Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Identification of Cytosolic Sialidase Neu2 Associated Proteins Bt Mass Spectrometric Analysis(Izmir Institute of Technology, 2013) Akyıldız Demir, Seçil; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologySialidases (Neuraminidases) are the enzymes which remove sialic acids from glycoproteins, oligosacharides and glycolipids. Four mammalian sialidases have been identified which are lysosomal sialidase (Neu1), cytosolic sialidase (Neu2), plasma membrane sialidase (Neu3), and mitochondrial/lysosomal sialidase (Neu4). These enzymes differ in their subcellular localizations, expression levels in different cells and tissues, substrate specificities and optimum pH levels. Cytosolic Neu2 enzyme has an active role on a wide range of subtances including oligosaccharides, glycopeptides and gangliosides. Studies on the Neu2 enzyme also showed that this enzyme is involved in different cellular events including cancer metabolism, neuronal differentiation and myoblast differentiation, proliferation and hypertrophy. However, it has not been shown whether Neu2 interacts with other proteins within the cell. Therefore, in this study we aimed to identify Neu2 associated proteins by using InterPlay Mammalian TAP System and ESI-LC-MS/MS analysis. Proteins in the Neu2 protein complex were identified by three different database search software such as PGLS, Mascot and X!Tandem. As a result of experiment Actin proteins (Alpha Actin, Gamma Actin and Beta Actin), and Calsyntenin-2 protein were found as a candidate protein for Neu2 association. The interaction between Neu2 and β-Actin proteins was confirmed by western blot analysis.Master Thesis Analysis of Lysosomal Neu4 Sialidase Associated Proteins by Using Mass Spectrometry (ms/Ms)(Izmir Institute of Technology, 2012) Öztürk, Süleyman Can; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologySialidases are glycohydrolytic enzymes which remove sialic acid residues from glycoproteins, oligosaccharides and glycolipids. There are 4 different sialidases known in mammalians. These are Neu1 (lysosomal), Neu2 (cytoplasmic), Neu3 (cell membrane) and Neu4 (lysosomal/mitochondrial) sialidase. Sialidases are involved in many metabolic and cellular processes interactioning with another proteins or work together in multiprotein complexes. For example, Neu1 is only active with betagalactosidase and cathepsin A enzyme in lysosome. Interactions of sialidases Neu2, Neu3 and Neu4 enzyme with other proteins remain unknown In our study, we aimed to identify proteins which have interaction with sialidase Neu4 as well as Neu1 by using mass spectrometry analysis to find new possible roles of sialidases. Our bait protein's cDNA was tagged with calmodulin binding protein as well as streptavidin binding protein. After transfection and expression of vectors to mammalian cells, proteins were purified using tandem affinity purification (TAP). We identified some associated proteins with sialidase Neu1 and Neu4 by using MS/MS analysis and bioinformatics.Master Thesis Method Development for Protein Identification With Maldi-tof/Tof by Using On-Surface Digestion(Izmir Institute of Technology, 2012) Dinç, Melike; Yalçın, Talat; Yalçın, Talat; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyProtein identification is predominantly carried out by searching tandem mass spectrometric data of peptides in a protein database. For this reason, proteins are converted to peptides through a digestion process by using some certain endoproteinases. Trypsin is mostly preferred in this sample preparation step due to its high activity and products having appropriate mass range. Whereas in-solution digestion method is applied for the proteins in solution, proteins trapped in the gel can be digested by using in-gel digestion technique. Alternative to these traditional digestion methods, it has been reported that proteins can be digested too while they were adsorbed onto solid surfaces. In this study, digestion process of the adsorbed proteins, namely on-surface digestion is examined widely by using both hydrophobic and ionic adsorbents on different proteins. Results of the on-surface digestion were compared with in-solution digestion and in-gel digestion methods. As a conclusion, on-surface digestion is applicable for the protein identification by mass spectrometry; however, its yield may change from one experiment to another, depending on two separate but related processes: protein adsorption before the digestion and peptide recovery after the digestion. Nevertheless on-surface digestion has the advantages of protein enrichment and protein purification prior to mass spectrometry. These processes are necessary and significant especially for the samples containing minute amounts of protein and an effective enzymatic activity. Last but not least, this method may be performed complementarily to other digestion methods since new and different peptides may be acquired from the same sample source.