Master Degree / Yüksek Lisans Tezleri

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

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Publisher: search.filters.publisher.01. Izmir Institute of TechnologySubject: search.filters.subject.Enzymes

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Now showing 1 - 4 of 4
  • Master Thesis
    Identification of Allosteric Control in Proteins Using Computational Methods
    (01. Izmir Institute of Technology, 2024) Güneş, Sude; Uyar, Arzu; Sezgin, Hümeyra Taşkent
    The prediction of orthosteric, allosteric, and cryptic sites through computational approaches is significant for drug discovery studies. To this extent, a ligand binding site prediction method called Essential Site Scanning Analysis (ESSA) was used to investigate allosteric and cryptic sites of TEM-1 beta-lactamase, cell division protein kinase 2, and galactokinase by applying various cutoff values (7 Å, 10 Å, 11 Å, and 13 Å) and combining 10/20 modes in this study. On the other hand, molecular dynamics (MD) and ClustENMD were performed to investigate hGALK1 enzyme dynamics. In addition, Principal Component Analysis (PCA) was applied to investigate collective motions in the presence and the absence of an allosteric inhibitor in hGALK1. The ligand binding sites of hGALK1 were investigated using frames obtained from MD and ClustENMD. According to the findings, the application of combined 10/20 modes improved the success of the ESSA method. Moreover, binding site prediction success demonstrated variation in the presence of different cutoff values and conformations. Different cutoff values demonstrated success in the prediction of allosteric and orthosteric sites highlighting the role of contacting atoms in the Gaussian Network Model (GNM) calculations. To this extent, the combination of results from various cutoff values has the potential to improve the allosteric site prediction success of the ESSA method.
  • Master Thesis
    Crude Pectinolytic Enzymes Production in Fed-Batch Shake Flask Cultivation
    (01. Izmir Institute of Technology, 2023) Esen, Büşra Nur; Uzuner, Sibel; Uzuner, Sibel; Taşkent Sezgin, Hümeyra
    The use of waste in the production of enzymes, which is one of the products with high added value, is one of the right strategies to reduce the production cost of the product and sustainability movement. In this study, the production of polygalacturonase (PGase) and pectin lyase (PLase) enzymes from Bacillus subtilis ATCC 6633 in fed batch submerged fermentation, the conditions and composition of the fermentation medium and the effects of pretreatment methods (thermal, thermo-chemical, microwave assisted dilute acid (MW- DA)) on the conversion of fermentable sugar from black carrot pulp were investigated. The MW-DA was chosen the best with higher fermentable sugar content (FSC). The three different powers (300, 600, 850 W) and 3 different treatment time (30, 60, 90 s) were examined by Taguchi design. The highest FSC was found at 300 Watt for 30 seconds. MW-DA followed by ES produced the most fermentable sugar (0.493 g/g, 87.3% conversion). The amount of fermentable sugar was enhanced from 15.8% to 87.3% when MW-DA treatment is combined with enzymatic saccharification (ES). Yeast extract, whey and pea protein were examined as nitrogen sources. According to the enzyme activity results obtained, the fermentation medium was modified with pea protein. Certain concentrations (2.5%, 5%, 10%, 15%) were fed to the fermentation medium. The highest PGase activity was determined at the 15% feed concentration and 72th hours (164.34±2.26 U/L) whereas the highest PLase activity was obtained at 72th hours (188.22±1.72 U/L) at 5% feed concentration.
  • 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.
  • Master Thesis
    Chemical Characterization of Caldanaerobacter Subterraneus Subsp. Tengcongensis Heme-Nitric Oxide/Oxygen Binding Protein
    (01. Izmir Institute of Technology, 2020) Erdal, Merve; Sürmeli, Nur Başak; Sürmeli, Nur Başak
    Hemoproteins, which contain the heme prosthetic group , take part in different biological processes in many stages of life. Their ability to catalyze important biosynthesis reactions makes them good candidates for understanding and elucidating complex mechanisms for biocatalysis. In this study, the catalytic properties of thermophilic Thermoanaerobacter tencogensis nitric oxide/oxygen binding protein, a heme protein reshaped by rational design, were investigated and chemical characterization was carried out. The peroxidase activity of the enzyme was investigated by the oxidation reactions of guaiacol, amplex red and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS). Kinetic parameters of the reactions were determined. These obtained results demonstrated that, in the presence of H2O2, wild type and Y140H TtH-NOX proteins are able to catalyze oxidation reactions of guaiacol, Amplex red and ABTS. Comparison of the kinetic parameters showed that Y140H mutant catalyzed the guaiacol and ABTS oxidation 3-fold and 15 -fold faster than wild type enzyme, respectively. The stability of TtH-NOX proteins were investigated in the presence of organic solvents. Results were demonstrated that WT TtH-NOX was more stable than Y140H mutant in the presence of organic solvents In addition to these, for the first time, thermophilic TtH-NOX proteins were immobilized with a novel enzyme immobilization method and organic-inorganic hybrid nanostrucrures were obtained. Copper ion incorporated TtH-NOX-based hybrid nanoflowers were synthesized at different pH values. SEM and EDX analysis of TtH-NOX-based hybrid nanoflowers proved that free TtH-NOXs were immobilized successfully.