Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Enhancing Electron Transfer in Cytochrome P450 Systems: Insights From CYP119-Putidaredoxin Interface Engineering(MDPI, 2025) Kakimova, Akbota; Surmeli, Nur BasakCytochrome P450 enzymes (CYPs) are versatile biocatalysts capable of performing selective oxidation reactions valuable for industrial and pharmaceutical applications. However, their catalytic efficiency is often constrained by dependence on costly electron donors, the requirement for redox partners, and uncoupling reactions that divert reducing power toward reactive oxygen species. Improving electron transfer efficiency through optimized redox partner interactions is therefore critical for developing effective CYP-based biocatalysts. In this study, we investigated the interaction between CYP119, a thermophilic CYP from Sulfolobus acidocaldarius, and putidaredoxin (Pdx), the redox partner of P450cam. Using rational design and computational modeling with PyRosetta 3, 14 CYP119 variants were modeled and analyzed by docking simulations on the Rosie Docking Server. Structural analysis identified three key mutations (N34E, D77R, and N34E/D77R) for site-directed mutagenesis. These mutations (N34E, D77R, and N34E/D77R) enhanced Pdx binding affinity by 20-, 3-, and 12-fold, respectively, without affecting substrate binding. Catalytic assays using lauric acid and indirect assays to monitor electron transfer revealed that, despite improved complex formation, the N34E variant showed reduced electron transfer efficiency compared to D77R. These findings highlight the delicate balance between redox partner binding affinity and catalytic turnover, emphasizing that fine-tuning electron transfer interfaces are essential for engineering efficient CYP biocatalysts.Article Citation - WoS: 5Citation - Scopus: 6A Novel Enzymatic Delamination Method for Sustainable Recycling of Crystal Silicon Photovoltaic (c-Si Pv) Modules(Elsevier, 2025) Karagoz, Sadik Can; Gundogdu, Tugba Keskin; Sarialtin, Huseyin; Celiktas, Melih SonerDue to the growing effects of global warming, there has been a surge in the demand for renewable energy sources. In particular, the most important player in this increase is the installation of photovoltaic (PV) modules. At this critical stage, it has become a priority to identify strategic approaches for the recycling of end-of-life PV panels with a strong focus on environmental protection. This study examined the impact of enzymatic delamination on the separation of the EVA (Ethylne Viniyl Aceate Co polymer) layer, a crucial stage in the recycling process of PV panels. Notably, this investigation is the first of its kind in the existing literature. To investigate this, delamination effects of lipase, laccase, and lecitase enzymes were analyzed according to experimental design methods. Furthermore, sunflower oil was employed for the first time in the existing body of literature to facilitate delamination, resulting in a delamination rate of 100 %. The environmental impacts of these biotechnological techniques, which serve as alternatives to the commonly used toluene, were also comparatively assessed by life cycle assessment (LCA) method to analyze the environmental impact. LCA methodology was performed from gate to gate and the Recipe impact methodology was used. Oil assisted enzymatic delamination method was shown to be an alternative from environmental point of view to solvent based method such as toluene.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.Book Part Citation - Scopus: 1Enzyme Technology in Value Addition of Wine and Beer Processing(Elsevier, 2022) Uzuner, SibelSome endogeneous and exogeneous enzymes participate in the brewery and winery technologies. Industrial enzymes provide quantitative advantages (increased juice yields) and qualitative advantages (enhanced extraction and flavor) for processing (shorter maceration, settling, and filtration time). This review aims to explain the flow process of brewing and wine-making, discuss different enzymes used in brewery and wine-making industry. Also, this chapter summarizes the key enzymes used at different stages of wine-making and brewing, and the challenges of the exogeneous, commercial and immobilized enzymes. Finally, the use of immobilized enzymes is presented as a significant strategy to improve catalyst during brewing and wine-making.Article Citation - WoS: 6Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(Wiley, 2021) Sakallı, Tuğçe; Sürmeli, Nur BaşakBiocatalysts 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.Article Citation - WoS: 13Citation - Scopus: 13Solid-Binding Peptide-Guided Spatially Directed Immobilization of Kinetically Matched Enzyme Cascades in Membrane Nanoreactors(American Chemical Society, 2021) Yücesoy, Deniz Tanıl; Akkineni, Susrut; Tamerler, Candan; Hinds, Bruce J.; Sarıkaya, MehmetBiocatalysis is a useful strategy for sustainable green synthesis of fine chemicals due to its high catalytic rate, reaction specificity, and operation under ambient conditions. Addressable immobilization of enzymes onto solid supports for one-pot multistep biocatalysis, however, remains a major challenge. In natural pathways, enzymes are spatially coupled to prevent side reactions, eradicate inhibitory products, and channel metabolites sequentially from one enzyme to another. Construction of a modular immobilization platform enabling spatially directed assembly of multiple biocatalysts would, therefore, not only allow the development of high-efficiency bioreactors but also provide novel synthetic routes for chemical synthesis. In this study, we developed a modular cascade flow reactor using a generalizable solid-binding peptide-directed immobilization strategy that allows selective immobilization of fusion enzymes on anodic aluminum oxide (AAO) monoliths with high positional precision. Here, the lactate dehydrogenase and formate dehydrogenase enzymes were fused with substrate-specific peptides to facilitate their self-immobilization through the membrane channels in cascade geometry. Using this cascade model, two-step biocatalytic