Introduction N-linked glycosylation is one of the most defined posttranslational modifications in... more Introduction N-linked glycosylation is one of the most defined posttranslational modifications in nature . Glycosylation regulates the critical functions of proteins and plays a vital role in healthy and diseased conditions . N-glycans have the potential to be used in the early diagnosis of some cancers . It is also known that most of the approved biomarkers are glycoproteins or glycoconjugates . Therefore, N-glycan analysis of glycoproteins derived from biological samples is crucial for discovering new biomarker candidates. Glycomics is the field that focuses on elucidating glycan structures and quantification of glycans . Clinical application of quantitative glycomics has attracted attention because aberrant glycosylation is associated with many diseases . The N-glycan release is one of the most critical steps for quantitative glycomics . N-glycans are released from glycoproteins by an enzyme namely PNGase F (N-glycosidase F). Glycoproteins are first denatured by detergents prior to enzymatic treatments to facilitate access of glycans to the PNGase F. It has been examined that many parameters in N-glycan release methods influence the profiles of N-glycans derived from glycoproteins . For example, the kinetics of N-glycan release by PNGase F enzyme resulted in different IgG glycosylation profiles . On the other hand, different N-glycan release protocols were examined for cell line analysis and, in-solution approach has been found to be the most robust . In addition, a study has showed that different PNGase F enzymes resulted in diverse IgG and human plasma N-glycosylation profiles . It is clearly seen that the studies for optimizing of N-glycan release methods are required to improve the clinical glycomics applications. The first step in sample preparation for glycomic experiments includes the extraction of proteins from biological samples. Since most of the glycoproteins are integral membrane proteins, the use of detergents is obligatory for maximizing the extraction of proteins . Many detergents have been introduced and compared regarding the efficient protein extraction for mass spectrometry-based proteomics . These detergents can also be used for quantitative glycomic experiments. However, the effects of commonly used detergents on the enzymatical N-glycan release process have not been examined yet.
Novel hydrazones based on (-)-carvone were synthesized via condensation of terpenoid with 4-R-phe... more Novel hydrazones based on (-)-carvone were synthesized via condensation of terpenoid with 4-R-phenoxyacetic acid hydrazides. The structure of target compounds was established by FT-IR, Raman, 1 H-NMR and 13 C-NMR spectral analysis, FAB/ESI mass spectrometry. (-)-Carvone hydrazones were proven to exist as Z/E geometrical isomers about C=N bond using ion mobility-tandem mass spectrometry (IM-MS/MS). Single crystal X-ray diffraction study was applied to determine molecular and crystal structure of compound 3e. Hydrazones 3a-3e were evaluated as potential anticonvulsant agents after their oral administration against maximal electroshock (MES) and pentylenetetrazole (PTZ)-induced seizures in mice. Analgesic activity of compounds was investigated by topical application on models of capsaicin and AITC-induced pain. The present findings indicate that (-)-carvone derivatives afforded seizure protection both at short (1 h) and long (24 h) time period by blocking electroshock-and chemical-induced convulsions. Hydrazones binding to TRPA1/TRPV1 ion channels was proposed as possible mechanism explaining significant analgesic effect of compounds.
Hacettepe journal of biology and chemistry, Dec 25, 2017
B u çalışmada, bazik bir trifenilmetan boyası olan "kristal moru"nun (CV) sulu çözeltilerde H 2 O... more B u çalışmada, bazik bir trifenilmetan boyası olan "kristal moru"nun (CV) sulu çözeltilerde H 2 O 2 varlığında uzaklaştırılması ve bozunması, tabakalı MnO 2 ve ayrıca MnO 2 @MnFe 2 O 4 nanokompozit katalizörler kullanılarak araştırıldı. CV'nin bozunmasının tabakalı MnO 2 yapısı ile daha hızlı gerçekleştiği görüldü. Katalitik bozunma ürünleri Elektrospray İyonlaşmalı-Dört Kutuplu-Uçuş Zamanlı Kütle Spektrometresi (ESI-Q-ToF-MS) kullanılarak izlendi ve analiz edildi. Ana parçalanma ürünleri olarak, biyo-iyileştirme ile mineralizasyon ürünlerine dönüşebilme potansiyeli olan 4-izosiyanobenzaldehit (A) ve Michler ketonu (B) tanımlandı. Böylece, MnO 2 /H 2 O 2 sisteminin CV'yi biyobozunabilir yapılara dönüştürebilen özendirici bir katalizör olduğu anlaşıldı. Kristal moru, boya bozunumu, katalitik oksidasyon, manganoksit katalizörleri.
Soil salinity is a major abiotic stress factor that limits agricultural productivity worldwide, a... more Soil salinity is a major abiotic stress factor that limits agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean is an important protein source in developing countries however highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were performed on both salt-tolerant and susceptible common bean genotypes in saline conditions. Transcriptomics has demonstrated increased photosynthesis in saline conditions for tolerant genotype while the susceptible genotype acted in contrast. Transcriptome also displayed active carbon and aminoacid metabolism for the tolerant genotype. Analysis of metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response. According to ion content comparison, the tolerant genotype managed to block accumulation of Na + in the leaves while accumulating significantly less Na + in the roots compared to susceptible genotype. K + levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn +2 and Mn +2 levels were dropped in the tolerant roots, while Mo +2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype. The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance.
