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Öğe Biofortified Whey/Deglycosylated Whey and Chickpea Protein Matrices: Functional Enrichment by Black Mulberry Polyphenols(Springer, 2022) Özleyen, Adem; Çınar, Zeynep Özlem; Karav, Sercan; Bayraktar, Ayşe; Arslan, Ayşenur; Kayılı, H. Mehmet; Salih, Bekir; Boyuneğmez Tümer, TuğbaMorus nigra L. (black mulberry-BM) is a promising nutraceutical fruit containing biologically active polyphenols like anthocyanins, proanthocyanidins, catechins, and stilbenes, with well-established anti-inflammatory, antidiabetic, anti-obesity, and anticancer biofunctions. However, these health-promoting properties in raw fruit are greatly masked due to the presence of soluble and insoluble carbohydrates in excess amounts restricting daily intake of the required dose to achieve targeted effects. In the current study, different protein sources (defatted whey and chickpea flours) were optimized through different conditions to capture polyphenols from BM juice while diminishing its glucose content. To optimize polyphenol-protein interactions, various pHs (3.7, 4.2, and 4.7), matrix concentrations (20, 50, and 80 g protein/L), and incubation times (5, 20, and 45 min) were tested. In the present work, optimized BM polyphenol enriched whey matrix inhibited pro-inflammatory mediators and promoted Nrf-2 dependent cytoprotective enzyme expressions in lipopolysaccharide (LPS) induced macrophages at low doses. In addition, whey proteins were also subjected to an enzymatic deglycosylation process by using recently identified EndoBI-1 enzyme for the specific cleavage of N-glycan core in all glycan types including high mannoses, hybrids as well as complex glycans found on defatted whey proteins. After this process, the polyphenol sorption capacity of deglycosylated whey proteins was found to be significantly higher (37%) than the capacity of non-treated normal whey protein under optimized conditions. In conclusion, deglycosylation of protein matrices could be a novel strategy for efficient sorption/concentration of polyphenols from fruits and vegetables, however, more detailed studies are needed to understand this effect.Öğe Characterization of branched and linear polyethyleneimine by trapped ion mobility-time of flight-mass spectrometry(Elsevier B.V., 2026) Atakay, Mehmet; Demirci, Sahin; Sahiner, Nurettin; Salih, BekirBackground: Polyethyleneimine (PEI) is a common polyelectrolyte that is used in many areas, such as drug delivery, gene therapy, and water treatment. This is because it has a highly branched structure, functional amine groups in its repeating unit, and a high cationic charge density. To understand the behavior and function of PEI, it is important to accurately describe its structure. The ion mobility-mass spectrometry method is expected to yield structural insights into PEI's molecular architecture, encompassing variations in branching patterns, chain conformations, and the potential presence of isomeric forms. Results: The difference in zeta potential values between B-PEI and L-PEI can be attributed to the distinct types of functional amine groups present in their structures. The trapped ion mobility-time of flight-mass spectrometry (TIMS-ToF-MS) technique was used in this study to elucidate the molecular architecture of linear and branched PEI with varying polymeric distributions of ion series and end groups, concentrating on its dimensions, morphology, conformational variations, variable cationic adducts (Na+, K+, Li+, and Ag+), and charge states (+1 and + 2). The singly charged ions, like those in the main series and fragment series of PEI, are more compact than doubly charged ions because of the change in charge repulsion. TIMS, in conjunction with mass spectrometry, facilitated high-resolution separation of PEI conformers according to their collision cross-section (CCS) values and charge states. Significance: The findings indicated that PEI displays a wide range of both compact and extended molecular conformations at various m/z ratios, with specific populations associated with varying branching levels, cationic adducts, and charge distribution. The influence of various metal ions on PEI conformation was examined, indicating substantial alterations in CCS values