Advanced computations and mass-spectrometric techniques to unravel the dynamics and interactions of proteins

Abstract: Proteins are an important class of biomolecules, involved in the metabolism, regulation, structure and transport in cells. Unfortunately, many diseases are caused by protein dysfunction. When proteins perform their normal function, they may interact with each other or change their conformation. Protein structure is therefore not static, that is the structure should instead be regarded as dynamic. Further understanding of proteins can in turn lead to new means to manipulate them for therapeutic purposes as well as for basic research.To address the challenges posed by the dynamic nature of protein structure and interactions, we combine molecular modelling and mass spectrometric techniques. This has shown to be very powerful, more so than using the techniques individually. With mass spectrometric techniques, proteins can be separated by their mass and shape. This allows for the selection of conformational and binding states. In contrast, computations, namely molecular dynamic simulations, take into account time, which is fundamental for a dynamical analysis.In this thesis, we investigated dihydroorotate dehydrogenase (DHODH) and alpha-synuclein (alphaSyn), two drug targets for cancer and Parkinson's disease, respectively. We also researched the electrospray process necessary for native mass spectrometry. The understanding of this process gives insights into mass spectrometry of native protein conformations and subsequently allows for further studies of disease related systems. Regarding the electrospray process, our findings confirm that charge states are not dependent on the protein surface chemistry, but instead on the surface area and is best described by a zwitterionic configuration model. We also proposed models for the electrospray process of protein associated with lipids and evaluated the lipid-protein interaction in the gas-phase. Regarding the disease related proteins, we show how DHODH can interact with ubiquinone-10 and this architecture is similar to respiratory chain complex I; intramolecular dityrosine crosslinks can prevent alphaSyn aggregation. These findings can help develop new drug strategies.