Korkmaz Özkan, Filiz
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Korkmaz Ozkan,Filiz
K.,Filiz
F.,Korkmaz Ozkan
Filiz, Korkmaz Özkan
Korkmaz Ozkan,F.
K.Ö.Filiz
Korkmaz Özkan,F.
K. O. Filiz
Korkmaz F.
F.,Korkmaz Özkan
F., Korkmaz Ozkan
Filiz, Korkmaz Ozkan
Filiz Korkmaz Özkan
F., Korkmaz Özkan
Korkmaz Ozkan, Filiz
Korkmaz Özkan, Filiz
K. Ö. Filiz
K., Filiz
Özkan, Filiz Korkmaz
Korkmaz, Filiz
K.,Filiz
F.,Korkmaz Ozkan
Filiz, Korkmaz Özkan
Korkmaz Ozkan,F.
K.Ö.Filiz
Korkmaz Özkan,F.
K. O. Filiz
Korkmaz F.
F.,Korkmaz Özkan
F., Korkmaz Ozkan
Filiz, Korkmaz Ozkan
Filiz Korkmaz Özkan
F., Korkmaz Özkan
Korkmaz Ozkan, Filiz
Korkmaz Özkan, Filiz
K. Ö. Filiz
K., Filiz
Özkan, Filiz Korkmaz
Korkmaz, Filiz
Job Title
Profesör Doktor
Email Address
filiz.korkmaz@atilim.edu.tr
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Scholarly Output
19
Articles
17
Citation Count
391
Supervised Theses
1
19 results
Scholarly Output Search Results
Now showing 1 - 10 of 19
Article Citation Count: 14K+-induced conformational changes in the trimeric betaine transporter BetP monitored by ATR-FTIR spectroscopy(Elsevier Science Bv, 2013) Korkmaz, Filiz; Ressl, Susanne; Ziegler, Christine; Maentele, Werner; Physics GroupThe trimeric Na+-coupled betaine symporter BetP from Corynebactrium glutamicum adjusts transport activity according to the external osmolality. BetP senses the increasing internal K+ concentration, which is an immediate consequence of osmotic upshift in C. glutamicum. It is assumed that BetP specifically binds potassium to yet unidentified binding sites, thereby inducing conformational changes resulting in activation. Atomic structures of BetP were obtained in the absence of potassium allowing only a speculative glimpse on a putative mechanism of K+-induced transport activation. The structural data suggest that activation in BetP is crucially linked to its trimeric state involving an interaction network between several arginines and glutamates and aspartates. Here, we describe the effect of K+-induced activation on the specific ionic interaction sites in terminal domains and loops and on the protomer-protomer interactions within the trimer studied by ATR-FTIR spectroscopy. We suggest that arginine and aspartate and/or glutamate residues at the trimeric interface rearrange upon K+-induced activation, although they remain assembled in an interaction network. Our data propose a two-step mechanism comprising first a change in solvent exposure of charged residues and second a modification of their interaction sites in a partner-switching manner. FTIR reveals a higher alpha-helical content than expected from the X-ray structures that we attribute to the structurally unresolved N-terminal domain modulating regulation. In situ H-1/H-2 exchange studies point toward an altered exposure of backbone regions to buffer solution upon activation, most likely due to conformational changes in both terminal domains, which further affects ionic interactions within the trimer. (C) 2013 Elsevier B.V. All rights reserved.Article Citation Count: 2Urinalysis of individuals with renal hyperfiltration using ATR-FTIR spectroscopy(Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, Filiz; Physics GroupAbnormal increased glomerular filtration rate (GFR), otherwise known as renal hyperfiltration (RHf), is associated with an increased risk of chronic kidney disease and cardiovascular mortality. Although it is not considered as a disease alone in medicine today, early detection of RHf is essential to reducing risk in a timely manner. However, detecting RHf is a challenge since it does not have a practical biochemical marker that can be followed or quantified. In this study, we tested the ability of ATR-FTIR spectroscopy to distinguish 17 individuals with RHf (hyperfiltraters; RHf (+)), from 20 who have normal GFR (normofiltraters; RHf(-)), using urine samples. Spectra collected from hyperfiltraters were significantly different from the control group at positions 1621, 1390, 1346, 933 and 783/cm. Intensity changes at these positions could be followed directly from the absorbance spectra without the