under diverse conditions of analysis. Hyphenated TIMS and MS technologies make a strong analytical platform for studying polymer structures in depth. © 2026Öğe Correction: Distinguishing Turkish pine honey from multi-foral honey through MALDI-MS-based N-glycomics and machine learning(Springer, 2024) Masri, Saad; Aksoy, Sena; Duman, Hatice; Karav, Sercan; Kayılı, Hacı Mehmet; Salih, Bekir[Anstract Not Available]Öğe Distinguishing Turkish pine honey from multi-floral honey through MALDI-MS-based N-glycomics and machine learning(Springer, 2024) Masri, Saad; Aksoy, Sena; Duman, Hatice; Karav, Sercan; Kayılı, Hacı Mehmet; Salih, BekirHoney, a multifaceted blend of sugars, amino acids, vitamins, proteins, and minerals, exhibits compositional variability dependent upon the floral source. While previous studies have attempted to categorize honey, the use of glycomic profiles for honey classification remains an unexplored avenue. This investigation seeks to establish a methodology for distinguishing honey types, specifically multi-floral and pine honey, employing mass spectrometry-based glycomic analysis in tandem with machine learning. In this search, seven samples of pine honey and eight samples of multi-floral honey were obtained from diverse regions of Turkey. Subsequently, the proteins within these honey samples were extracted, and glycans were enzymatically released. The released glycans were labeled with 2-aminobenzoic acid (2-AA) and subjected to analysis via matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The glycan profiles of pine and multi-floral honey were determined through these analytical procedures, revealing a total of 76 distinct N-glycan structures. Among these, 13 N-glycan profiles consistently established at high levels across experimental replicates and were incorporated in subsequent analyses. Following the quantification of individual glycan abundances, statistically significant differences in glycan profiles were determined. Notably, N-glycans Hex5HexNAc2, Hex4HexNAc3, and Hex5HexNAc3 displayed considerable differences. Using the 13 N-glycan profiles, an accuracy rate of 93.5% was obtained from machine learning analysis, which increased to 100% when incorporating the identified significantly changed glycans. The most productive models were identified as subspace and fine k-nearest neighbors (KNN). The findings underscore the potential of mass spectrometry-based glycomics in conjunction with machine learning as a robust tool for precise honey type classification and its prospective utility in quality control and honey product authentication.Öğe ESI-IM-MS characterization of cyclodextrin complexes and their chemically cross-linked alpha (α-), beta (β-) and gamma (γ-) cyclodextrin particles as promising drug delivery materials with improved bioavailability(Elsevier, 2023) Yılmaz, Aynur Sanem; Öztürk, Serhat; Salih, Bekir; Ayyala, Ramesh S.; Şahiner, NurettinCyclodextrins (CDs) are natural cyclic oligosaccharides with a relatively hydrophobic cavity and a hydrophilic outer surface. In this study, alpha (alpha-), beta (beta-) and gamma (gamma-) CD particles were prepared by directly using alpha-, beta-, and gamma-CDs as monomeric units and divinyl sulfone (DVS) as a crosslinker in a single-step via reverse micelle microemulsion crosslinking technique. Particles of p(alpha-CD), p(beta-CD), and p(gamma-CD) were perfectly spherical in sub 10 mu m size ranges. The prepared p(CD) particles at 1.0 mg/mL concentrations were found biocompatible with > 95 % cell viability against L929 fibroblasts. Furthermore, p(alpha-CD) and p(beta-CD) particles were found non-hemolytic with < 2 % hemolysis ratios, whereas p(gamma-CD) particles were found to be slightly hemolytic with its 2.1 +/- 0.4 % hemolysis ratio at 1.0 mg/mL concentration. Furthermore, a toxic compound, Bisphenol A (BPA) and a highly antioxidant polyphenol, curcumin (CUR) complexation with alpha-, beta-, and gamma-CD molecules was investigated via Electrospray-Ion Mobility-Mass Spectrometry (ESI-IM-MS) and tandem mass spectrometry (MS/MS) analysis. It was determined that the most stable noncovalent complex was in the case of beta-CD, but the complex stoichiometry was changed by the hydrophobic nature of the guest molecules. In addition, BPA and CUR were separately loaded into prepared p(CD) particles as active agents. The drug loading and release studies showed that p (CD) particles possess governable loading and releasing profiles.