production of l-lactate is demonstrated with concomitant regeneration of soluble nicotinamide adenine dinucleotide (NADH). Both fusion enzymes retained their catalytic activity upon immobilization, suggesting their optimal display on the support surface. The 85% cascading reaction efficiency was achieved at a flow rate that kinetically matches the residence time of the slowest enzyme. In addition, 84% of initial catalytic activity was preserved after 10 days of continuous operation at room temperature. The peptide-directed modular approach described herein is a highly effective strategy to control surface orientation, spatial localization, and loading of multiple enzymes on solid supports. The implications of this work provide insight for the single-step construction of high-power cascadic devices by enabling co-expression, purification, and immobilization of a variety of engineered fusion enzymes on patterned surfaces. © 2021 The Authors. Published by American Chemical Society.Article Citation - WoS: 3Citation - Scopus: 5A Novel Thermophilic Hemoprotein Scaffold for Rational Design of Biocatalysts(Springer Verlag, 2018) Efua Aggrey Fynn, Joana; Sürmeli, Nur BaşakHemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design. [GRAPHICS] .Article Citation - WoS: 40Citation - Scopus: 50Hyaluronidase 1 and Ss-Hexosaminidase Have Redundant Functions in Hyaluronan and Chondroitin Sulfate Degradation(American Society for Biochemistry and Molecular Biology, 2012) Gushulak, Lara; Hemming, Richard; Martin, Dianna; Seyrantepe, Volkan; Pshezhetsky, Alexey; Triggs-Raine, BarbaraHyaluronan (HA), a member of the glycosaminoglycan (GAG) family, is a critical component of the extracellular matrix. A model for HA degradation that invokes the activity of both hyaluronidases and exoglycosidases has been advanced. However, no in vivo studies have been done to determine the extent to which these enzymes contribute to HA breakdown. Herein, we used mouse models to investigate the contributions of the endoglycosidase HYAL1 and the exoglycosidase β-hexosaminidase to the lysosomal degradation of HA. We employed histochemistry and fluorophore-assisted carbohydrate electrophoresis to determine the degree of HA accumulation in mice deficient in one or both enzyme activities. Global HA accumulation was present in mice deficient in both enzymes, with the highest levels found in the lymph node and liver. Chondroitin, a GAG similar in structure to HA, also broadly accumulated in mice deficient in both enzymes. Accumulation of chondroitin sulfate derivatives was detected in mice deficient in both enzymes, as well as in β-hexosaminidase-deficient mice, indicating that both enzymes play a significant role in chondroitin sulfate breakdown. Extensive accumulation of HA and chondroitin when both enzymes are lacking was not observed in mice deficient in only one of these enzymes, suggesting that HYAL1 and β-hexosaminidase are functionally redundant in HA and chondroitin breakdown. Furthermore, accumulation of sulfated chondroitin in tissues provides in vivo evidence that both HYAL1 and β-hexosaminidase cleave chondroitin sulfate, but it is a preferred substrate for β-hexosaminidase. These studies provide in vivo evidence to support and extend existing knowledge of GAG breakdown.Article Citation - WoS: 62Citation - Scopus: 67Thermal Stability of Carbonic Anhydrase Immobilized Within Polyurethane Foam(John Wiley and Sons Inc., 2010) Kanbar, Bora; Özdemir, EkremThermal stability of carbonic anhydrase (CA) immobilized within polyurethane (PU) foam was investigated. The catalytic activity of the enzyme was estimated by using p-nitrophenyl acetate (p-NPA) as the substrate in tris buffer containing 10% acetonitrile. The immobilized CA was stable during the repeatable washings and stability tests over 45 days stored in tris buffer at ambient conditions indicating that the CA was covalently attached to the polyurethane (PU) foam by crosslinking. The immobilized CA was found to be 98% stable below 50°C, whereas a drastic decrease was seen at temperatures between 50 and 60°C. The optimum temperature for the immobilized CA was found to be 45°C and it lost its activity completely at 60°C. Thermal deactivation energies for the free and immobilized CA were estimated to be 29 and 86 kcal/mol, respectively. The association of unfolded CA with the polymeric backbone chains of the PU foam was also addressed. It was concluded that the immobilized CA was highly stable at temperatures less than 50°C and could be used in biomimetic CO sequestration processes. © 2010 American Institute of Chemical EngineersArticle Citation - WoS: 125Citation - Scopus: 147Incorporation of Partially Purified Hen Egg White Lysozyme Into Zein Films for Antimicrobial Food Packaging(Elsevier Ltd., 2006) Mecitoğlu, Çiğdem; Yemenicioğlu, Ahmet; Arslanoğlu, Alper; Elmacı, Zehra Seda; Korel, Figen; Çetin, Ali EmrahLysozyme, partially purified from hen egg white by precipitation of non-enzyme protein with ethanol and lyophilized after dialysis, was incorporated into zein films. The recovery and specific activity of the enzyme after partial purification varied between 45% and 72% and 2173 and 3448 U/mg, whereas the activity of the lyophilized enzyme varied between 2900 and 3351 U/mg. The partially purified enzyme was very stable and lost almost no activity in lyophilized form or in zein films stored at -18 and 4°C for up to 8 and 4 months, respectively. During partial purification and in zein film preparation, ethanol treatment caused 123-137% and 132-315% activation of the enzyme, respectively. In zein films incorporated with 187-1318 U/cm2 (63-455 μg/cm2) lysozyme, the release rates at 4°C, changed between 7 and 29 U/cm2/min, increased at high lysozyme concentrations. Zein films incorporated with partially purified lysozyme showed antimicrobial effect on Bacillus subtilis and Lactobacillus plantarum. By the addition of disodium EDTA, the films also became effective on Escherichia coli. The results of this study showed that the partially purified lysozyme may be used in antimicrobial packaging to increase food safety.