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    Bioinformatics and 3D homology modelling of AsAlaDH fromAmycolatopsis sulphurea
    (2021) Aktaş, Fatih
    Alanine dehydrogenase (AlaDH) (E.C.1.4.1.1) is an enzyme that catalyzes the interconversion of pyruvate and alanine. This enzymehas the key catalytic role for the sporulation of microorganisms and synthesis of the many amino acids, proteins, and peptidoglycanlayers in the microorganisms. Amycolatopsis sulphurea one of the strains of Amycolatopsis genus within the familyPseudonocardiaceae has capable to produce different antibiotics such as Ristocetin, Vancomycin, and Epoxyquinomicin as well as tobiodegrade the bioplastic (poly-lactic acid (PLA) films). The 3D homology model of Alanine dehydrogenase from Amycolatopsissulphurea was carried out through I-TASSER. The interaction of L-alanine and active site amino acids of the enzyme was determinedby docking in silico via AutoDock Vina program. Protein secondary structures were predicted with EMBOSS tool garnier. Structuraland functional analysis and determination of Physico-chemical properties of AsAlaDH were performed by using differentbioinformatics tools. The secondary structure and multiple alignment analysis of alanine dehydrogenase displayed that there areconserved amino acid residues of AlaDH's from different microorganisms.
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    High-level heterologous expression of active Chaetomium thermophilum FDH in Pichia pastoris
    (Elsevier Inc., 2020) Duman, Zeynep Efsun; Duraksoy, Bedri Burak; Aktaş, Fatih; Woodley, John M.; Binay, Barış
    Nowadays, the use of formate dehydrogenase (FDH, EC 1.17.1.9) is well established as a means of NADH regeneration from NAD+ via the coupled conversion of formate into carbon dioxide. Recent studies have been reported that specifically Chaetomium thermophilum FDH (CtFDH) is the most efficient FDH catalyzing this reaction in reverse (i.e. using CO2 as a substrate to produce formate, and thereby regenerating NAD+). However, to date the production of active CtFDH at high protein expression levels has received relatively little attention. In this study, we have tested the effect of batch and high cell density fermentation (HCDF) strategies in a small stirred fermenter, as well as the effect of supplementing the medium with casamino acids, on the expressed level of secreted CtFDH using P. pastoris. We have established that the amount of expressed CtFDH was indeed enhanced via a HCDF strategy and that extracellular protease activity was eliminated via the addition of casamino acids into the fermentation medium. On this basis, secreted CtFDH in an active form can be easily separated from the fermentation and can be used for subsequent biotechnological applications. © 2020 Elsevier Inc.
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    Isolation, Purification and Characterization of New Cold Active Subtilisin-like Protease from Bacillus sp. strain EL-GU1
    (2019) Guduk, Elif; Yasar, Gulhan; Gulhan, Unzile Guven; Aktaş, Fatih
    One of the important hydrolytic enzymes are proteases that slice peptide bonds between amino acid residues.Proteases have various industrial applications including detergent, food, pharmaceutical, leather and diagnosticreagent industries. Among them, the most commercialized enzymes are alkaline proteases in the industry. Due totheir potential applications in the detergent industry as cleaning additives, they are of particular interest. In thisstudy, a novel protease from Bacillus sp. strain EL-GU1 was reported showing highest activity at pH 6 and20°C. The novel protease was purified by using ammonium sulfate precipitation and identified by 16S rDNAsequencing. Highest activity was observed as 3300 µmol/min-1mg-1 when casein used as a substrate. Kineticparameters of the enzyme were determined; KM, Vmax, kcat and catalytic efficiency values were calculated as 1.4mM, 1 mM/s, 2.10-7s-1, 0.14 10-7s-1M-1, respectively. These results indicated that the novel cold active proteasefrom Bacillus sp. strain EL- GU1 can be a good candidate for the detergent industry.
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    Partial purification and characterization of the novel halotolerant and alkalophilic laccase produced by a new isolate of Bacillus subtilis LP2
    (Taylor & Francis Ltd, 2019) Yaşar, Gülhan; Guven, Ünzile Gülhan; Güdük, Elif; Aktaş, Fatih
    Laccases (benzenediol: oxygen oxidoreductases, [EC1.10.3.2] are mostly known as members of the blue multicopper oxidase family that are used in very different industrial applications: textile, pulp and paper, food, cosmetics industries, bioremediation process, biosensor, biofuel and organic synthesis. Stability against the extreme conditions is an important property and it makes laccase suitable for several industrial processes. Laccase should have salt resistance to be used in textile dye degradation because the textile wastewaters include dyes with high concentrations of salts, especially NaCl. Bacterial laccases are preferable to be used for bioremediation process due to their high stability to extremely salt contaminated and alkalophilic environment. Bacillus subtilis LP2 was identified as a source of alkali-tolerant, salt resistant laccase. Laccase showed activity over a wide pH (4-10) and temperature (30-80 degrees C) range. Maximum laccase activity was observed as 140.4U/mg (umol/min*mg) at pH 8 and 50 degrees C with the substrate guaiacol. Stability of laccase was determined as 60% and 20% after incubation of the enzyme for different time intervals of 20 and 40min at 50 degrees C and pH 8. SDS (10mM) and EDTA (5mM) decreased laccase activity from 100% to 0% and 56%, respectively. Despite the other inhibitors, NaCI increased the activity of laccase to 167% at 500mM concentration. Laccase from Bacillus subtilis LP2 barely showed the activity on the substrates vanillin and L-tyrosine. These results clearly show that laccase from Bacillus subtilis LP2 has high potential to be used for several applications in textile industry.