Glycosylation and phosphorylation are two of the most commonly seen and important post-translatio... more Glycosylation and phosphorylation are two of the most commonly seen and important post-translational modifications (PTMs) of proteins. Both play key role in many vital biological processes. Mass spectrometry is the most favored technique used for monitoring the dynamics of PTMs. Mass spectrometric analysis of phosphopeptide and glycopeptide is a crucial step in phosphoproteomics and glycoproteomics to understand the role of these modifications in the cellular pathways. Enrichment and purification of (phosphoand glyco-) peptides and glycans are recommended prior to mass spectrometric analysis because of the lower amount of modified peptides in a peptide mixture. Herein, we present titanium/silica and zirconium/silica sol-gel materials for the enrichment of (phospho-and glyco-) peptides and glycans to enhance MALDI-MS analysis performance. Enrichment of (phospho-and glyco-) peptides was successfully applied using standard proteins including β-casein, fetuin, and IgG as well as some complex medium. The solgel materials were compared with commercial metal oxides regarding their modified peptide enrichment performances.
Proceedings of 5th International Electronic Conference on Medicinal Chemistry, Oct 30, 2019
Nowadays, a significant number of antiepileptic drugs aimed at influencing the main inhibitory tr... more Nowadays, a significant number of antiepileptic drugs aimed at influencing the main inhibitory transmitter -gamma-aminobutyric acid (GABA). Compounds with various chemical structures, binding to different GABA A sites, potentiate the action of amino acid. Recent studies have reported that terpenoids such as l-menthone and its derivatives were found to act as modulators of GABA A receptors, thereby demonstrating anticonvulsant activity. On the other hand, neuroprotective and anticonvulsant potentialities were revealed in phenoxyacetic acid derivatives. Based on the foregoing, the combination of l-menthone and phenoxyacetic acid residues into one molecule is feasible for obtaining the pharmacological agents with antiseizure action. In order to achieve the above-mentioned goal, l-menthone hydrazones were synthesized via condensation of terpenoid with 4-R-phenoxyacetic acid hydrazides in the presence of a catalytic amount of glacial acetic acid. The structure of the target compounds has been established by FTIR-ATR, Raman, 1 H-NMR and 13 C-NMR spectral analysis and EI/FAB/ESI mass spectrometry. Thermal properties of hydrazones were elucidated by DSC and their purity -by HPLC coupled to mass spectrometry. Synthesized compounds were found to exist as Z/E geometrical isomers about C=N bond and cis/trans amide conformers. At the present study, the influence of obtained derivatives on the central nervous system was reliably confirmed by evaluating their anticonvulsant activity. The present findings indicate that all aforementioned compounds possess antiseizure action after oral administration on PTZ-induced convulsion and maximal electroshock-induced (MES) seizures.
Zinc oxide (ZnO) as a multi-function semiconductor is widely known for photocatalysis and electro... more Zinc oxide (ZnO) as a multi-function semiconductor is widely known for photocatalysis and electronic applications but exceptionally new in Solid State Ionics. In this study, a new semiconducting-ionic conductor is reported for solid oxide fuel cells (SOFCs) applications by composing ZnO with an ionic conductor La/Pr codoped CeO 2 (LCP) in various mass ratios. The prepared composites acting as membranes are sandwiched between two Ni 0.8 Co 0.15 Al 0.05 LiO 2-δ (NCAL) electrodes to construct fuel cells. A remarkable maximum power output of 1055 mW cm -2 is attained along with a high open circuit voltage (OCV) of 1.04 V at 550 °C by the fuel cell using an optimal composition of 7LCP-3ZnO. The electrical properties of the composites as a function of LCP/ZnO ratio are studied through EIS measurements and polarization curves. It has been found that the composite of 7LCP-3ZnO exhibits a higher ionic conductivity than other composite samples at 475-550 °C, while possessing both high electronic and ionic conduction. Our further investigation also verifies the appreciable protonic conduction in LCP-ZnO, suggesting that the developed composite is a triple O 2-/H + /e -conducting material. Additionally, rectification characteristic of the best-performance cell is also measured to interpret the high OCVs and power outputs of LCP-ZnO fuel cells.
ABSTRACT 4,4′-Isopropylidendioxydiphenyl bridged bis-metallophthalocyanines Zn(II) (5) and Co(II)... more ABSTRACT 4,4′-Isopropylidendioxydiphenyl bridged bis-metallophthalocyanines Zn(II) (5) and Co(II) (6) were synthesized from the compound 4,4′-isopropylidendioxydiphthalonitrile (3) and 4,5-bis(hexylthio)phthalonitrile (4). The new cofacial bis-phthalocyanines Zn(II) (7) and Co(II) (8) were synthesized from the corresponding 3 which can be obtained by the reaction of 4,4′-isopropylidendiphenol (1) with 4-nitrophthalonitrile (2). These complexes have been characterized by elemental analysis, UV/Vis, FT-IR, 1H NMR and MALDI-TOF mass spectroscopies. The electrochemical properties of the complexes were examined by cyclic voltammetry, differential pulse voltammetry and controlled potential coulometry in nonaqueous media. Electrochemical results showed that while there is not any considerable interaction between the two phthalocyanine rings in bisphthalocyanine complexes 5 and 6, the splitting of the molecular orbitals occurs as a result of the strong interaction between the phthalocyanine rings in cofacial complexes 7 and 8.Measurements of capacitance showed a well defined decrease with increasing frequency and an increase with increasing temperature at lower frequencies.
