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Article Citation - WoS: 2Citation - Scopus: 2Biosorption of Reactive Dyes by Novel Bacterium Leclercia Adecarboxylata: Complete Removal of Reactive Black 5 and Molecular Insights Into the Adsorption Mechanism(Wiley, 2025) Sen, Seda; Korkmaz, Filiz; Kilic, Nur KocberberLeclercia adecarboxylata isolated from the D & uuml;den Waterfall (Turkey) was utilized as a biosorbent for the removal of Reactive Black 5 (RB5), Setazol Blue BRF-X (BRF-X), Setazol Navy Blue SBG (SNB), and Setazol Turquoise Blue G (STBG). Of the dyes, RB5 was removed with the highest efficiency, 97.4% after 60 min. The effect of parameters such as pH (3-9), initial biosorbent dose (0.1-2.0 g/L), and initial dye concentration (25-1200 mg/L) on the biosorption of RB5 was investigated. Increasing the biosorbent dosage from 0.1 to 2.0 g/L enhanced the RB5 removal from 55.3% to 100% within 10 min. The complete removal (100%) of RB5 was achieved in media with 2.0 g/L biosorbent and 25 mg/L RB5 at pH 3 after 10 min. Additionally, the soluble extracellular polymeric substances (EPS) of L. adecarboxylata were found to consist of proteins, lipids, nucleic acids, and polysaccharides according to Fourier transform infrared spectroscopy (FTIR) analysis. The EPS was found to play a crucial role in dye removal, forming chemical interactions with dye molecules. Zeta potential analysis was used to evaluate the charge distribution on the biosorbent surface (-12.6 +/- 1.1 mV) and its interactions in the biosorption process. Kinetic and isotherm models suggested a complex interaction mechanism between the biomass and the dye. Adsorption isotherm data were analyzed via nine isotherm models. Among them, the Hill model was found to be the best fit for describing the equilibrium adsorption process of the RB5 (R2 = 0.9993). Overall, the applied models elucidated the influence of both physical and chemical interactions on the mechanism. Kinetic studies revealed that the adsorption of RB5 fit a pseudo-second-order kinetic model. The unique biochemical composition of the indigenous L. adecarboxylata biosorbent provided a high affinity for RB5, offering a sustainable, rapid, and economical solution for the treatment of dye-polluted water.Article Citation - WoS: 9Citation - Scopus: 9Ir-Spectroscopic Characterization of an Elongated Ompg Mutant(Elsevier Science inc, 2015) Korkmaz, Filiz; van Pee, Katharina; Yildiz, OezkanOmpG is a nonselective, pH dependent outer membrane protein from Escherichia coli. It consists of 281 residues, forming a 14-stranded beta-sheet structure. In this study, OmpG is extended by 38 amino acids to produce a 16-stranded beta-barrel (OmpG-16S). The resulting protein is investigated by IR-spectroscopy. The secondary structure, pH-dependent opening/closing mechanism, buffer accessibility and thermal stability of OmpG-16S are compared to OmpG-WT. The results show that OmpG-16S is responsive to pH change as indicated by the Amide I band shift upon a switch from acidic to neutral pH. This spectral shift is consistent with that observed in OmpG-WT, which confirms the existence of structural differences consistent with the presence of the open or closed state. Secondary structure analysis after curve-fitting of Amide I band revealed that the additional residues do not fold into beta-sheet; rather they are in the form of turns and unordered structure. In thermal stability experiments, OmpG-16S is found to be as stable as OmpG-WT. Additionally, H/D exchange experiments showed no difference in the exchange rate of OmpG-16S between the acidic and alkaline pH, suggesting that the loop L6 is no longer sufficient to block the pore entrance at acidic pH. (C) 2015 Elsevier Inc. All rights reserved.Article Citation - WoS: 3Citation - Scopus: 4Nanoremediation of Toxic Dyes Using a Bacterial Consortium Immobilized on Cellulose Acetate Nanofiber Mats(Wiley, 2024) Erkoc, Esra; Tuzun, Imre; Korkmaz, Filiz; San Keskin, Nalan Oya; Kocberber Kilic, NurStenotrophomonas maltophilia and Ochrobactrum sp. demonstrated the highest rates of dye bioremediation. The trials were performed at pH 8, which resulted in the highest bioremediation rate of 64.6% in media containing 21.2 mg L-1 dye. As the dye concentration increased, the pollutant removal decreased, with the maximum bioremoval rate of 70.3%. The removal capacity was increased with an increase in biomass concentration; the highest yield of 91.3% was obtained in media containing 14.2 mg L-1 dye and 12% (v/v) biomass. In nanoremediation studies, the bacterial consortium was immobilized