Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Author: search.filters.author.Ceylan, ÇağatayPublisher: search.filters.publisher.01. Izmir Institute of Technology

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Now showing 1 - 4 of 4
  • Master Thesis
    Computational investigation of allostery in hydroxyacid oxidase
    (01. Izmir Institute of Technology, 2024) Gökoğlu, Gizem; Uyar, Arzu; Ceylan, Çağatay
    Understanding 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
    Anti-Microbial Properties and Biochemical Characterization of Maillard Reaction Products From Legume Protein Hydrolysates and D-Glucose
    (01. Izmir Institute of Technology, 2024) Gündoğan, Bengihan; Ceylan, Çağatay; Baysal, Ayşe Handan
    Bu tez, çeşitli termal koşullarda (175°C ila 275°C) D-glukoz ile reaksiyona sokulan nohut, bakla, adi fasulye ve soya fasulyesi protein hidrolizatlarından elde edilen Maillard Reaksiyon Ürünlerinin (MRP'ler) antimikrobiyal özelliklerini ve biyokimyasal karakterizasyonunu araştırmaktadır. Çalışmada bu MRP'lerin Escherichia coli, Staphylococcus aureus, Lactococcus lactis, Candida albicans, Saccharomyces var. boulardii ve Saccharomyces cerevisiae'ye karşı antimikrobiyal aktivitesi değerlendirilmiştir. Sonuçlar nohut MRP'lerinin en yüksek antimikrobiyal aktiviteyi sergilediğini, bunu bakla MRP'lerinin izlediğini, bakteri ve maya sayılarında önemli azalmalar olduğunu göstermiştir; antimikrobiyal etkinlik işleme sıcaklığına göre değişiklik göstermiş ve belirli koşullarda optimum aktiviteye işaret etmiştir. UV-Vis spektroskopisi, FTIR, HPLC ve NMR analizleri kullanılarak yapılan biyokimyasal karakterizasyon, melanoidin içeriğinde ve yapısal özelliklerinde baklagil kaynağına ve ısıl işleme bağlı olarak farklılıklar olduğunu ortaya koymuştur. Kolorimetrik analiz ve esmerleşme indeksi tayini, daha yüksek sıcaklıkların daha koyu MRP'lere yol açtığını ve esmerleşme indekslerinin arttığını göstermiştir. Bu bulgular, baklagil bazlı MRP'lerin gıda muhafazasında doğal antimikrobiyal ajanlar olarak potansiyele sahip olduğunu ve gelişmiş sağlık yararları ve güvenliği ile yeni gıda ürünlerinin geliştirilmesine katkıda bulunduğunu göstermektedir.
  • Master Thesis
    Investigation of Structural and Biological Activities of D-Glucose D-Glucose and Bread Melanoidins
    (01. Izmir Institute of Technology, 2022) Elci, Ferhat; Ceylan, Çağatay; Şahin, İpek
    As a result of Maillard reactions, high molecular weight compounds known melanoidins are formed from the proteins and sugars in food. Amino acids and reducing sugars combine, making them common ingredients in meals, fruit juices, coffee, and baked products that are consumed on a regular basis. Food melanoidins can affect human health, thus it's critical to assess and understand their chemical composition. Understanding the relationship between melanoidins' structural analysis and their activity was the main objective of this work. According to our observations, melanoidins have an antibacterial effect on the microorganisms E. coli and S. aureus. Melanoidins demonstrated excellent antibacterial action against E. coli at low doses, whereas S. aureus was more resistant at higher concentrations. These data suggested that melanoidins have a significant level of activity against gram-negative bacteria. The antioxidant capacity of melanoidins was assessed using the ABTS test. The bread melanoid exhibited the lowest antioxidant value, whereas the Gly - Glc melanoid model system had the strongest antioxidant property. Fourier transform Infrared (FTIR) spectroscopy was utilized to identify the functional groups of melanoidins and to analyze these groups. HPLC was used to identify melanoidins. We investigated the structural and functional properties of melanoidins utilizing spectroscopic methods such as FTIR spectroscopy, UV-Visible Spectroscopy, Scanning Electron Microscopy, and biochemical approaches. Studies on their biological activities and structures have enhanced our understanding of them; yet the complexity of the structures and variety of melanoidins provide the greatest obstacle to the knowledge.
  • Master Thesis
    The Effect of Enzyme Use on the Formation of Carbonyls and Structural Properties of Cakes
    (01. Izmir Institute of Technology, 2021) Er, Ayşe Ege; Ceylan, Çağatay; Şanlı Mohamed, Gülşah
    Enzymes are used as additives to improve the quality parameters of cakes. However, high temperature conditions produce carbonyl-containing compounds as precursors of toxic maillard reaction products. In this study three food grade enzymes were used as agents to decrease the formation of carbonyl-containig compounds while preserving the cake quality factors. For this purpose transglutaminase, lipase and amylase enzymes were used. All of the three enzymes lowered the amounts of carbonyls with the largest decrease by lipase of 31.83% (p<0.05) with respect to the control cake. Transglutaminase and lipase addition changed the carbonyl profile of cakes. Both transglutaminase and lipase caused important changes in protein secondary structures with large increases in alpha helix, turns and anti-parallel beta structures, however, amylase did not cause such large changes. The three enzymes used caused the lipid/protein ratio to decrease. The level of lipid unsaturation did not change for transglutaminase and lipase, however, the level unsaturation decreased in the case of amylase indicating the formation of dicarbonyls was via Maillard reaction not due to lipid peroxidation. However, the GC-MS analysis results indicated that there was no change in the formation of neither the Maillard reaction products nor the lipid oxidation products in the head space analysis. The amorphous structure of the starch in cake samples increased depending on the enzyme concentration used.