ABSTRACT Novel ABA-type block copolymers were prepared using end-groups activated poly(ethylene g... more ABSTRACT Novel ABA-type block copolymers were prepared using end-groups activated poly(ethylene glycol) (PEG) as an initiator for hydrogen transfer polymerization (HTP). For this purpose, PEG with average molar mass of 1450 Da (PEG-1450) was firstly treated with the equivalent amount of sodium hydride to synthesize PEG with dialkoxide end-groups, namely PEG-dialkoxide. Using the PEG-dialkoxide as a macroinitiator, base-catalyzed HTP of acrylamide, N-methoxypropyl acrylamide, and 2-hydroxyethyl acrylate were then performed to achieve the novel ABA-type block copolymers. The copolymers were obtained with high yields of about 90%. Characterization of the ABA-type copolymers was carried out using Fourier Transform Infrared Spectroscopy (FTIR spectroscopy) and Matrix Assisted Laser Desorption Ioizaton (MALDI) mass spectrometry. FTIR spectra of the copolymers exhibited some characteristic bands assigned to the functional groups arising from the mechanism of HTP. Molar mass distributions of the copolymers from the MALDI mass study pointed out that chain extensions by mass in each copolymer were almost equal. Hence, the MALDI mass spectra of the copolymers revealed that chain extensions of telechelic PEGs by β-alanine, 2-hydroxyethyl acrylate, and N-methoxypropyl β-alanine units were successfully fulfilled.
In this work, novel silica hybrid magnetic particles with biocompatible surface were designed as ... more In this work, novel silica hybrid magnetic particles with biocompatible surface were designed as a support for enzyme immobilization, and the immobilized chymotrypsin (CT) performance was clarified as a model biocatalyst. CT is used in food technology for drink clarification and protein hydrolysis. The enzyme was directly immobilized onto polydopamine-grafted magnetic silica particles (MNP@SiO 2 @PDA-CT) via the Schiff base reaction. Immobilized enzyme had broadened for both pH and temperature profiles compared with the native CT. The MNP@SiO 2 @PDA-CT system also improved in thermostability compared with the native enzyme. The immobilized CT was operated in a continuous enzyme reactor (CER) for the hydrolysis of different proteins (i.e., cytochrome c (Cyt c), human serum albumin (HSA), human immunoglobulin G (HIgG), and lysozyme (Lys)). The peptide synthesis rate was shown to decrease as a function of increasing flow rate. The catalytic activity of the CER remained stable for 6.0 h in a continuous operation period; thus, the presented method may increase applicability in the food technology area. The immobilized CT in the CER showed a good hydrolysis performance for all the tested model proteins. The peptides hydrolyzed from the tested proteins were analyzed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS). Results show that the MNP@SiO 2 @PDA-CT system also permits for the applicability in the area of proteomic research.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Oligomers of 2-methyl nylon3 (2mN3) and 3-methyl nylon3 (3mN3) were synthesized by base-catalyzed... more Oligomers of 2-methyl nylon3 (2mN3) and 3-methyl nylon3 (3mN3) were synthesized by base-catalyzed hydrogen transfer polymerization (HTP) of methacrylamide and crotonamide, respectively. The detailed structural analyses of 2mN3 and 3mN3 were performed using MALDI-MS, 1 H-NMR, elemental analysis and several end-group analyses to ascertain polymerization mechanism and exact chemical structures of final products. The structural analyses revealed that (1) basecatalyzed HTP of methacrylamide and crotonamide follows the sequence of: hydrogen abstraction from amide group of monomer by basic catalyst (NatBuO), addition of monomeric units to the anionic center, intramolecular hydrogen migration and finally, termination by hydrogen transfer from protonated catalyst (tBuOH) to anionic end-group, (2) both oligomeric products have olefinic chainends resulting from the initiation mechanism. The specific behavior of basic catalyst leads to the formation of olefinic chain-ends that are apt to possible end-group functionalization. Since the functional end-groups of a well-defined macromonomer are of importance in terms of chain extension, grafting, chemical modification, click chemistry, monolayer surface modification, etc., it was aimed to create more reactive functional end-groups by epoxylation and bromination. Disappearance of the signals belonging to the olefinic protons in 1 H-NMR spectra of modified oligomers and existence of bromine and epoxy adducts in MALDI MS spectra of the modified oligomers were attributed to end-group modification as intended. Hence, & Efkan C ¸atıker
Hydrazones were obtained in 76-78% yield via condensation of (2S,5R)-2-isopropyl-5methylcyclohexa... more Hydrazones were obtained in 76-78% yield via condensation of (2S,5R)-2-isopropyl-5methylcyclohexanone with 4-R-phenoxyacetic acid hydrazides in the presence of a catalytic amount of glacial acetic acid. The structure of the target compounds has been established by FTIR-ATR, Raman, 1 H-NMR and 13 C-NMR spectral analysis and EI/FAB/ESI mass spectrometry. Thermal properties of hydrazones 3a-3e were elucidated by differential scanning calorimetry (DSC) and their purity by HPLC coupled to mass spectrometry. Synthesized compounds were found to exist as Z/E geometrical isomers about C=N bond and cis/trans amide conformers.
