Korkmaz Özkan, Filiz

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https://hdl.handle.net/20.500.14411/6821
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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
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Profesör Doktor
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filiz.korkmaz@atilim.edu.tr
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Physics Group
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0000-0003-3512-3521
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8664101000
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4NU4lXwAAAAJ
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2752134

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24

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27

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22

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4

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597

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618

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Scientific Reports4
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy2
Physica B: Condensed Matter2
Archives of Biochemistry and Biophysics2
Journal of Biomolecular Structure and Dynamics1
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Author: Korkmaz, FilizHas files: false

Scholarly Output Search Results

Now showing 1 - 10 of 13
  • Thumbnail Image
    Article
    Citation - WoS: 355
    Citation - Scopus: 373
    A New Artificial Urine Protocol To Better Imitate Human Urine
    (Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, Ilhan
    Artificial 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.
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    Article
    Citation - WoS: 9
    Citation - Scopus: 9
    Ir-Spectroscopic Characterization of an Elongated Ompg Mutant
    (Elsevier Science inc, 2015) Korkmaz, Filiz; van Pee, Katharina; Yildiz, Oezkan
    OmpG 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.
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    Article
    Citation - WoS: 9
    Citation - Scopus: 9
    Urinalysis of Individuals With Renal Hyperfiltration Using Atr-Ftir Spectroscopy
    (Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, Filiz
    Abnormal 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.
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    Article
    Citation - WoS: 32
    Citation - Scopus: 32
    Urine 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
    Urine 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.
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    Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy
    (Elsevier, 2022) Yilmaz, Irem; Korkmaz, Filiz
    In 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.
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    Article
    Author Correction: Using Urine Ftir Spectra To Screen Autism Spectrum Disorder
    (Nature Portfolio, 2024) Sarigul, Neslihan; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, Filiz
    [No Abstract Available]
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    Editorial
    Citation - WoS: 1
    Citation - Scopus: 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, Filiz
    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.
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    Article
    Structural and Electronic Properties of the Dppc Molecule
    (World Scientific Publ Co Pte Ltd, 2006) Erkoc, Sakir; Korkmaz, Filiz
    The 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.
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    Article
    Citation - WoS: 15
    Citation - Scopus: 13
    K+-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
    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.
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    Article
    Citation - WoS: 17
    Citation - Scopus: 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, Filiz; Koester, Stefan; Yildiz, Oezkan; Maentele, Werner
    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.