and load sessions for sharing spectra including analysis or depositing them for publication. The ease of use and the instructive auxiliary tools make it a valuable addition to the suite of software available for the analysis of native mass spectrometry.