PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.Article Citation - WoS: 3Citation - Scopus: 4Enhanced Thermostability of the Immobilized Thermoalkalophilic Esterase Onto Magnetic-Cornstarch Nanoparticle(Wiley, 2022) Öz, Yasin; Sürmeli, Yusuf; Şanlı Mohamed, GülşahThe immobilization of the biocatalysts onto magnetic nanoparticles has been extensively applied as the external magnetic field facilitates the enzyme recovery from the reaction mixture. In the present study, glutaraldehyde-modified magnetite-cornstarch nanoparticles (MCNs) were successfully synthesized, elaborately characterized by ZetaSizer and surface-enhanced Raman spectroscopy, and used for the immobilization of a thermoalkalophilic esterase from Geobacillus sp. The optimal immobilization conditions were obtained at 65 degrees C, 2:3 molar ratios of Fe2+:Fe3+, and 1 g cornstarch resulted in approximately 90 nm magnetic particles in size. Also, immobilization yield and immobilization efficiency of the esterase were found as 74% and 82%, respectively. Scanning electron microscopy micrographs showed that MCNs were uniform, spherical in shape, and well dispersed and esterase immobilized MCNs displayed similar morphology as free MCNs. The maximum activity of free and immobilized esterase was obtained at 65 degrees C and pH 9. Immobilization onto glutaraldehyde-modified MCNs significantly enhanced the esterase thermostability. Additionally, the immobilized esterase kept its residual activity of 75% after three sequential cycles, suggesting that it has favorable operational stability.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: 2Citation - Scopus: 2Cloning, Expression, and Characterization of a Novel Sericin-Like Protein(Wiley, 2022) Bostan, Fatmanur; Sürmeli, Nur BaşakSilk consists of two proteins called fibroin and sericin. While fibroin is used in the textile industry and has various biomaterial applications, sericin has been considered as waste material until recently. Sericin is a multicomponent protein and it has important properties such as biocompatibility, biodegradability, cryoprotectivity, and antioxidant. Sericin from silkworm cocoons can be obtained by chemical, enzymatic, and heat treatment methods. However, sericin obtained with these treatment methods is not of consistent and high quality. Moreover, the exposure of sericin to harsh conditions during extraction leads to inconsistencies in the composition and structure of the sericin obtained. The inconsistencies in sericin structure and composition decrease application of sericin as a biomaterial. Here, we produce a sericin-like protein (Ser4mer) with native sequence of sericin encoding four repeats of the conserved 38 amino acid motif recombinantly in Escherichia coli and characterize its structural properties. Ser4mer protein shows similar structure to native sericin and higher solubility than previously obtained recombinant sericin-like proteins. Recombinant production of a soluble sericin-like protein will significantly expand its applications as a biomaterial. In addition, recombinant production of silk proteins will allow us to understand sequence-structure relationships in these proteins.Article Citation - WoS: 3Citation - Scopus: 3Monolayer Aste2: Stable Robust Metal in 2d, 1d and 0d(Wiley, 2018) Badalov, S. V.; Kandemir, Ali; Şahin, HasanThe structural, phononic, and electronic properties of the monolayer structures of AsTe2 are characterized by performing density functional theory (DFT) calculations. Total energy optimization and phonon calculations reveal that single layers of the 2H-AsTe2 and 1T-AsTe2 phases form dynamically stable crystal structures. Electronic structure analysis also shows that both 2H and 1T phases have nonmagnetic metallic character. It is also predicted that the metallic nature of the ultra-thin both 2H-AsTe2 and 1T-AsTe2 structures remain unchanged even under high biaxial strain values. For further examination of the dimensionality effect in the robust metallicity in 2D AsTe2 phases, electronic characteristics of 1D nanoribbons and 0D quantum dots are also investigated. It is found that independent from the dimension and crystallographic orientations 0D and 1D structures of 2H- and 1T-AsTe2 structures have metallic behavior. It is found that single layers of AsTe2 are quite promising materials for nanodevice applications owing to the robust metallic character.