Proteinlerin Çözelti ve Gaz Fazındaki Konformasyonlarının Tuzaklı İyon Hareketliliği-Kütle Spektrometrisi Kullanılarak İncelenmesi

Abstract

The issue on protein conformation in the gas phase has not been fully clarified yet. The protein conformation in the gas phase may be affected by conformational changes in the solution phase, which occur due to the changes in the parameters such as pH, temperature, ionic strength concentrations, and the types of solvents in the solution phase. This thesis has been tried to clarify how much of the protein conformation in the gas phase reflects the protein conformation in the solution phase. In addition to various solution conditions, studies have been carried out on whether the changes that occur in the solution result from the interaction of the proteins with the polystyrene sulfonate polyelectrolyte. In this study, it was observed that the changes in the solution phase (the addition of methanol, changein the ion source temperature, and pH change) affect the conformational properties of the protein in the gas phase. Many studies in the literature examine the effects of pH, the presence of organic solvent, and how they affect the conformation of model proteins. For this reason, it was thought that this thesis's analyses should be carried out under physiological conditions, which can contribute more to the literature. Within the scope of the thesis, the effects of ammonium acetate, which is widely used salt in ESI-MS analyses of proteins to provide nearly physiological conditions were investigated. It was concluded that the protein has more compact conformation in ammonium acetate solution than just in water. The change in ammonium acetate concentration also affects the polyelectrolyte-protein interactions. The polyelectrolyte-protein complexes formed in the solution were also seen in the gas phase and the compaction of these complexes at some charge states were observed. The protein becomes more compact with the increase in the chain length of the polyelectrolyte. Molecular dynamics simulations were also performed to explain the polyelectrolyte-protein interactions.The simulations were carried out with GROMACS molecular dynamics program and Martini3 Force-Field with the coarse-grained model. According to the simulation results, most of this complexation occurs in the solution phase and the complex is preserved in the gas phase.