Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 9Citation - Scopus: 9Development of an Improved Amplex Red Peroxidation Activity Assay for Screening Cytochrome P450 Variants and Identification of a Novel Mutant of the Thermophilic Cyp119(Springer, 2020) Başlar, M. Semih; Sakallı, Tuğçe; Güralp, Gülce; Kestevur Doğru, Ekin; Haklı, Emre; Sürmeli, Nur BaşakBiocatalysts are increasingly utilized in the synthesis of drugs and agrochemicals as an alternative to chemical catalysis. They are preferred in the synthesis of enantiopure products due to their high regioselectivity and enantioselectivity. Cytochrome P450 (P450) oxygenases are valuable biocatalysts, since they catalyze the oxidation of carbon-hydrogen bonds with high efficiency and selectivity. However, practical use of P450s is limited due to their need for expensive cofactors and electron transport partners. P450s can employ hydrogen peroxide (H2O2) as an oxygen and electron donor, but the reaction with H(2)O(2)is inefficient. The development of P450s that can use H(2)O(2)will expand their applications. Here, an assay that utilizes Amplex Red peroxidation, to rapidly screen H2O2-dependent activity of P450 mutants in cell lysate was developed. This assay was employed to identify mutants of CYP119, a thermophilic P450 fromSulfolobus acidocaldarius, with increased peroxidation activity. A mutant library of CYP119 containing substitutions in the heme active site was constructed via combinatorial active-site saturation test and screened for improved activity. Screening of 158 colonies led to five mutants with higher activity. Among improved variants, T213R/T214I was characterized. T213R/T214I exhibited fivefold higherk(cat)for Amplex Red peroxidation and twofold higherk(cat)for styrene epoxidation. T213R/T214I showed higher stability towards heme degradation by H2O2. While theK(m)for H(2)O(2)and styrene were not altered by the mutation, a fourfold decrease in the affinity for another substrate, lauric acid, was observed. In conclusion, Amplex Red peroxidation screening of CYP119 mutants yielded enzymes with increased peroxide-dependent activity. [GRAPHICS] .Article Citation - WoS: 21Citation - Scopus: 29Partial Purification and Kinetic Characterization of Mushroom Stem Polyphenoloxidase and Determination of Its Storage Stability in Different Lyophilized Forms(Elsevier Ltd., 2007) Şimşek, Şebnem; Yemenicioğlu, AhmetMonophenolase (1011 ± 626 U/g AP) and diphenolase activities (5163 ± 3059 U/g AP) of PPO in acetone powders (APs) of different mushroom stems varied considerably. However, the limited variation of average dipenolase (L-DOPA) to monophenolase (L-tyrosine) activity ratio (5.4 ± 0.7) in crude extracts showed the homogeneity of PPO from different mushroom stems. The change in extraction material or partial purification method (ammonium sulfate or acetone precipitation) did not affect the temperature stability, temperature and pH dependency and Km of monophenolase activity considerably. However, some changes were observed in pH stability and substrate specificity of PPO in different parties of mushroom stems. The most important aspects of mushroom stem PPO are its lower diphenolase to monophenolase activity ratio than mushroom cap PPO, low temperature dependency of activity between 25 and 40 °C (Ea = 30 kJ/mol), broad optimum pH between 6 and 8, but lack of activity pH ≤5, and ability to use phloridzin as substrate. The mushroom stem PPOs partially purified and lyophilized by using sucrose, dextran or alginate showed moderate to high stability at -18 °C for 6-6.5 months. Thus, the mushroom stems obtained as a waste material during mushroom processing may be used as a more homogenous source than whole mushrooms to obtain PPO used for different industrial, clinical or research purposes.Article Citation - WoS: 110Citation - Scopus: 120Alkaline Protease Production From Alkalophilic Bacillus Sp. Isolated From Natural Habitats(Elsevier Ltd., 2006) Gençkal, Hande; Tarı, CananBacillus strains isolated under extreme alkaline conditions (Izmir, Turkey), were screened and identified for high alkaline protease activity. Strains with high protease yields were optimized with respect to inoculum concentration, temperature, agitation speed, initial medium pH and incubation time. Three Bacillus strains coded as I18, L18 and L21 showed high potential, for alkaline protease activity (160-222 U/ml) among 85 isolates. The specific growth rates were estimated from the growth curves as 0.49 h-1 for I18, as 0.6 and 0.7 h-1 for L18 and L21, respectively. The optimum temperatures were determined as 30 °C for strain I18 and 37 °C for the strains L18 and L21. Similarly, the optimum agitation speeds were 100 rpm for I18 and 180 rpm for L18 and L21. For all three strains, the optimum inoculation ratio and incubation time, were determined as 5% (v/v) and 96 h, respectively. The optimum initial media pH was found as pH 10 for strain L18 and L21. Bacillus sp. L21 with the highest specific protease activity (60 U/mg protein) and a broader pH range was chosen for further study. The biomass and product yield for this strain was determined as 0.023 g cell/g glucose and 0.021 U/g glucose, respectively. The crude enzyme of this strain was further characterized and was determined as a bleach stable, serine alkaline protease with an optimum temperature of 60 °C and a pH of 11, with a potential to be a candidate for the applications in the detergent industry.Article Citation - WoS: 56Citation - Scopus: 63Thioredoxin Is Required for Deoxyribonucleotide Pool Maintenance During S Phase(American Society for Biochemistry and Molecular Biology, 2006) Koç, Ahmet; Mathews, Christopher K.; Wheeler, Linda J.; Gross, Michael K.; Merrill, Gary FredericThioredoxin was initially identified by its ability to serve as an electron donor for ribonucleotide reductase in vitro. Whether it serves a similar function in vivo is unclear. In Saccharomyces cerevisiae, it was previously shown that Δtrx1 Δtrx2 mutants lacking the two genes for cytosolic thioredoxin have a slower growth rate because of a longer S phase, but the basis for S phase elongation was not identified. The hypothesis that S phase protraction was due to inefficient dNTP synthesis was investigated by measuring dNTP levels in asynchronous and synchronized wild-type and Δtrx1 Δtrx2 yeast. In contrast to wild-type cells, Δtrx1 Δtrx2 cells were unable to accumulate or maintain high levels of dNTPs when α-factor- or cdc15-arrested cells were allowed to reenter the cell cycle. At 80 min after release, when the fraction of cells in S phase was maximal, the dNTP pools in Δtrx1 Δtrx2 cells were 60% that of wild-type cells. The data suggest that, in the absence of thioredoxin, cells cannot support the high rate of dNTP synthesis required for efficient DNA synthesis during S phase. The results constitute in vivo evidence for thioredoxin being a physiologically relevant electron donor for ribonucleotide reductase during DNA precursor synthesis.