on cellulose acetate nanofiber mats (CA-NFM). Scanning electron microscopic micrographs showed that bead-free nanofiber mats were effective in immobilizing bacterial cells. Moreover, nanofiber structures were capable of supporting exopolysaccharides formation, as confirmed by Fourier transform & imath;nfrared spectroscopy. The bacterial consortium immobilized on CA-NFM showed a maximum bioremoval rate of 56.5%. Reusability tests demonstrated that the consortium immobilized CA-NFM could be used at least five times. Furthermore, after leaving the mat for 1 month at 4 degrees C, it was still usable, and the removal efficiency was found to be 45.4%. Based on our findings, bacteria immobilized on CA-NFM have the potential to be used as highly effective and versatile nanobiotechnological biological sorbents in the treatment of wastewater containing dyes.Article Citation - WoS: 32Citation - Scopus: 32Urine Analysis Using Ftir Spectroscopy: a Study on Healthy Adults and Children(Wiley-v C H verlag Gmbh, 2021) Sarigul, Neslihan; Kurultak, Ilhan; Gokceoglu, Arife Uslu; Korkmaz, FilizUrine spectra from 108 healthy volunteers are studied by attenuated total refraction-Fourier transform infrared (ATR-FTIR) spectroscopy. The spectral features are correlated with observable urine components. The variation of spectra within a healthy population is quantified and a library of reference spectra is constructed. Using the band assignments, these spectra are compared with both age-wise and gender-wise. Children show the least intensity variations compared to both adult groups. Young adults show the highest variation, particularly in the 1650 to 1400 cm(-1) and 1200 to 900 cm(-1) regions. These results indicate the importance of the size of the control group in comparative studies utilizing FTIR. Age-wise comparisons reveal that phosphate and sulfate excretion decreases with age, and that the variance of phosphate among individuals is higher with adults. As for gender-wise comparisons, females show a slightly higher citrate content at 1390 cm(-1) regardless of the age and they show a higher variance in the 1200 to 1000 cm(-1) region when compared to men.Article Citation - WoS: 2Citation - Scopus: 2Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, FilizIn this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 beta-strands in its structure, the mutant is designed to have 16 beta-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the H-1/H-2 exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.Article Structural and Electronic Properties of the Dppc Molecule(World Scientific Publ Co Pte Ltd, 2006) Erkoc, Sakir; Korkmaz, FilizThe structural and electronic properties of the DPPC molecule have been investigated theoretically by performing semi-empirical self-consistent-field molecular-orbital theory calculations at the PM3 level in its ground state.Article Citation - WoS: 5Citation - Scopus: 5Structural Properties of an Engineered Outer Membrane Protein G Mutant, Ompg-16sl, Investigated With Infrared Spectroscopy(Taylor & Francis inc, 2020) Yilmaz, Irem; Yildiz, Ozkan; Korkmaz, FilizThe structural and functional differences between wild type (WT) outer membrane protein G and its two mutants are investigated with Fourier transform infrared spectroscopy. Both mutants have a long extension to the primary sequence to increase the number of beta-strands from 14 (wild type) to 16 in an attempt to enlarge the pore diameter. The comparison among proteins is made in terms of pH-dependent conformational changes and thermal stability. Results show that all proteins respond to pH change but at different degrees. At acidic environment, all proteins contain the same number of residues participated in beta-sheet structure. However, at neutral pH, the mutants have less ordered structure compared to WT porin. Thermal stability tests show that mutants differ significantly from WT porin at neutral pH. Although the transition temperature is directly proportional with the amount of beta-sheet content, the changes in the pre-transition phase that pave the way to structural breakdown are shown to involve interactions among charged residues by two-dimensional correlation spectroscopy analysis. Results of the analysis show that side chain interactions play an active role under increasing temperature. Both mutants have more unordered secondary structure but they respond to pH change in tertiary structure level. Findings of this study provided deeper insight on the active players in structural stability of the WT porin. Communicated by Ramaswamy H. Sarma
