Filiz Korkmaz Özkan

Korkmaz Özkan, Filiz

Name Variants

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

Job Title

Profesör Doktor

Email Address

filiz.korkmaz@atilim.edu.tr

Scholarly Output

19

Articles

17

Citation Count

391

Supervised Theses

1 Scholarly Output Search Results

Now showing 1 - 10 of 19

Citation Count: 0
Author Correction: Using urine FTIR spectra to screen autism spectrum disorder
(Nature Portfolio, 2024) Korkmaz Özkan, Filiz; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, Filiz; Physics Group
[No Abstract Available]
Citation Count: 1
Using urine FTIR spectra to screen autism spectrum disorder
(Nature Portfolio, 2023) Korkmaz Özkan, Filiz; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, Filiz; Physics Group
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder caused by multiple factors, lacking clear biomarkers. Diagnosing ASD still relies on behavioural and developmental signs and usually requires lengthy observation periods, all of which are demanding for both clinicians and parents. Although many studies have revealed valuable knowledge in this field, no clearly defined, practical, and widely acceptable diagnostic tool exists. In this study, 26 children with ASD (ASD+), aged 3-5 years, and 26 sex and age-matched controls are studied to investigate the diagnostic potential of the Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy. The urine FTIR spectrum results show a downward trend in the 3000-2600/cm region for ASD+ children when compared to the typically developing (TD) children of the same age. The average area of this region is 25% less in ASD+ level 3 children, 29% less in ASD+ level 2 children, and 16% less in ASD+ level 1 children compared to that of the TD children. Principal component analysis was applied to the two groups using the entire spectrum window and five peaks were identified for further analysis. The correlation between the peaks and natural urine components is validated by artificial urine solutions. Less-than-normal levels of uric acid, phosphate groups, and ammonium (NH4+) can be listed as probable causes. This study shows that ATR-FTIR can serve as a practical and non-invasive method to screen ASD using the high-frequency region of the urine spectrum.
Citation Count: 18
In 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 Özkan, Filiz; Koester, Stefan; Yildiz, Oezkan; Maentele, Werner; Physics Group
The 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.
Citation Count: 0
Simultaneous Removal of Setazol Navy Blue and Cr(VI) By Mixed Microbial Culture Isolated from the Çubuk Stream
(Springer int Publ Ag, 2024) Korkmaz Özkan, Filiz; Erkoc, Esra; Korkmaz, Filiz; Kilic, Nur Kocberber; Physics Group
Water 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.
Citation Count: 5
Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy
(Taylor & Francis inc, 2020) Yılmaz, İrem; Yildiz, Ozkan; Korkmaz Özkan, Filiz; Avionics; Physics Group
The 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
Citation Count: 1
Commentary on "Spectral characterization of the binding and conformational changes of serum albumins upon interaction with an anticancer drug, anastrozole"
(Pergamon-elsevier Science Ltd, 2015) Korkmaz Özkan, Filiz; Physics Group
The manuscript by R. Punith and J. Seetharamappa (http://dx.doi.org/10.1016/j.saa.201202.038) presents the interaction between serum albumin from human (HAS) and from bovine (BSA) with a drug called Anastrozole (AZ). The drug is on the market for treating patients with breast cancer after surgery and for metastasis in women. The study utilizes various spectroscopic techniques such as; fluorescence, synchronous fluorescence, 3D fluorescence measurements, FTIR, CD and UV. Although there are some relatively minor comments on the paper, the main point that needs to be reviewed by the authors is the result of FTIR measurements. Based on the data provided in the text (there is no figure), the protein sample is not in its native state, which makes the data inconvenient to be used in drawing conclusions. Authors are kindly requested to take another look at the FUR experiments. (C) 2014 Elsevier B.V. All rights reserved.
İnsan idrarları arasında gözlenen çeşitliliğin yapay idrar sistemi ve FTIR spektroskopisi kullanılarak anlaşılması