Membrane vesicle production in H. caseinilytica KB2 was studied under low, optimal, and high sali... more Membrane vesicle production in H. caseinilytica KB2 was studied under low, optimal, and high saline conditions. Vesiculation decreased with increase in salt concentration but suggested no direct adaptive role to changes in salinity
Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their se... more Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their selective stimulation of beneficial microbes. These compounds are glycosidically attached to proteins through N-acetylglucosamines via specific asparagine residue (AsN-X-Ser/Thr). Certain bacteria such as Bifidobacterium longum subspecies infantis (B. infantis) have been shown to be capable of utilizing conjugated N-glycans, owing to their specialized genomic abilities. B. infantis possess a unique enzyme, Endo-ß-N-acetylglucosaminidase (EndoBI-1), which cleaves all types of conjugated N-glycans from glycoproteins. In this study, recombinantly cloned EndoBI-1 enzyme activity was investigated using various immobilization methods: 1) adsorption, 2) entrapment-based alginate immobilization, 3) SulfoLink-, and 4) AminoLink-based covalent bonding immobilization techniques were compared to develop the optimum application of EndoBI-1 to food processes. The yield of enzyme immobilization and the a...
A series of novel poly(α-methyl β-alanine-b-lactone)s were prepared by a combination of hydrogen-... more A series of novel poly(α-methyl β-alanine-b-lactone)s were prepared by a combination of hydrogen-transfer polymerization (HTP) of methacrylamide (MAm) and anionic ring-opening polymerization (AROP) of β-propiolactone (BPL), β-butyrolactone (BBL), and δ-valerolactone (DVL). For this purpose, poly(α-methyl β-alanine) (PmBA) having a living anionic end-group for a further extension was obtained via HTP of MAm. The anionic end-group on PmBA chains were used as initiation sites for AROP of BPL, BBL, and DVL. Fourier Transform Infrared Spectroscopy (FTIR) and Proton Nuclear Magnetic Resonance Spectroscopy (1H-NMR) confirmed the existence of both ester and α-methyl β-alanine (mBA) units in the final products. MALDI-MS analysis revealed that the poly(α-methyl β-alanine-b-lactone)s with average molar masses of several thousand g·mol−1 were obtained. DSC and TGA thermograms of each copolymer showed that the copolymers comprised the mBA and the corresponding ester units.
The Eurasia Proceedings of Science Technology Engineering and Mathematics, 2021
Novel ABA-type amphiphilic copolymers were prepared using end-groups activated poly (ethylene gly... more Novel ABA-type amphiphilic copolymers were prepared using end-groups activated poly (ethylene glycol) (PEG) as an initiator of hydrogen-transfer polymerization (HTP). For this purpose, PEG with 1450 Da (PEG-1450) was treated with the equivalent amount of sodium hydride to synthesize PEG with dialkoxide end-groups, namely PEG-dialkoxide. Using the PEG-dialkoxide as a macroinitiator, base-catalysed HTP of 2-hydroxypropyl acrylate (HPA), and N-isobutoxymethyl acrylamide (BMA) were performed to achieve the novel ABA-type block copolymers. The copolymers were obtained with relatively high yields. Characterization of the ABA-type amphiphilic copolymers was carried out using FTIR and MALDI mass spectrometry. FTIR spectra of the copolymers exhibited some characteristic bands assigning to the functional groups arising from the mechanism of HTP. Molar mass distributions of the copolymers from the MALDI mass study pointed out that chain extensions by mass in each copolymer were almost equal. H...
Nowadays, the use of microalgae species as raw materials in biopharmaceutical production is on th... more Nowadays, the use of microalgae species as raw materials in biopharmaceutical production is on the agenda. The reason behind this idea is that microalgae are cell factories that are able to efficiently utilize carbon dioxide for the production of numerous biologically active compounds. However, there are several problems that remain to be solved in the production of recombinant protein from microalgaes. One of the critical requirements is to produce a bio-compatible N-glycosylation profile from the secreted recombinant proteins. However, the knowledge about the glycosylation machinery and N-glycan profiles of microalgae spices are quite limited. In the study, it was aimed to characterize N-glycan profiles of a green microalgae, Chlorella zofingiensis. To achieve this, photoautotrophically grown Chlorella zofingiensis extracts including (glyco-)proteins were enzymatically deglycosylated and labelled with 2-aminobenzoic acid tag. Released N-glycans were purified with a HILIC-based app...
Propolis (ari tutkali) yuzyillardir terapotik bir ajan olarak yaygin bir sekilde kullanilmaktadir... more Propolis (ari tutkali) yuzyillardir terapotik bir ajan olarak yaygin bir sekilde kullanilmaktadir. Farmakolojik ve biyolojik ozelliklerinden dolayi bu konu uzerindeki bilimsel ilgi son yillarda giderek artmaktadir. Bu calismanin amaci, propolisin ethanol ekstraktinin (EEP) kimyasal komposizyonunu belirlemek ve ayrica Ames/Salmonella ve E. coli WP2 test sistemlerini kullanarak propolisin genotoksik ve antigenotoksik etkilerini degerlendirmektir. Canlilik testlerinden elde edilen sonuclar, EEP’nin 1mg/plate ve daha yuksek konsantrasyonlarinin oldukca toksik oldugunu, daha dusuk konsantrasyonlarin ise toksik etkisinin olmadigini gostermistir. Genotoksisite test sonuclari ise, EEP’nin 1 mg/plate ve daha dusuk konsantrasyonlarda, S. typhimurium TA1535, 1537 ve E. coli WP2uvrA test suslari icin genotoksik etkisinin olmadigini gostermistir. Ayrica, ayni test suslari icin mutajen etkiye sahip NaN3 , 9-AA and MNNG gibi mutajenlere karsi EEP’nin, belirgin bir sekilde antigenotoksik etkiye sah...
