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
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Physics Group
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Sustainable Development Goals
2
ZERO HUNGER
0
Research Products
14
LIFE BELOW WATER
0
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17
PARTNERSHIPS FOR THE GOALS
0
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5
GENDER EQUALITY
0
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16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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8
DECENT WORK AND ECONOMIC GROWTH
0
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4
QUALITY EDUCATION
0
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6
CLEAN WATER AND SANITATION
3
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7
AFFORDABLE AND CLEAN ENERGY
0
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10
REDUCED INEQUALITIES
0
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11
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0
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9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
0
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1
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0
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3
GOOD HEALTH AND WELL-BEING
3
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12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
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13
CLIMATE ACTION
0
Research Products
15
LIFE ON LAND
2
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Documents
24
Citations
665
h-index
9
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0
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0
Scholarly Output
27
Articles
22
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6/0
Supervised MSc Theses
4
Supervised PhD Theses
0
WoS Citation Count
600
Scopus Citation Count
619
WoS h-index
9
Scopus h-index
8
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0
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0
WoS Citations per Publication
22.22
Scopus Citations per Publication
22.93
Open Access Source
9
Supervised Theses
4
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| Journal | Count |
|---|---|
| Scientific Reports | 4 |
| Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy | 2 |
| Physica B: Condensed Matter | 2 |
| Archives of Biochemistry and Biophysics | 2 |
| Journal of Biomolecular Structure and Dynamics | 1 |
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27 results
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Now showing 1 - 10 of 27
Article Web Server-Based Structure Prediction as a Supplementary Tool for Basic and Acidic Fgf Secondary Structure Analysis Using Ftir Spectroscopy and a Case Study Comparing Curve-Fit With the Model-Based Structure Inspection of the Ftir Data(DergiPark, 2023) Korkmaz,F.; Mollaoglu,A.; Adiguzel,Y.Fourier Transform Infrared (FTIR) spectroscopy can provide relative proportion of secondary structure elements in a protein. However, extracting this information from the Amide I band area of an FTIR spectrum is difficult. In addition to experimental methods, several protein secondary structure prediction algorithms serving on the Web can be used as supplementary tools requiring only protein amino acid sequences as inputs. In addition, web-server based docking tools can provide structure information when proteins are mixed and potentially interacting. Accordingly, we aimed to utilize web-server based structure predictors in fibroblast growth factor (FGF) protein structure determination through the FTIR data. Seven such predictors were selected and tested on basic FGF (bFGF) protein, to predict FGF secondary structure. Results were compared to available structure-files deposited in the Protein Data Bank (PDB). Then, FTIR spectra of bFGF and the acidic form of the protein with 50 folds more bovine serum albumin as carrier protein (1FGFA/50BSA) were collected. Optimized Amide I curve-fit parameters of bFGF with low (<5) root mean square deviation (RMSD) in the PDB data and the predictions were obtained. Those parameters were applied in curve-fitting of 1FGFA/50BSA data. Secondary structure was inspected also through applying models derived from the previously established methods. Results of model-based secondary structure estimation from FTIR data were compared with secondary structure calculated as 1 part contribution from 1FGFA/1BSA complex and 49 parts contribution from BSA. Complex structure was obtained through docking. RMSD in the PDB data and the predictions were respectively 3.05 and 2.39 with the optimized parameters. Those parameters did not work well for the 1FGFA/50BSA data. Models are better in this case, wherein one model (Model-1’) with the lowest average RMSD has 8.38 RMSD in the bFGF and 4.78 RMSD in the 1FGFA/50BSA structures. Model-based secondary structure predictions are better for determining bFGF and 1FGFA/50BSA secondary structures through the curve-fit approach that we followed, under non-optimal conditions like protein/BSA mixtures. Web servers can assist experimental studies investigating structures with unknown structures. Any web-based structure prediction supporting the experimental results would be enforcing the findings, but the unsupported results would not necessarily falsify the experimental data. © (2023), (DergiPark). 