Öğe Exploring the Activity of a Novel N-Glycosidase (EndoBI-2): Recombinant Production to Release Bioactive Glycans(Mdpi, 2025) Duman, Hatice; Avci, Izzet; Salih, Bekir; Kayili, Haci Mehmet; Bechelany, Mikhael; Karav, SercanThe gut microbiome evolves in response to host development, health state, lifestyle, nutrition, and microbial interactions. The survival of gut microbiota depends on its ability to utilize its host-indigestible complex oligosaccharides. Certain gut microbes produce glycosidases that cleave N-glycoproteins to release N-glycans that are then used as a carbon source. However, commercial glycosidases are inefficient and, thus, require improved deglycosylation strategies to study their functions and scale up their production. Therefore, the main objective of this study was to recombinantly produce and characterize the novel endo-beta-N-acetylglucosaminidase 2 (EndoBI-2) from Bifidobacterium longum subsp. infantis (B. infantis) and to evaluate its enzymatic performance for controlled N-glycan release. Furthermore, the optimum reaction conditions for EndoBI-2 were investigated on model glycoprotein RNAse B using model glycoprotein. The released N-glycans were profiled by hydrophilic interaction liquid chromatography-fluorescence detection-quadrupole time-of-flight tandem mass spectrometry (HILIC-FLD-QTOF-MS/MS). We demonstrated that EndoBI-2 possesses a strong temperature tolerance and efficiently cleaves N-glycans under mild reaction conditions, exhibiting high activity at pH 5. These findings highlight EndoBI-2 as a robust and efficient biocatalyst for the production of bioactive N-glycans from diverse N-glycoproteins, with potential applications in glycobiotechnology.Öğe Identification and comparison of N-glycome profiles from common dietary protein sources(Elsevier, 2025) Bolino, Matthew; Avcı, İzzet; Kayılı, Hacı Mehmet; Duman, Hatice; Salih, Bekir; Karav, Sercan; Frese, Steven A.The N-glycomes of bovine whey, egg white, pea, and soy protein isolates are described here. N-glycans from four protein isolates were analyzed by HILIC high performance liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (HILIC-FLD-QTOF-MS/MS). In total, 33 N-glycans from bovine whey and egg white and 10 N-glycans from soy and pea glycoproteins were identified. The type of N-glycans per glycoprotein source were attributable to differences in biosynthetic glycosylation pathways. Animal glycoprotein sources favored a combination of complex and hybrid glycan configurations, while the plant proteins were dominated by oligomannosidic N-glycans. Bovine whey glycoprotein isolate contained the most diverse N-glycans by monosaccharide composition as well as structure, while plant sources such as pea and soy glycoprotein isolates contained an overlap of oligomannosidic N-glycans. The results suggest N-glycan structure and composition is dependent on the host organism which are driven by the differences in N-glycan biosynthetic pathways.Öğe Modification of cyclodextrin-based microgels with 2-hydroxymethyl-12-crown ether-4 for higher and selective Li+ ion adsorption from aqueous medium(Taylor & Francis Inc, 2026) Demirci, Sahin; Salih, Bekir; Sahiner, NurettinThe cyclodextrin (CD) oligosaccharides derived materials, e.g., p(alpha-CD), p(beta-CD), and p(gamma-CD) microgels were used in Li + ion adsorption studies, which revealed 55.4 +/- 3.9, 85.1 +/- 3.8, and 117.8 +/- 4.9 mg Li+/g, respectively, in 12 h from 500 mg/L 100 mL aqueous solutions. The Li+ ion adsorption by p(CD)-based microgels is best described by pseudo-first-order adsorption kinetics and Freundlich adsorption isotherms, with higher R-2 values. There is no significant selectivity observed for any microgels to Li + ions in the presence of Na+, K+, and Ca2+ ions. However, the relative selectivity (kl) calculation among the adsorbents revealed that p(beta-CD) microgels afforded higher selectivity than p(alpha-CD) and p(gamma-CD) microgels, with kl values greater than 1. Therefore, to further increase selectivity, p(beta-CD) microgels were modified (M-p(beta-CD)) with 2-hydroxymethyl-12-crown ether-4, known for its specificity for Li + ion. The adsorbed amount of Li+ ions by M-p(beta-CD) microgels was determined as 91.9 +/- 1.9 mg Li+/g, a slight increase with respect to the unmodified microgel upon 12 h contact time. Interestingly, the selectivity of M-p(beta-CD) microgels toward Li+ ion for Li+/Na+, Li+/K+, and Li+/Ca2+ was measured as 3.1, 4.5, and 5.1-fold higher, respectively, than bare p(beta-CD) microgels. Also, M-p(beta-CD) microgels retained >80% adsorption capacity of Li+ ions after 5 consecutive uses. Microgels employing cyclodextrin, particularly beta-CD systems demonstrated an effective and reusable adsorption capability for Li+, and the selectivity is markedly enhanced amid competing ions via the functionalization with crown ethers. [GRAPHICS]Öğe Proteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro(Amer Soc Microbiology, 2025) Bolino, Matthew; Duman, Hatice; Avci, Izzet; Kayili, Haci Mehmet; Petereit, Juli; Zundel, Chandler; Salih, BekirAdvances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly beta-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome.IMPORTANCERecent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.Öğe Superporous poly(β-Cyclodextrin) cryogels as promising materials for simultaneous delivery of both hydrophilic and hydrophobic drugs(Pergamon-Elsevier Science Ltd, 2022) Ari, Betül; Demirci, Şahin; Ayyala, Ramesh S.; Salih, Bekir; Şahiner, NurettinHere, one step, simple preparation of superporous p(beta-cyclodextrin) (p(beta-CD)) cryogels in the presence of various ratios of crosslinker, divinyl sulfone (DVS) e.g., 100, 150, 200% mole with respect to the mole ratio of 6 hydroxyl groups on beta-CD unit under cryogenic conditions were reported for the first time. The swelling properties, and hydrolytic degradation of p(beta-CD) cryogels was directly related to the used crosslinker ratio. It was observed that the p(beta-CD) cryogels showed higher swelling% in DMSO and DMF than in DI water. The prepared p(beta-CD)-1 cryogel that was 100% crosslinked exhibited 14 +/- 3.7%, 34 +/- 4.8%, and 45 +/- 6.2% weight losses within 20 days in pH 5.4, 7.4, and 9.0 buffer solutions, respectively. An acceptable hemolysis index of < 5% and a blood coagulation index, >89% were observed for the p(beta-CD) cryogels at 1 mg/mL concentrations. Additionally, the potential useability of p(beta-CD) cryogels as in vitro drug delivery systems for both hydrophilic vancomycin, and hydrophobic tetracycline as model drugs were individually illustrated at pH 7.4 in PBS. The cumulative drug release from p(beta-CD) cryogels, in sustained release profiles with 76.7 +/- 9.0 mg/g of vancomycin (89.9 +/- 10.5% of the loaded amount) and 146.5 +/- 19.4 mg/g tetracycline g (83.1 +/- 6.3% of the loaded amount) were attained in 6 and 54 h, respectively at pH 7.4 in PBS. Most importantly, p(beta-CD) cryogels exhibited simultaneous loading and releasing the ability for both hydrophilic vancomycin, and hydrophobic tetracycline drugs by concurrently releasing 37.0 +/- 2.7 mg/g (23.4 +/- 1.8% of the loaded amount), and 36.3 +/- 1.3 mg/g (23.6 +/- 0.8% of the loaded amount), respectively at pH 7.4 (PBS) in 10 h.Öğe Synthesis, characterization and thermal study of some tetradentate Schiff base transition metal complexes(Springer, 2009) Doğan, Fatih; Ulusoy, Mahmut; Özturk, Ömer F.; Kaya, İsmet; Salih, BekirSeveral mononuclear Co(II), Ni(II), Cu(II), and Fe(II) complexes of tetradentate salpren-type diimine, obtained from 3,5-di-tert-butyl-2-hydroxybenzaldehyde and 1,3-diaminopropane have been prepared and characterized by analytical, spectroscopic (FT-IR, UV-VIS) techniques, magnetic susceptibility measurements and thermogravimetric analyses (TG). The thermodynamic and thermal properties of complexes have been investigated. For further characterization Direct Insertion Probe-Mass Spectrometry (DIP-MS) was used and the fragmentation pattern and also stability of the ions were evaluated. The characterization of the end products of the decomposition was achieved by X-ray diffraction. The thermal stabilities of metal complexes of N,N'-bis(3,5-di-t-butylsalicylidene)-1,3-propanediamine ligand (L) were found as Ni(II) > Cu(II) > Co(II) > Fe(II).