Introduction N-linked glycosylation is one of the most defined posttranslational modifications in... more Introduction N-linked glycosylation is one of the most defined posttranslational modifications in nature . Glycosylation regulates the critical functions of proteins and plays a vital role in healthy and diseased conditions . N-glycans have the potential to be used in the early diagnosis of some cancers . It is also known that most of the approved biomarkers are glycoproteins or glycoconjugates . Therefore, N-glycan analysis of glycoproteins derived from biological samples is crucial for discovering new biomarker candidates. Glycomics is the field that focuses on elucidating glycan structures and quantification of glycans . Clinical application of quantitative glycomics has attracted attention because aberrant glycosylation is associated with many diseases . The N-glycan release is one of the most critical steps for quantitative glycomics . N-glycans are released from glycoproteins by an enzyme namely PNGase F (N-glycosidase F). Glycoproteins are first denatured by detergents prior to enzymatic treatments to facilitate access of glycans to the PNGase F. It has been examined that many parameters in N-glycan release methods influence the profiles of N-glycans derived from glycoproteins . For example, the kinetics of N-glycan release by PNGase F enzyme resulted in different IgG glycosylation profiles . On the other hand, different N-glycan release protocols were examined for cell line analysis and, in-solution approach has been found to be the most robust . In addition, a study has showed that different PNGase F enzymes resulted in diverse IgG and human plasma N-glycosylation profiles . It is clearly seen that the studies for optimizing of N-glycan release methods are required to improve the clinical glycomics applications. The first step in sample preparation for glycomic experiments includes the extraction of proteins from biological samples. Since most of the glycoproteins are integral membrane proteins, the use of detergents is obligatory for maximizing the extraction of proteins . Many detergents have been introduced and compared regarding the efficient protein extraction for mass spectrometry-based proteomics . These detergents can also be used for quantitative glycomic experiments. However, the effects of commonly used detergents on the enzymatical N-glycan release process have not been examined yet.
Novel hydrazones based on (-)-carvone were synthesized via condensation of terpenoid with 4-R-phe... more Novel hydrazones based on (-)-carvone were synthesized via condensation of terpenoid with 4-R-phenoxyacetic acid hydrazides. The structure of target compounds was established by FT-IR, Raman, 1 H-NMR and 13 C-NMR spectral analysis, FAB/ESI mass spectrometry. (-)-Carvone hydrazones were proven to exist as Z/E geometrical isomers about C=N bond using ion mobility-tandem mass spectrometry (IM-MS/MS). Single crystal X-ray diffraction study was applied to determine molecular and crystal structure of compound 3e. Hydrazones 3a-3e were evaluated as potential anticonvulsant agents after their oral administration against maximal electroshock (MES) and pentylenetetrazole (PTZ)-induced seizures in mice. Analgesic activity of compounds was investigated by topical application on models of capsaicin and AITC-induced pain. The present findings indicate that (-)-carvone derivatives afforded seizure protection both at short (1 h) and long (24 h) time period by blocking electroshock-and chemical-induced convulsions. Hydrazones binding to TRPA1/TRPV1 ion channels was proposed as possible mechanism explaining significant analgesic effect of compounds.
Hacettepe journal of biology and chemistry, Dec 25, 2017
B u çalışmada, bazik bir trifenilmetan boyası olan "kristal moru"nun (CV) sulu çözeltilerde H 2 O... more B u çalışmada, bazik bir trifenilmetan boyası olan "kristal moru"nun (CV) sulu çözeltilerde H 2 O 2 varlığında uzaklaştırılması ve bozunması, tabakalı MnO 2 ve ayrıca MnO 2 @MnFe 2 O 4 nanokompozit katalizörler kullanılarak araştırıldı. CV'nin bozunmasının tabakalı MnO 2 yapısı ile daha hızlı gerçekleştiği görüldü. Katalitik bozunma ürünleri Elektrospray İyonlaşmalı-Dört Kutuplu-Uçuş Zamanlı Kütle Spektrometresi (ESI-Q-ToF-MS) kullanılarak izlendi ve analiz edildi. Ana parçalanma ürünleri olarak, biyo-iyileştirme ile mineralizasyon ürünlerine dönüşebilme potansiyeli olan 4-izosiyanobenzaldehit (A) ve Michler ketonu (B) tanımlandı. Böylece, MnO 2 /H 2 O 2 sisteminin CV'yi biyobozunabilir yapılara dönüştürebilen özendirici bir katalizör olduğu anlaşıldı. Kristal moru, boya bozunumu, katalitik oksidasyon, manganoksit katalizörleri.
Soil salinity is a major abiotic stress factor that limits agricultural productivity worldwide, a... more Soil salinity is a major abiotic stress factor that limits agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean is an important protein source in developing countries however highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were performed on both salt-tolerant and susceptible common bean genotypes in saline conditions. Transcriptomics has demonstrated increased photosynthesis in saline conditions for tolerant genotype while the susceptible genotype acted in contrast. Transcriptome also displayed active carbon and aminoacid metabolism for the tolerant genotype. Analysis of metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response. According to ion content comparison, the tolerant genotype managed to block accumulation of Na + in the leaves while accumulating significantly less Na + in the roots compared to susceptible genotype. K + levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn +2 and Mn +2 levels were dropped in the tolerant roots, while Mo +2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype. The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance.
