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: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, NuranIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.Letter Prof. Dr. O. Yavuz Ataman(TÜBİTAK, 2021) Eroğlu, Ahmet EminProf. Dr. O. Yavuz Ataman passed away on August 15, 2020, in Ankara. He was an academic as well as a social figure throughout his life. He had remarkable achievements in academy as a researcher, an educator, and an administrator. He was known for his unique approaches to the events in all aspects of life. With his beloved character, he was really special. With Prof. Ataman's passing away, the chemistry and especially analytical chemistry community have lost a very special member.Article Citation - WoS: 1Citation - Scopus: 1Fabrication and in Vitro Evaluation of Thermally Cross-Linked Gelatin Nanofibers for Drug Delivery Applications(Taylor & Francis, 2022) Mete, Derya; Göktaş, Gözde; Şanlı Mohamed, GülşahIn this study, four different nanofibers consisting of gelatin (Gel), doxorubicin (DOX) with gel (DOX@Gel), a composite of gel with poly(ethylene glycol) (PEGylated-gel), and DOX@PEGylated-gel were fabricated. Subsequently, the nanofibers were thermally cross-linked in order to offer a stable and biocompatible alternative for the biological applications of nanofibers such as drug delivery and tissue engineering. Nanofibers were characterized by scanning electron microscopy, Fourier Transform-Infrared Spectroscopy (FT-IR), and confocal microscopy. The formation of smooth, continuous, and uniform nanofibers was observed and the addition of PEG resulted in an increase whereas the incorporation of DOX into nanofibers had no significant change in the diameter of nanofibers. Crosslinking also enlarged the diameter of all nanofibers and the most dramatic increase was observed 53% by DOX@PEGylated-gel. Afterward, the biological performance of the nanofibers was investigated by drug release profile, cytotoxicity on A549 cell line as well as antimicrobial activity with E. coli and S. aureus. The results indicate an enhanced drug release profile, moderate antimicrobial activity, and reasonable cytotoxic efficiency for thermally cross-linked nanofibers compared to uncross-linked nanofibers.Article Citation - WoS: 15Citation - Scopus: 17Improved Activity of Alpha-L From Geobacillus Vulcani Gs90 by Directed Evolution: Investigation on Thermal and Alkaline Stability(John Wiley and Sons Inc., 2019) Sürmeli, Yusuf; İlgü, Hüseyin; Şanlı Mohamed, Gülşahalpha-L-Arabinofuranosidase (Abf) is a potential enzyme because of its synergistic effect with other hemicellulases in agro-industrial field. In this study, directed evolution was applied to Abf from Geobacillus vulcani GS90 (GvAbf) using one round error-prone PCR and constructed a library of 73 enzyme variants of GvAbf. The activity screening of the enzyme variants was performed on soluble protein extracts using p-nitrophenyl alpha-L-arabinofuranoside as substrate. Two high activity displaying variants (GvAbf L307S and GvAbf Q90H/L307S) were selected, purified, partially characterized, and structurally analyzed. The specific activities of both variants were almost 2.5-fold more than that of GvAbf. Both GvAbf variants also exhibited higher thermal stability but lower alkaline stability in reference to GvAbf. The structural analysis of GvAbf model indicated that two mutation sites Q90H and L307S in both GvAbf variants are located in TIM barrel domain, responsible for catalytic action in many Glycoside Hydrolase Families including GH51. The structure of GvAbf model displayed that the position of L307S mutation is closer to the catalytic residues of GvAbf compared with Q90H mutation and also L307S mutation is conserved in both variants of GvAbf. Therefore, it was hypothesized that L307S amino acid substitution may play a critical role in catalytic activity of GvAbf. (C) 2018 International Union of Biochemistry and Molecular Biology, Inc.Article Citation - WoS: 15Citation - Scopus: 15Bodipy-Conjugated Chitosan Nanoparticles as a Fluorescent Probe(Taylor and Francis Ltd., 2017) Bor, Gizem; Üçüncü, Muhammed; Emrullahoğlu, Mustafa; Tomak, Aysel; Şanlı Mohamed, GülşahRecently, development of fluorescent nanoparticle-based probes for various bioimaging applications has attracted great attention. This work aims to develop a new type fluorescent nanoparticle conjugate and evaluate its cytotoxic effects on A549 and BEAS 2B cell lines. Throughout the study, ionically crosslinked chitosan nanoparticles (CNs) were conjugated with carboxylated 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY-COOH). The results of conjugates (BODIPY-CNs) were investigated with regard to their physic-chemical, optical, cytotoxic properties and cellular internalization. The morphology of BODIPY-CNs was found to be spherical in shape and quite uniform having average diameter of 70.25 ± 11.99 nm. Cytotoxicty studies indicated that