need for pre-processing. They were tentatively attributed to urea, citrate, creatinine, phosphate groups, and uric acid, respectively. Using principal component analysis (PCA), major peaks of the second derivative forms for the classification of two groups were determined. Peaks at 1540, 1492, 1390, 1200, 1000 and 840/cm were significantly different between the two groups. Statistical analysis showed that the spectra of normofiltraters are similar; however, those of hyperfiltraters show diversity at multiple positions that can be observed both from the absorbance spectra and the second derivative profiles. This observation implies that RHf can simultaneously affect the excretion of many substances, and that a spectroscopic analysis of urine can be used as a rapid and non-invasive pre-screening tool.Article Citation Count: 19Urine 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, Filiz; Physics GroupUrine 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 İlaç Araştırmalarında Yeni Nesil Uygulamalar: Kontrollü İlaç Salımı(Bilim ve Teknoloji, 2012) İşgör, Belgin S.; Korkmaz Özkan, Filiz; Physics Group16.yüzyılda yaşamış olan ve bugünkü Modern tıbbın kurucularından sayılan Paracelsus’un “Her şey zehirdir. Zehirle ilacı ayıran dozudur” sözü, bugünkü modern toksikolojinin temeli olan doz-cevap ilişkisine dikkat çekmesi açısından son derece önemlidir. Günümüzde ilaç olarak sunulan sentetik ve doğal kaynaklı kimyasal bileşiklerin vücuda alımı genel olarak ağızdan (oral) katı veya sıvı formlarda, damar ve kas içerisine sıvı enjeksiyonuyla, nazal yol aracılığıyla sprey veya toz formunda inhalatör yardımıyla, veya deriden lokal uygulamalarla gerçekleşmektedir. Vücuda verilen ilaç ilk olarak dolaşım sistemine alınır ve tedavi için hedeflenen dokuya kan damarları ile taşınır. Hedef dokulara ise bu dokulara nüfuz etmiş kılcal damarlar yoluyla ulaşır. İlacın vücuda alımından hedef dokuya taşınması sürecinde, damar yolu üzerinde bulunan tüm dokularca alınıp hücresel mekanizmalarca işlenmesi mümkündür.Article Citation Count: 199A New Artificial Urine Protocol to Better Imitate Human Urine(Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, Ilhan; Physics GroupArtificial urine has many advantages over human urine for research and educational purposes. By closely mimicking healthy individuals' urine, it may also be important in discovering novel biomarkers. However, up until now, there has not been any specific protocol to prove the similarity in terms of the chemical composition at the molecular level. In this study, a new artificial urine protocol is established to mimics the urine of healthy individuals. The multi-purpose artificial urine (MP-AU) presented here is compared with two other protocols most cited in literature. Furthermore, these three protocols are also compared with samples from 28 healthy young individuals. To do so, attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is used, according to which MP-AU shows a significantly close similarity with human urine. In formulating MP-AU, the infrared spectra of nine compounds is provided, making possible the band assignment of some absorption bands to certain compounds. Given its properties, the MP-AU protocol introduced here is both economical and practical, making it useful when designing comparative-controlled experiments.Article Citation Count: 2Investigations of pH-dependent dynamic properties of OmpG-16SL, an outer membrane protein G mutant by ATR-FTIR spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, Filiz; Avionics; Physics GroupIn 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 Citation Count: 18In situ opening/closing of OmpG from E. coli and the splitting of β-sheet signals in ATR-FTIR spectroscopy(Pergamon-elsevier Science Ltd, 2012) Korkmaz, Filiz; Koester, Stefan; Yildiz, Oezkan; Maentele, Werner; Physics GroupThe pH dependent opening and closure of Escherichia coli OmpG is driven by the formation and breaking of hydrogen bridges in beta-strands S11-S13. We have investigated the in situ secondary structural changes of OmpG with ATR-FTIR difference spectroscopy in order to detect