Glycosylation and phosphorylation are two of the most commonly seen and important post-translatio... more Glycosylation and phosphorylation are two of the most commonly seen and important post-translational modifications (PTMs) of proteins. Both play key role in many vital biological processes. Mass spectrometry is the most favored technique used for monitoring the dynamics of PTMs. Mass spectrometric analysis of phosphopeptide and glycopeptide is a crucial step in phosphoproteomics and glycoproteomics to understand the role of these modifications in the cellular pathways. Enrichment and purification of (phosphoand glyco-) peptides and glycans are recommended prior to mass spectrometric analysis because of the lower amount of modified peptides in a peptide mixture. Herein, we present titanium/silica and zirconium/silica sol-gel materials for the enrichment of (phospho-and glyco-) peptides and glycans to enhance MALDI-MS analysis performance. Enrichment of (phospho-and glyco-) peptides was successfully applied using standard proteins including β-casein, fetuin, and IgG as well as some complex medium. The solgel materials were compared with commercial metal oxides regarding their modified peptide enrichment performances.
Proceedings of 5th International Electronic Conference on Medicinal Chemistry, Oct 30, 2019
Nowadays, a significant number of antiepileptic drugs aimed at influencing the main inhibitory tr... more Nowadays, a significant number of antiepileptic drugs aimed at influencing the main inhibitory transmitter -gamma-aminobutyric acid (GABA). Compounds with various chemical structures, binding to different GABA A sites, potentiate the action of amino acid. Recent studies have reported that terpenoids such as l-menthone and its derivatives were found to act as modulators of GABA A receptors, thereby demonstrating anticonvulsant activity. On the other hand, neuroprotective and anticonvulsant potentialities were revealed in phenoxyacetic acid derivatives. Based on the foregoing, the combination of l-menthone and phenoxyacetic acid residues into one molecule is feasible for obtaining the pharmacological agents with antiseizure action. In order to achieve the above-mentioned goal, l-menthone hydrazones were synthesized via condensation of terpenoid with 4-R-phenoxyacetic acid hydrazides in the presence of a catalytic amount of glacial acetic acid. The structure of the target compounds has been established by FTIR-ATR, Raman, 1 H-NMR and 13 C-NMR spectral analysis and EI/FAB/ESI mass spectrometry. Thermal properties of hydrazones were elucidated by DSC and their purity -by HPLC coupled to mass spectrometry. Synthesized compounds were found to exist as Z/E geometrical isomers about C=N bond and cis/trans amide conformers. At the present study, the influence of obtained derivatives on the central nervous system was reliably confirmed by evaluating their anticonvulsant activity. The present findings indicate that all aforementioned compounds possess antiseizure action after oral administration on PTZ-induced convulsion and maximal electroshock-induced (MES) seizures.
Zinc oxide (ZnO) as a multi-function semiconductor is widely known for photocatalysis and electro... more Zinc oxide (ZnO) as a multi-function semiconductor is widely known for photocatalysis and electronic applications but exceptionally new in Solid State Ionics. In this study, a new semiconducting-ionic conductor is reported for solid oxide fuel cells (SOFCs) applications by composing ZnO with an ionic conductor La/Pr codoped CeO 2 (LCP) in various mass ratios. The prepared composites acting as membranes are sandwiched between two Ni 0.8 Co 0.15 Al 0.05 LiO 2-δ (NCAL) electrodes to construct fuel cells. A remarkable maximum power output of 1055 mW cm -2 is attained along with a high open circuit voltage (OCV) of 1.04 V at 550 °C by the fuel cell using an optimal composition of 7LCP-3ZnO. The electrical properties of the composites as a function of LCP/ZnO ratio are studied through EIS measurements and polarization curves. It has been found that the composite of 7LCP-3ZnO exhibits a higher ionic conductivity than other composite samples at 475-550 °C, while possessing both high electronic and ionic conduction. Our further investigation also verifies the appreciable protonic conduction in LCP-ZnO, suggesting that the developed composite is a triple O 2-/H + /e -conducting material. Additionally, rectification characteristic of the best-performance cell is also measured to interpret the high OCVs and power outputs of LCP-ZnO fuel cells.
ABSTRACT 4,4′-Isopropylidendioxydiphenyl bridged bis-metallophthalocyanines Zn(II) (5) and Co(II)... more ABSTRACT 4,4′-Isopropylidendioxydiphenyl bridged bis-metallophthalocyanines Zn(II) (5) and Co(II) (6) were synthesized from the compound 4,4′-isopropylidendioxydiphthalonitrile (3) and 4,5-bis(hexylthio)phthalonitrile (4). The new cofacial bis-phthalocyanines Zn(II) (7) and Co(II) (8) were synthesized from the corresponding 3 which can be obtained by the reaction of 4,4′-isopropylidendiphenol (1) with 4-nitrophthalonitrile (2). These complexes have been characterized by elemental analysis, UV/Vis, FT-IR, 1H NMR and MALDI-TOF mass spectroscopies. The electrochemical properties of the complexes were examined by cyclic voltammetry, differential pulse voltammetry and controlled potential coulometry in nonaqueous media. Electrochemical results showed that while there is not any considerable interaction between the two phthalocyanine rings in bisphthalocyanine complexes 5 and 6, the splitting of the molecular orbitals occurs as a result of the strong interaction between the phthalocyanine rings in cofacial complexes 7 and 8.Measurements of capacitance showed a well defined decrease with increasing frequency and an increase with increasing temperature at lower frequencies.