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.Master Thesis Gas(x)se(1-x) Katmanlı Karışım Kristallerinin Yapısal ve Elipsometrik Özellikleri(2017) Habaibi, Om-alhana; Işık, Mehmet; Özkan, Filiz KorkmazGaSxSe1-x katmanlı karışım kristalleri yapısal ve optiksel karakterizasyon teknikleri kullanılarak incelendi. Bridgman metodu ile büyütülen örneklerin yapısal karakterizasyonu x-ışını kırınımı (XRD), enerji saçılım spektroskopisi (EDS) ve Fourier transform kızılötesi spektroskopisi teknikleri kullanılarak başarıldı. Karışım kristallerinin kompozisyonal bağımlılığı EDS deneyleri ile elde edildi. Ölçümlerin sonuçları, kullanılan örneklerin x değerinin 0.25 aralıklar ile 0 ile 1 arasında olduğu kompozisyona denk geldiğini gösterdi. Örneklerin kristal yapısı XRD ölçümlerinin sonuçlarını ve analiz için bir yazılım programı kullanarak açığa çıkarıldı. FTIR tayfları x=0, 0.25 ve 0.50 kompozisyonlarındaki örneklerin içerisinde çoklu fonon emiliminin var olduğunu gösterdi. XRD ve FTIR deneylerinin sonuçları kullanılan kompozisyonlar arasında ilişkilendirildi. Örneklerin optiksel karakterizasyonu 1.2-6.0 eV spektral aralıpında gerçekleştirilen elipsometri deneyleri ile tamamlandı. Ölçüm sisteminin çıkış datası optiksel parametrelerin spektraş bağımlılığını gösteren dataya çevrildi. Elipsometrik data örneklerin bant boşluğu enerjilerini elde etmek için kullanıldı. Elde edilen bant enerjisi değerleri karışım kristallerinde sülfür kompozisyonu arttıkça bant enerjisinin 2.4 eV'tan (x = 0) 2.57 eV'a (x = 1) arttığını gösterdi. Ortaya çıkarılan bant enerji değerlerine göre bant boşluğu enerjisinin kompozisyona bağlılığını gösteren bir grafik çizildi.Article Citation - WoS: 96Citation - Scopus: 100Effect of Progesterone on Dppc Membrane: Evidence for Lateral Phase Separation and Inverse Action in Lipid Dynamics(Elsevier Science inc, 2005) Korkmaz, F; Severcan, FInteractions 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.Article Citation - WoS: 5Citation - Scopus: 5Concentration Dependent Different Action of Progesterone on the Order, Dynamics and Hydration States of the Head Group of Dipalmitoyl-Phosphatidylcholine Membrane(Hindawi Ltd, 2005) Korkmaz, F; Kirbiyik, H; Severcan, FInteractions 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.Article Citation - WoS: 15Citation - Scopus: 13K+-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, WernerThe 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 - WoS: 9Citation - Scopus: 9Urinalysis of Individuals With Renal Hyperfiltration Using Atr-Ftir Spectroscopy(Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, FilizAbnormal 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.Master Thesis İnsan İdrarları Arasında Gözlenen Çeşitliliğin Yapay İdrar Sistemi ve Ftır Spektroskopisi Kullanılarak Anlaşılması(2023) Ahmed, Marıam Hany Farouk Mohamed; Özkan, Filiz Korkmazİdrar 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.Article Citation - WoS: 357Citation - Scopus: 374A New Artificial Urine Protocol To Better Imitate Human Urine(Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, IlhanArtificial 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.Master Thesis N-(piridin-2-il) metilen benznamine içeren platin(II) kompleksinin sentezi, karakterizasyonu ve spektroskopik yöntemlerle DNA, HSA ve BSA'ya bağlanma davranımları(2017) Abdalla, Rema A İbrahim; Yaman, Şeniz Özalp; Özkan, Filiz KorkmazCisplatinin (Pt(NH3)2Cl2) yapısal analogları DNA ile benzer şekilde etkileştiği için, yeni platin temelli antitümör ilaçlarının, cisplatinden daha aktif olması ve çeşitli nedenlerle oluşabilecek ilaç direncini yenebilmesi beklenilmektedir. Bu amaçla, N-(piridin-2-il)metilen benzamin (L) ligandı içeren PtCl2 kompleksi sentezlenmiş ve karakterizasyonu tamamlanmıştır. Pt(L)Cl2 bileşiğinin buzağı DNA'sı ve serum albumin (BSA ve HSA) ile etkileşimleri test edilmiştir. Pt(L)Cl2 kompleksinin DNA'ya bağlanma mekanizmasını belirleyebilmek için çeşitli spektroskopik yöntemler kullanılmıştır. Platin kompleksi varlığında DNA çözeltisi ile gerçekleştirilen elektronik soğurma spektrumu, termal davranım, viskosite ölçümleri ve florometrik titrasyon deneyleri Pt(L)Cl2'nin DNA ile elektrostatik etkileşim yaptığını kanıtlamıştır. Aynı şekilde, spektroskopik ve viskometrik bulgular Pt(L)Cl2'nin serum proteinleri ile elektrostatik olarak etkileştiğini göstermiştir. Etkileşimin her iki protein için de hidrofobik bölgede olduğu, triptofan etrafında hidrofilite artışı ve alfa heliksler etrafında hidrofilite artışı ile ortaya konulmuştur. Öte yandan sürdürülen detaylı FTIR ölçümlerinden Pt(L)Cl2'nin BSA ya da HSA ile etkileşim noktası husunda net bir bilgi edinilememiştir.
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