although BODIPY-COOH itself was quite toxic on both A549- and BEAS 2B-treated cells, CNs increased the cell viability of both cell lines via conjugation to BODIPY-COOH fluorescent molecule up to 67% for A549 and 74% for BEAS 2B cells. These results may suggest a possible utilization of the new fluorescent nanoparticle-based probe for bioimaging in biology and medicine.Article Citation - WoS: 23Citation - Scopus: 25Molecular Cloning, Over Expression and Characterization of Thermoalkalophilic Esterases Isolated From Geobacillus Sp(Springer Verlag, 2011) Tekedar, Hasan Cihad; Şanlı Mohamed, GülşahDue to potential use for variety of biotechnological applications, genes encoding thermoalkalophilic esterase from three different Geobacillus strains isolated from thermal environmental samples in Balçova (Agamemnon) geothermal site were cloned and respective proteins were expressed in Escherichia coli (E. coli) and characterized in detail. Three esterases (Est1, Est2, Est3) were cloned directly by PCR amplification using consensus degenerate primers from genomic DNA of the strains Est1, Est2 and Est3 which were from mud, reinjection water and uncontrolled thermal leak, respectively. The genes contained an open reading frame (ORF) consisting of 741 bp for Est1 and Est2, which encoded 246 amino acids and ORF of Est3 was 729 bp encoded 242 amino acids. The esterase genes were expressed in E. coli and purified using His-Select HF nickel affinity gel. The molecular mass of the recombinant enzyme for each esterase was approximately 27. 5 kDa. The three esterases showed high specific activity toward short chain p-NP esters. Recombinant Est1, Est2, Est3 have exhibited similar activity and the highest esterase activity of 1,100 U/mg with p-nitrophenyl acetate (pNPC2) as substrate was observed with Est1. All three esterase were most active around 65°C and pH 9.5-10.0. The effect of organic solvents, several metal ions, inhibitors and detergents on enzyme activity for purified Est1, Est2, Est3 were determined separately and compared.Article Citation - WoS: 28Citation - Scopus: 27Determination of Thiamine Hcl and Pyridoxine Hcl in Pharmaceutical Preparations Using Uv-Visible Spectrophotometry and Genetic Algorithm Based Multivariate Calibration Methods(Pharmaceutical Society of Japan, 2004) Özdemir, Durmuş; Dinç, ErdalSimultaneous determination of binary mixtures pyridoxine hydrochloride and thiamine hydrochloride in a vitamin combination using UV-visible spectrophotometry and classical least squares (CLS) and three newly developed genetic algorithm (GA) based multivariate calibration methods was demonstrated. The three genetic multivariate calibration methods are Genetic Classical Least Squares (GCLS), Genetic Inverse Least Squares (GILS) and Genetic Regression (GR). The sample data set contains the UV-visible spectra of 30 synthetic mixtures (8 to 40 μg/ml) of these vitamins and 10 tablets containing 250 mg from each vitamin. The spectra cover the range from 200 to 330 nm in 0.1 nm intervals. Several calibration models were built with the four methods for the two components. Overall, the standard error of calibration (SEC) and the standard error of prediction (SEP) for the synthetic data were in the range of <0.01 and 0.43 μg/ml for all the four methods. The SEP values for the tablets were in the range of 2.91 and 11.51 mg/tablets. A comparison of genetic algorithm selected wavelengths for each component using GR method was also includedArticle Citation - WoS: 16Citation - Scopus: 19N,n-Dialkylaniline Tetraethynylethenes: a New Class of Chromophores Possessing an Emitting Charge-Transfer State. Experimental and Computational Studies(John Wiley and Sons Inc., 2001) Gobbi, Luca; Elmacı, Nuran; Lüthi, Hans Peter; Diederich, FrançoisThe photophysical properties of N,N-dimethylaniline- (DMA) substituted tetraethynylethene (TEE; 3,4-diethynylhex-3-ene-1,5-diyne) and related derivatives were investigated in a joint experimental and computational study. Measurements of the electronic emission spectra showed that these novel chromophores display a dual fluorescence which strongly depends on solvent polarity. Computational studies suggest that the twisted intramolecular charge-transfer state (TICT) model offers a possible explanation for the experimentally observed dual fluorescence. Time-dependent density functional calculations revealed that the initial excited state reached upon photoirradiation relaxes to a lower-energy TICT state in which either the dimethylamino group is twisted into an orthogonal position with respect to the remaining planar arylated TEE moiety or the entire DMA donor group takes an orthogonal orientation with respect to the rigid, planar TEE acceptor moiety. For the compounds investigated, the charge-transfer state responsible for the strongly solvent-dependent luminescence is directly connected with the initial excited state, namely, no crossing of states is involved.