ABSTRACT Novel ABA-type block copolymers were prepared using end-groups activated poly(ethylene g... more ABSTRACT Novel ABA-type block copolymers were prepared using end-groups activated poly(ethylene glycol) (PEG) as an initiator for hydrogen transfer polymerization (HTP). For this purpose, PEG with average molar mass of 1450 Da (PEG-1450) was firstly treated with the equivalent amount of sodium hydride to synthesize PEG with dialkoxide end-groups, namely PEG-dialkoxide. Using the PEG-dialkoxide as a macroinitiator, base-catalyzed HTP of acrylamide, N-methoxypropyl acrylamide, and 2-hydroxyethyl acrylate were then performed to achieve the novel ABA-type block copolymers. The copolymers were obtained with high yields of about 90%. Characterization of the ABA-type copolymers was carried out using Fourier Transform Infrared Spectroscopy (FTIR spectroscopy) and Matrix Assisted Laser Desorption Ioizaton (MALDI) mass spectrometry. FTIR spectra of the copolymers exhibited some characteristic bands assigned to the functional groups arising from the mechanism of HTP. Molar mass distributions of the copolymers from the MALDI mass study pointed out that chain extensions by mass in each copolymer were almost equal. Hence, the MALDI mass spectra of the copolymers revealed that chain extensions of telechelic PEGs by β-alanine, 2-hydroxyethyl acrylate, and N-methoxypropyl β-alanine units were successfully fulfilled.
In this work, novel silica hybrid magnetic particles with biocompatible surface were designed as ... more In this work, novel silica hybrid magnetic particles with biocompatible surface were designed as a support for enzyme immobilization, and the immobilized chymotrypsin (CT) performance was clarified as a model biocatalyst. CT is used in food technology for drink clarification and protein hydrolysis. The enzyme was directly immobilized onto polydopamine-grafted magnetic silica particles (MNP@SiO 2 @PDA-CT) via the Schiff base reaction. Immobilized enzyme had broadened for both pH and temperature profiles compared with the native CT. The MNP@SiO 2 @PDA-CT system also improved in thermostability compared with the native enzyme. The immobilized CT was operated in a continuous enzyme reactor (CER) for the hydrolysis of different proteins (i.e., cytochrome c (Cyt c), human serum albumin (HSA), human immunoglobulin G (HIgG), and lysozyme (Lys)). The peptide synthesis rate was shown to decrease as a function of increasing flow rate. The catalytic activity of the CER remained stable for 6.0 h in a continuous operation period; thus, the presented method may increase applicability in the food technology area. The immobilized CT in the CER showed a good hydrolysis performance for all the tested model proteins. The peptides hydrolyzed from the tested proteins were analyzed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS). Results show that the MNP@SiO 2 @PDA-CT system also permits for the applicability in the area of proteomic research.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Oligomers of 2-methyl nylon3 (2mN3) and 3-methyl nylon3 (3mN3) were synthesized by base-catalyzed... more Oligomers of 2-methyl nylon3 (2mN3) and 3-methyl nylon3 (3mN3) were synthesized by base-catalyzed hydrogen transfer polymerization (HTP) of methacrylamide and crotonamide, respectively. The detailed structural analyses of 2mN3 and 3mN3 were performed using MALDI-MS, 1 H-NMR, elemental analysis and several end-group analyses to ascertain polymerization mechanism and exact chemical structures of final products. The structural analyses revealed that (1) basecatalyzed HTP of methacrylamide and crotonamide follows the sequence of: hydrogen abstraction from amide group of monomer by basic catalyst (NatBuO), addition of monomeric units to the anionic center, intramolecular hydrogen migration and finally, termination by hydrogen transfer from protonated catalyst (tBuOH) to anionic end-group, (2) both oligomeric products have olefinic chainends resulting from the initiation mechanism. The specific behavior of basic catalyst leads to the formation of olefinic chain-ends that are apt to possible end-group functionalization. Since the functional end-groups of a well-defined macromonomer are of importance in terms of chain extension, grafting, chemical modification, click chemistry, monolayer surface modification, etc., it was aimed to create more reactive functional end-groups by epoxylation and bromination. Disappearance of the signals belonging to the olefinic protons in 1 H-NMR spectra of modified oligomers and existence of bromine and epoxy adducts in MALDI MS spectra of the modified oligomers were attributed to end-group modification as intended. Hence, & Efkan C ¸atıker
Hydrazones were obtained in 76-78% yield via condensation of (2S,5R)-2-isopropyl-5methylcyclohexa... more Hydrazones were obtained in 76-78% yield via condensation of (2S,5R)-2-isopropyl-5methylcyclohexanone with 4-R-phenoxyacetic acid hydrazides in the presence of a catalytic amount of glacial acetic acid. The structure of the target compounds has been established by FTIR-ATR, Raman, 1 H-NMR and 13 C-NMR spectral analysis and EI/FAB/ESI mass spectrometry. Thermal properties of hydrazones 3a-3e were elucidated by differential scanning calorimetry (DSC) and their purity by HPLC coupled to mass spectrometry. Synthesized compounds were found to exist as Z/E geometrical isomers about C=N bond and cis/trans amide conformers.