(2023) Korkmaz Özkan, Filiz; Özkan, Filiz Korkmaz; Physics Group
İdrar testleri, çeşitli tıbbi bozuklukları tanımlamanın ve teşhis etmenin yaygın ve uygun bir yoludur. Bu çalışmada, 9 yapay idrar bileşeninin normal minimum ve maksimum değerlerinin spektrumunu belirlemek için yeni bir yapay idrar protokolünü (MP-AU) kullanıyoruz. Fourier Transform Infrared (FTIR) spektroskopisi, varsa bozuklukların erken saptanmasına yardımcı olacak bu spektrumları oluşturmak için kullanılmıştır. Hastanın idrar numunesinden elde edilen spektrum, minimum ve maksimum normal değerler için yapay idrar çözeltilerinden elde edilen spektrumlarla karşılaştırılabilir. Bu karşılaştırmanın sonucu hastanın sağlığı ile ilgili olacaktır. Hastanın spektrumu bu iki normal spektrum arasında yer alıyorsa, hastanın sağlık olduğu düşünülebilir. Buna bağlı olarak, hastanın spektrumu normal aralığın dışına çıkarsa, anomaliyi saptamak için daha fazla test istenebilir. Bu çalışmanın bulguları, yapay idrar sistemi içindeki bileşenlerin miktarının, FTIR spektrumundaki tepe noktalarının genlikleri ile ilişkili olduğunu ortaya koymaktadır. Ayrıca, daha sonraki çalışmalarda referans olarak kullanılmak üzere, test edilen idrar bileşenlerinin karakteristik bant pozisyonları da belirlenmiştir. Bu çalışma Atılım Üniversitesi Araştırma Destek programı çerçevesinde ATÜ-ADP-2122-01 numaralı proje ile finansal olarak desteklenmiştir.
Citation Count: 91
Effect of progesterone on DPPC membrane: Evidence for lateral phase separation and inverse action in lipid dynamics
(Elsevier Science inc, 2005) Korkmaz Özkan, Filiz; Severcan, F; Physics Group
Interactions of progesterone with zwitterionic dipalmitoyl phosphatidylcholine (DPPC) triultilamellar liposomes were investigated as a function of temperature and progesterone concentration by using three non-invasive techniques namely Fourier transform infrared spectroscopy, turbidity at 440 nm, and differential scanning calorimetry. The results reveal that progesterone changes the physical properties of DPPC bilayers by decreasing the main phase-transition temperature, abolishing the pre-transition, broadening the phase-transition profile, disordering the system both in gel and liquid crystalline phase, increasing the dynamics at low concentrations whereas stabilizing the membrane at high concentrations, and inducing phase separation. Progesterone does not change the hydration of the C=O groups, while it strengthens the hydrogen bonding between the PO (2) over bar groups of lipids and the water molecules around. (c) 2005 Elsevier Inc. All rights reserved.
Citation Count: 5
Concentration dependent different action of progesterone on the order, dynamics and hydration states of the head group of dipalmitoyl-phosphatidylcholine membrane
(Hindawi Ltd, 2005) Korkmaz Özkan, Filiz; Kirbiyik, H; Severcan, F; Physics Group
Interactions of progesterone with zwitterionic dipalmitoyl phosphatidylcholine (DPPC) multilamellar liposomes (MLVs) were investigated as a function of progesterone concentration at selected temperatures monitoring both the gel and liquid crystalline phase, by using Fourier Transform Infrared spectroscopy (FTIR). It has been show that the effect of progesterone on membrane dynamics is dependent on progesterone concentration. At 1 mol%, which is close to physiological level, progesterone behaves differently. At this concentration the decrease in dynamics is more noticeable. Additionally a dramatic decrease in the strength of hydrogen bonding in the interfacial region of the bilayer is also observed. When concentration increases up to 12 mol% opposite behaviour is observed at all interactions. Above 12 mol%, progesterone-DPPC interactions shows almost linear plot.
Citation Count: 14
K⁺-induced conformational changes in the trimeric betaine transporter BetP monitored by ATR-FTIR spectroscopy
(Elsevier Science Bv, 2013) Korkmaz Özkan, Filiz; Ressl, Susanne; Ziegler, Christine; Maentele, Werner; Physics Group
The 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.

Korkmaz Özkan, Filiz

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Scholarly Output

19

Articles

17

Citation Count

391

Supervised Theses

1

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