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
Main Affiliation
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
Research Products
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
Research Products
7
AFFORDABLE AND CLEAN ENERGY
0
Research Products
10
REDUCED INEQUALITIES
0
Research Products
11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
0
Research Products
1
NO POVERTY
0
Research Products
3
GOOD HEALTH AND WELL-BEING
3
Research Products
12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
Research Products
13
CLIMATE ACTION
0
Research Products
15
LIFE ON LAND
2
Research Products
Documents
24
Citations
665
h-index
9
Documents
0
Citations
0
Scholarly Output
27
Articles
22
Views / Downloads
6/0
Supervised MSc Theses
4
Supervised PhD Theses
0
WoS Citation Count
597
Scopus Citation Count
618
WoS h-index
9
Scopus h-index
8
Patents
0
Projects
0
WoS Citations per Publication
22.11
Scopus Citations per Publication
22.89
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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Now showing 1 - 10 of 20
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: 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 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: 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.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 İlaç Araştırmalarında Yeni Nesil Uygulamalar: Kontrollü İlaç Salımı(Bilim ve Teknoloji, 2012) İşgör, Belgin S.; Korkmaz Özkan, Filiz16.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 - WoS: 355Citation - Scopus: 373A 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.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.