Membrane vesicle production in H. caseinilytica KB2 was studied under low, optimal, and high sali... more Membrane vesicle production in H. caseinilytica KB2 was studied under low, optimal, and high saline conditions. Vesiculation decreased with increase in salt concentration but suggested no direct adaptive role to changes in salinity
Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their se... more Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their selective stimulation of beneficial microbes. These compounds are glycosidically attached to proteins through N-acetylglucosamines via specific asparagine residue (AsN-X-Ser/Thr). Certain bacteria such as Bifidobacterium longum subspecies infantis (B. infantis) have been shown to be capable of utilizing conjugated N-glycans, owing to their specialized genomic abilities. B. infantis possess a unique enzyme, Endo-ß-N-acetylglucosaminidase (EndoBI-1), which cleaves all types of conjugated N-glycans from glycoproteins. In this study, recombinantly cloned EndoBI-1 enzyme activity was investigated using various immobilization methods: 1) adsorption, 2) entrapment-based alginate immobilization, 3) SulfoLink-, and 4) AminoLink-based covalent bonding immobilization techniques were compared to develop the optimum application of EndoBI-1 to food processes. The yield of enzyme immobilization and the a...
A series of novel poly(α-methyl β-alanine-b-lactone)s were prepared by a combination of hydrogen-... more A series of novel poly(α-methyl β-alanine-b-lactone)s were prepared by a combination of hydrogen-transfer polymerization (HTP) of methacrylamide (MAm) and anionic ring-opening polymerization (AROP) of β-propiolactone (BPL), β-butyrolactone (BBL), and δ-valerolactone (DVL). For this purpose, poly(α-methyl β-alanine) (PmBA) having a living anionic end-group for a further extension was obtained via HTP of MAm. The anionic end-group on PmBA chains were used as initiation sites for AROP of BPL, BBL, and DVL. Fourier Transform Infrared Spectroscopy (FTIR) and Proton Nuclear Magnetic Resonance Spectroscopy (1H-NMR) confirmed the existence of both ester and α-methyl β-alanine (mBA) units in the final products. MALDI-MS analysis revealed that the poly(α-methyl β-alanine-b-lactone)s with average molar masses of several thousand g·mol−1 were obtained. DSC and TGA thermograms of each copolymer showed that the copolymers comprised the mBA and the corresponding ester units.
The Eurasia Proceedings of Science Technology Engineering and Mathematics, 2021
Novel ABA-type amphiphilic copolymers were prepared using end-groups activated poly (ethylene gly... more Novel ABA-type amphiphilic copolymers were prepared using end-groups activated poly (ethylene glycol) (PEG) as an initiator of hydrogen-transfer polymerization (HTP). For this purpose, PEG with 1450 Da (PEG-1450) was treated with the equivalent amount of sodium hydride to synthesize PEG with dialkoxide end-groups, namely PEG-dialkoxide. Using the PEG-dialkoxide as a macroinitiator, base-catalysed HTP of 2-hydroxypropyl acrylate (HPA), and N-isobutoxymethyl acrylamide (BMA) were performed to achieve the novel ABA-type block copolymers. The copolymers were obtained with relatively high yields. Characterization of the ABA-type amphiphilic copolymers was carried out using FTIR and MALDI mass spectrometry. FTIR spectra of the copolymers exhibited some characteristic bands assigning to the functional groups arising from the mechanism of HTP. Molar mass distributions of the copolymers from the MALDI mass study pointed out that chain extensions by mass in each copolymer were almost equal. H...
Nowadays, the use of microalgae species as raw materials in biopharmaceutical production is on th... more Nowadays, the use of microalgae species as raw materials in biopharmaceutical production is on the agenda. The reason behind this idea is that microalgae are cell factories that are able to efficiently utilize carbon dioxide for the production of numerous biologically active compounds. However, there are several problems that remain to be solved in the production of recombinant protein from microalgaes. One of the critical requirements is to produce a bio-compatible N-glycosylation profile from the secreted recombinant proteins. However, the knowledge about the glycosylation machinery and N-glycan profiles of microalgae spices are quite limited. In the study, it was aimed to characterize N-glycan profiles of a green microalgae, Chlorella zofingiensis. To achieve this, photoautotrophically grown Chlorella zofingiensis extracts including (glyco-)proteins were enzymatically deglycosylated and labelled with 2-aminobenzoic acid tag. Released N-glycans were purified with a HILIC-based app...
Propolis (ari tutkali) yuzyillardir terapotik bir ajan olarak yaygin bir sekilde kullanilmaktadir... more Propolis (ari tutkali) yuzyillardir terapotik bir ajan olarak yaygin bir sekilde kullanilmaktadir. Farmakolojik ve biyolojik ozelliklerinden dolayi bu konu uzerindeki bilimsel ilgi son yillarda giderek artmaktadir. Bu calismanin amaci, propolisin ethanol ekstraktinin (EEP) kimyasal komposizyonunu belirlemek ve ayrica Ames/Salmonella ve E. coli WP2 test sistemlerini kullanarak propolisin genotoksik ve antigenotoksik etkilerini degerlendirmektir. Canlilik testlerinden elde edilen sonuclar, EEP’nin 1mg/plate ve daha yuksek konsantrasyonlarinin oldukca toksik oldugunu, daha dusuk konsantrasyonlarin ise toksik etkisinin olmadigini gostermistir. Genotoksisite test sonuclari ise, EEP’nin 1 mg/plate ve daha dusuk konsantrasyonlarda, S. typhimurium TA1535, 1537 ve E. coli WP2uvrA test suslari icin genotoksik etkisinin olmadigini gostermistir. Ayrica, ayni test suslari icin mutajen etkiye sahip NaN3 , 9-AA and MNNG gibi mutajenlere karsi EEP’nin, belirgin bir sekilde antigenotoksik etkiye sah...
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