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    Conserved amino acid residues that affect structural stability of candida boidinii formate dehydrogenase
    (Springer, 2021) Bulut, Huri; Yüksel, Büşra; Gül, Mehmet; Eren, Meryem; Karataş, Ersin; Kara, Nazlı; Yılmazer, Berin; Koçyiğit, Abdurrahim; Labrou, Nikolaos E.; Bi?nay, Barış
    The NAD+-dependent formate dehydrogenase (FDH; EC 1.2.1.2) from Candida boidinii (CboFDH) has been extensively used in NAD(H)-dependent industrial biocatalysis as well as in the production of renewable fuels and chemicals from carbon dioxide. In the present work, the effect of amino acid residues Phe285, Gln287, and His311 on structural stability was investigated by site-directed mutagenesis. The wild-type and mutant enzymes (Gln287Glu, His311Gln, and Phe285Thr/His311Gln) were cloned and expressed in Escherichia coli. Circular dichroism (CD) spectroscopy was used to determine the effect of each mutation on thermostability. The results showed the decisive roles of Phe285, Gln287, and His311 on enhancing the enzyme’s thermostability. The melting temperatures for the wild-type and the mutant enzymes Gln287Glu, His311Gln, and Phe285Thr/His311Gln were 64, 70, 77, and 73 °C, respectively. The effects of pH and temperature on catalytic activity of the wild-type and mutant enzymes were also investigated. Interestingly, the mutant enzyme His311Gln exhibits a large shift of pH optimum at the basic pH range (1 pH unit) and substantial increase of the optimum temperature (25 °C). The present work supports the multifunctional role of the conserved residues Phe285, Gln287, and His311 and further underlines their pivotal roles as targets in protein engineering studies.
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    Investigation of diagnostic proteins by 2D electrophoresis in major de-pression model induced by forced swim test in rats
    (2021) Duman, Tuğçe; Akyüz, Enes; Bulut, Huri; Koçyiğit, Abdurrahim; Tülek, Ahmet; Karataş, Ersin; Kırpınar, İsmet
    Background: Aside from its pervasiveness, whereby it affects as much as 20% of the world's population, depression continues to be one of the most crucial psychiatric problems due to the loss of power it causes by disrupting daily life functioning, containing economic consequences, and having a high suicidal tendency. Major depression (MD) is a systemic and multifactorial disorder involving complex interactions between genetic predisposition and disturbances of various molecular pathways. Objectives: In our current study, we aimed to identify the proteins obtained from serum samples that change during depression with the MD model. Methods: The MD model was applied through the forced swim test in rats. 14 Winstar Albino male rats were divided into two equal groupsas follows: depression and control groups. Serum samples were separated by chromatographic methods and then compared with two-dimensional (2D) electrophoresis. Results: A total of 9 potential diagnostic protein sequences were identified, which were distinguished with computer soft-ware. During the last phase of the study,the Matrix-Assisted Laser Desorption/Ionization -Time of Flight (MALDI-TOF) analysis, the previous expression sequences identified among the groups were determined and classified. By comparing protein expressions, it was concluded that 9 different points could be used together as a potential biomarker. Conclusion: Results can help us identify a new diagnostic system that can be used to diagnose MD.