the signals associated with the newly established interactions. Curve-fitting of OmpG in two pH conditions revealed the splitting and shifting of beta-sheet signals upon opening of the channel. Besides secondary structure changes, there are also amino acid side chain signals that play active role in opening/closing of the channel. An interaction among positively charged arginines and negatively charged aspartic and glutamic acid residues is suggested upon closure of the channel while this interaction is abolished when the channel opens at higher pH. (C) 2012 Elsevier B.V. All rights reserved.Article Citation Count: 0Simultaneous Removal of Setazol Navy Blue and Cr(VI) By Mixed Microbial Culture Isolated from the Çubuk Stream(Springer int Publ Ag, 2024) Gunduz, A. Irem; Erkoc, Esra; Korkmaz, Filiz; Kilic, Nur Kocberber; Physics GroupWater samples taken from the & Ccedil;ubuk Stream (Ankara, Turkey) were inoculated into nutrient broth media containing Setazol Navy Blue SBG (SNB), an organic pollutant, and heavy metal Cr(VI), an inorganic pollutant, to obtain a pollutant-resistant mixed microbial culture. Experiments were conducted with this culture to remove SNB and heavy metal. The optimum conditions, where the mixed bacterial culture removed the pollutants most effectively, were determined, showing that the highest capacity for removal took place at pH 8 with removal percentages 96.3% for Cr(VI) and 78.5% for SNB. In media with 50.4 mg/L SNB and 9.7 mg/L Cr(VI), the SNB removal was 87.3%, and the Cr(VI) removal was 96.6% at the end of the 7-day incubation period. The highest removal was observed with a biomass concentration of 8% (v/v) of mixed culture [50 mg/L SNB dye+25 mg/L Cr(VI)]. The removal was 100% for both Cr(VI) and the SNB dye. The bacteria with the highest removal were isolated and identified using 16S rDNA gene sequence analysis as Microbacterium oxydans and Leucobacter aridicollis. The role of various functional groups and the structures of the microorganisms that might be involved in the removal mechanisms were discussed using their FTIR spectra. This report is the first study that investigates a mixed bacterial culture and pure cultures (M. oxydans and L. aridicollis) isolated from that mixed culture, removing both SNB and Cr(VI) simultaneously.Article Citation Count: 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, Filiz; Avionics; Physics GroupThe 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. SarmaArticle Citation Count: 25Interaction of a novel platinum drug with bovine serum albumin: FTIR and UV-Vis spectroscopy analysis(Royal Soc Chemistry, 2015) Korkmaz, Filiz; Erdogan, Deniz Altunoz; Ozalp-Yaman, Seniz; Physics Group; Chemical EngineeringPlatinum complexes have proven to be very effective in cancer treatment. However, severe side effects of these drugs have lead scientists to pursue new platinum complex derivatives. A novel blue platinum compound, called Platinum-Blue (Pt-Blue), is one of the promising candidate platinum compounds to be used for tumor treatment. In this study, the interaction of Pt-Blue with bovine serum albumin (BSA) has been investigated using UV-Vis and FTIR spectroscopy. One of the findings is that the drug-protein interaction type depends on the drug concentration. Though Pt-Blue is attached to the surface of BSA at high concentrations, it interacts with a hydrophobic region of the protein at low concentrations with a binding constant of 1.93 x 10(5) M-1. Spectroscopic results indicate the hydrophobic docking position to be around Trp 213 in domain II, which is surrounded by a number of Asp and Glu. During this interaction, helices such as helix-10, helix-18, helix-19 and helix-24 change orientation and/or partially unfold to make room for the compound. Binding constants at high and low concentrations of Pt-Blue are determined using UV-Vis spectroscopy, which are found to be comparable to cisplatin. FTIR spectroscopy also reveals that the interaction between Pt-Blue and BSA is noncovalent, which makes the candidate drug favorable because it is available for DNA binding while being carried by albumin.
