PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(John Wiley and Sons Inc, 2022) Sakalli, T.; Surmeli, N.B.Biocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry. © 2021 International Union of Biochemistry and Molecular Biology, Inc.Article Citation - Scopus: 4Quasi-Supervised Strategies for Compound-Protein Interaction Prediction(John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.Article Citation - Scopus: 4Comparative Proteomic Analysis of Leishmania Parasites Isolated From Visceral and Cutaneous Leishmaniasis Patients(Cambridge University Press, 2022) Dinç, M.; Yalçln, T.; Çavuş, I.; Özbilgin, A.Leishmaniasis is an infectious disease in which different clinical manifestations are classified into three primary forms: visceral, cutaneous and mucocutaneous. These disease forms are associated with parasite species of the protozoan genus Leishmania. For instance, Leishmania infantum and Leishmania tropica are typically linked with visceral (VL) and cutaneous (CL) leishmaniasis, respectively; however, these two species can also cause other form to a lesser extent. What is more alarming is this characteristic, which threatens current medical diagnosis and treatment, is started to be acquired by other species. Our purpose was to address this issue; therefore, gel-based and gel-free proteomic analyses were carried out on the species L. infantum to determine the proteins differentiating between the parasites caused VL and CL. In addition, L. tropica parasites representing the typical cases for CL were included. According to our results, electrophoresis gels of parasites caused to VL were distinguishable regarding the repetitive down-regulation on some specific locations. In addition, a distinct spot of an antioxidant enzyme, superoxide dismutase, was shown up only on the gels of CL samples regardless of the species. In the gel-free approach, 37 proteins that were verified with a second database search using a different search engine, were recognized from the comparison between VL and CL samples. Among them, 31 proteins for the CL group and six proteins for the VL group were determined differentially abundant. Two proteins from the gel-based analysis, pyruvate kinase and succinyl-coA:3-ketoacid-coenzyme A transferase analysis were encountered in the protein list of the CL group. Copyright © The Author(s), 2021. Published by Cambridge University Press.Article Citation - WoS: 1Citation - Scopus: 2Recycling of Gas-To Sludge as a Potential Organic Amendment: Effect on Soil and Cotton Properties Under Hyperarid Conditions(Academic Press, 2023) Mabrouk, O.; Hamdi, H.; Sayadi, S.; Al-Ghouti, M.A.; Abu-Dieyeh, M.; Kogbara, R.; Al-Sharshani, A.Gas-to-liquid (GTL) sludge is a specific wastewater treatment by-product, which is generated during the industrial process of natural gas conversion to transportation fuels. This least studied sludge is pathogen-free and rich in organic carbon and plant nutrients. Therefore, it can be reused for soil enhancement as a sustainable management strategy to mitigate landfill gas emissions. In this field study, we compared the performance of soil treatments with GTL sludge to the more conventional chemical fertilizers and cow manure compost for the cultivation of cotton under hyperarid conditions. After a complete growing season, GTL sludge application resulted in the enhancement of soil properties and plant growth compared to conventional inputs. As such, there was a significant dose-dependent increase of soil organic matter (4.01% and 4.54%), phosphorus (534 and 1090 mg kg−1), and cumulative lint yield (4.68 and 5.67 t ha−1) for GTL sludge application rates of 1.5% and 3%, respectively. The produced fiber quality was adequate for an upland cotton variety (Gossypium hirsutum var. MAY 344) and appeared more dependent on the prevailing climate conditions than soil treatments. On the other hand, the adverse effects generally related to industrial sludge reuse were not significant and did not affect the designed agro-environmental system. Accordingly, plants grown on GTL sludge-amended soils showed lower antioxidant activity despite significant salinity increase. In addition, the concentrations of detected heavy metals in soil were within the standards’ limits, which did not pose environmental issues under the described experimental conditions. Leachate analysis revealed no risks for groundwater contamination with phytotoxic metals, which were mostly retained by the soil matrix. Therefore, recycling GTL sludge as an organic amendment can be a sustainable solution to improve soil quality and lower carbon footprint. To reduce any environmental concerns, an application rate of 1.5% could be provisionally recommended since a two-fold increase in sludge dose did not result in a significant yield improvement. © 2023 Elsevier Ltd