Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Computational investigation of allostery in hydroxyacid oxidase(01. Izmir Institute of Technology, 2024) Gökoğlu, Gizem; Uyar, Arzu; Ceylan, ÇağatayUnderstanding allosteric regulation in proteins may enable the development of effective new-generation therapeutics for disease treatments. Computational methods are gaining importance daily due to their fast and effective nature in examining protein dynamics and discovering potential allosteric binding sites. In this context, computational methods were used to determine the potential binding sites of the human hydroxyacid oxidase 1 (hHAO1) protein, which is effective in the rare disease Primary hyperoxaluria type 1 (PH1). Then, potential binding sites were predicted in monomeric and homotetrameric crystal and modeled structures of hHAO1 using the Fragment–Based Mapping (FTMap) web server and the Essential Site Scanning Analysis (ESSA) method. In ESSA, first, the default parameters cut-off 10 Å and mode 10 were applied. Then, to examine the effect of the cut-off value (distance) (Å), the parameters cut-off 7 Å and cumulative mode 20, and cut-off 13 Å and cumulative mode 20 were applied in ESSA. The modeled structures for hHAO1 were successful in terms of conformation and predicted binding sites. In the results of hHAO1, more binding sites were determined in the monomeric forms of hHAO1 than in tetrameric forms. FTMap and especially ESSA successfully predicted allosteric and potential new binding sites for hHAO1. This thesis might contribute to the improvement of computational methods and the development of allosteric therapeutics for hHAO1 and PH1.Master Thesis Characterization of Antioxdant Activity and Protein Functionality in Some Legume Cultivars Grown in Turkey(Izmir Institute of Technology, 2008) Aydemir, Levent Yurdaer; Yemenicioğlu, AhmetTurkish chickpeas (4 cultivars) and lentils (6 cultivars) show similar total phenolic contents and free radical scavenging capacities in aqueous extracts ranging between 2869 and 4312 mg gallic acid equivalents/kg legume and 24.42 and 38.20 mmol Trolox equivalents/kg legume, respectively. However, the free radical scavenging capacity of lentil and chickpea protein extracts, range between 110 and 185 mmol Trolox/kg protein and 58 and 144 mmol Trolox/kg protein, respectively, clearly showed the higher free radical scavenging capacity of lentil proteins than chickpea proteins.Protein extracts of chickpeas and lentils showed considerable emulsifying and foaming capacities in almost at the same range, but emulsions and foams formed by chickpea proteins are more stable than those of lentil proteins. The lentil protein extracts are highly soluble and showed poor water absorption and gelling characteristics. In contrast, chickpea protein extracts showed moderate water absorption and gelling capacity.Chickpea protein extracts are also good oil absorbers with almost 1.5 to 2 fold better oil adsorption capacity than lentil protein extracts. Thus, chickpea proteins are suggested as soy and whey protein alternatives for functional proteins used in the food, drug and cosmetics industries. Considering functional properties of proteins for different cultivars, the outstanding Turkish chickpea cultivars are Gökçe and Cevdetbey, while the outstanding Turkish lentil cultivar is Alidayı. Variations in the functional properties of protein suggest the diversity of genes in chickpeas and lentils responsible for these properties. Thus, this study showed the possibility of improving functional properties of chickpeas and lentils by breeding programs.Master Thesis Characterization and Modification of Antioxidant Proteins From Plat Materials(Izmir Institute of Technology, 2005) Arcan, İskender; Yemenicioğlu, AhmetIn this study, the radical scavenging and iron chelating capacity of proteins from heat treated (20 min at 90 oC) or thermally processed (20 min at 121 oC) chick-peas andkidney-beans were compared. Lyophilized crude protein extracts from chick-peas contained more protein (1.5-3 fold) and showed higher free radical scavenging (up to 2.3 fold) and iron binding capacity (up to 3 fold) than lyophilized crude protein extracts form kidney-beans. The thermal processing of chick-peas did not cause a significant change in the radical scavenging capacity of their lyophilized crude protein extracts, but improved the iron chelating capacity of these proteins almost 80 %. However, the thermal processing reduced both the radical scavenging and iron binding capacity of crude lyophilized proteins form kidney beans by 20-40 % and 60 %, respectively.Partial purification by ammonium sulfate precipitation or DEAE-cellulose chromatography increased the antioxidant capacity of thermally processed chick-pea proteins. The DEAE cellulose chromatography also showed the presence of 5 and 3 antioxidant protein fractions in heat treated and thermally processed chick-peas, respectively. Hot acidic hydrolysis at 80 oC for 30 min in presence of 1.5 M HCl increases the specific antioxidant activity of protein extracts, but causes the formation of undesired Maillard reaction products. Hot extraction at 85 oC for 30 min at pH 2.5 extracts the antioxidant proteins selectively, whereas 85 oC for 30 min at pH 9.5 extracts both antioxidant proteins and other proteins.