Korkmaz Özkan, Filiz

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Profile URL
https://hdl.handle.net/20.500.14411/6821
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
Main Affiliation
Physics Group
Status
Website
https
ORCID ID
0000-0003-3512-3521
Scopus Author ID
8664101000
Turkish CoHE Profile ID
Google Scholar ID
4NU4lXwAAAAJ
WoS Researcher ID
2752134

Sustainable Development Goals

NO POVERTY1
NO POVERTY
0
Research Products
ZERO HUNGER2
ZERO HUNGER
0
Research Products
GOOD HEALTH AND WELL-BEING3
GOOD HEALTH AND WELL-BEING
3
Research Products
QUALITY EDUCATION4
QUALITY EDUCATION
0
Research Products
GENDER EQUALITY5
GENDER EQUALITY
0
Research Products
CLEAN WATER AND SANITATION6
CLEAN WATER AND SANITATION
3
Research Products
AFFORDABLE AND CLEAN ENERGY7
AFFORDABLE AND CLEAN ENERGY
0
Research Products
DECENT WORK AND ECONOMIC GROWTH8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
INDUSTRY, INNOVATION AND INFRASTRUCTURE9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
0
Research Products
REDUCED INEQUALITIES10
REDUCED INEQUALITIES
0
Research Products
SUSTAINABLE CITIES AND COMMUNITIES11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
RESPONSIBLE CONSUMPTION AND PRODUCTION12
RESPONSIBLE CONSUMPTION AND PRODUCTION
0
Research Products
CLIMATE ACTION13
CLIMATE ACTION
0
Research Products
LIFE BELOW WATER14
LIFE BELOW WATER
0
Research Products
LIFE ON LAND15
LIFE ON LAND
2
Research Products
PEACE, JUSTICE AND STRONG INSTITUTIONS16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
PARTNERSHIPS FOR THE GOALS17
PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents

24

Citations

665

h-index

9

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Documents

0

Citations

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Scholarly Output

27

Articles

22

Views / Downloads

6/0

Supervised MSc Theses

4

Supervised PhD Theses

0

WoS Citation Count

600

Scopus Citation Count

619

Patents

0

Projects

0

WoS Citations per Publication

22.22

Scopus Citations per Publication

22.93

Open Access Source

9

Supervised Theses

4

JournalCount
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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End date: 2019

Scholarly Output Search Results

Now showing 1 - 10 of 16
  • Thumbnail Image
    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; Mäntele, 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 - Scopus: 1
    Infrared and Raman Scattering Spectra of Layered Structured Ga3inse4< Crystals
    (Elsevier Science Bv, 2013) Isik, M.; Gasanly, N. M.; Korkmaz, F.
    The infrared reflectivity and transmittance and Raman scattering in Ga3InSe4 layered crystals were investigated in the frequency ranges of 100-400, 400-4000 and 25-500 cm(-1). The refractive and absorption indices, the frequencies of transverse and longitudinal optical modes, high- and low-frequency dielectric constants were obtained from the analysis of the IR reflectivity spectra. The bands observed in IR transmittance spectra were interpreted in terms of two-phonon absorption processes. (C) 2012 Elsevier B.V. All rights reserved.
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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
    İlaç Araştırmalarında Yeni Nesil Uygulamalar: Kontrollü İlaç Salımı
    (Bilim ve Teknoloji, 2012) İşgör, Belgin S.; Korkmaz Özkan, Filiz
    16.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.
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    Article
    Citation - WoS: 357
    Citation - Scopus: 374
    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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    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 Korkmaz
    Cisplatinin (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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    Master Thesis
    Gas(x)se(1-x) Katmanlı Karışım Kristallerinin Yapısal ve Elipsometrik Özellikleri
    (2017) Habaibi, Om-alhana; Işık, Mehmet; Özkan, Filiz Korkmaz
    GaSxSe1-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.
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    Article
    Citation - WoS: 96
    Citation - Scopus: 100
    Effect of Progesterone on Dppc Membrane: Evidence for Lateral Phase Separation and Inverse Action in Lipid Dynamics
    (Elsevier Science inc, 2005) Korkmaz, F; Severcan, F
    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.
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    Article
    Citation - WoS: 5
    Citation - Scopus: 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, F; Kirbiyik, H; Severcan, F
    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.