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Öğe Calcitonin Gene Related Peptide Gene Polymorphism in Migraine Patients(Cambridge Univ Press, 2013) Guldiken, Baburhan; Sipahi, Tammam; Tekinarslan, Remziye; Kabayel, Levent; Ozkan, Hulya; Unlu, Ayhan; Yamasan, Bilge ErenObjective: Calcitonin gene related peptide (CGRP), which has a vasodilator effect, is held responsible for neurogenic inflammation and vasodilatation of the cranial vessels in migraine pathophysiology. In this study, we investigated the association between alpha CGRP gene polymorphism (CALCA T-692C) and migraine. Material and Methods: One hundred and thirty-four female migraineurs and 96 healthy female cases were enrolled in the study. The patient group was further subdivided into migraine with and without aura groups. The CALCA T-692C gene polymorphism was identified using polymerase chain reaction (PCR) technique and restriction fragment length polymorphism (RFLP). Results: The genotype and allele frequencies of CALCA T-692C gene polymorphism did not differ between the migraine and control groups. Between the migraine with and without aura subgroups, there was no difference. No association was seen between the CALCA T-692C gene polymorphisms and migraine attack severity and frequency. Conclusion: Our study did not show any association between CALCA T-692C gene polymorphism and migraine.Öğe Characterization of short-length multi-walled carbon nanotubes and cytotoxicity on MDA-MB-231 and HUVEC cell lines(Springer Japan Kk, 2020) Dinc, Bircan; Unlu, Ayhan; Bektas, MuhammetMulti-walled carbon nanotubes (MWNTs) are suitable for delivering large biomolecules with lower cytotoxicity values and low prime cost. Surface modifications of MWNTs affect interaction with cells and proteins. Oxidation with strong acids decreases cytotoxicity of CNTs and increases protein-loading capacity. Here, after oxidation, TEM images revealed more aligned structure and carboxylated groups at the surface which decreases toxicity. Functionalized MWNTs showed more gradual degradation than the pristine MWNTs and mass loss increased by 2% in the same temperature range. Raman spectroscopy corrected graphitic structure with characteristic D and G bands at 1330 and 1579 cm(-1) and increased intensity after oxidation. FTIR spectroscopy peaks at 1443 cm(-1), 1560, 1640 cm(-1), 2100-2200 cm(-1) and 3426 cm(-1) are ascribed to C-O-C vibrational stretch, C=C bonds, vibration of C equivalent to C bonds and stretch of hydroxyl groups, respectively. The sonication-driven dispersion of in phosphate-buffered saline, distilled water and cell culture medium were detected by UV-vis-NIR spectroscopy, water-dispersed functionalized MWNTs revealed the highest absorbance value. Cytotoxicity of MWNTs was investigated before and after functionalization in breast cancer (MDA-MB-231) and human vein endothelial (HUVEC) cells. Relatively low-toxicity results were obtained in functionalized MWNTs and cellular uptake of MWNTs were corrected with fluorescent imaging of cells and cell lysates. Protein-loading capacity of fsMWNTs (functionalized short-length multi-walled carbon nanotubes) was evaluated by using bovine serum albumin (BSA) and with an equal amount of fsMWNTs and BSA; 36% binding yield was obtained. Protein corona after covalent functionalization potentially lowered cytotoxicity up to 6%.Öğe A Comparative Study of Short Multi-Walled Carbon Nanotubes with Different Bulk Densities(Maik Nauka/Interperiodica/Springer, 2022) Dinc, Bircan; Ustunsoy, Recep; Unlu, Ayhan; Meran, Mehdi; Karatepe, Nilgun; Bektas, MuhammetMulti-walled carbon nanotubes (MWNTs) were investigated before and after carboxylic acid functionalization. Here, the comparative analysis of MWNTs with different bulk densities reveals similar Raman and FTIR spectra before and after acid functionalization except for minor differences. However thermal analyses exhibited some basic differences for both MWNTs before and after acid treatment. We investigated the cytotoxicity of two MWNTs on HT-29 and HEK293-T cells through three different methods: MTT assay, DAPI staining, and xCELLigence real-time cell analyzing method. It was observed that high bulk density affects the cytotoxicity for both cell lines and in all methods. Because the acid treatment lowered the bulk density, after acid treatment, the MWNTs with the higher bulk density (C150P) elicited similar cytotoxicity compared to the lower one (C70P).Öğe Computational prediction of actin-actin interaction(Springer, 2014) Unlu, AyhanActin is one of the most abundant proteins in eukaryotic cells, where it plays key roles in cell shape, motility, and regulation. Actin is found in globular (G) and filamentous (F) structure in the cell. The helix of actin occurs as a result of polymerization of monomeric G-actin molecules through sequential rowing, is called F-actin. Recently, the crystal structure of an actin dimer has been reported, which details molecular interface in F-actin. In this study, the computational prediction model of actin and actin complex has been constructed base on the atomic model structure of G-actin. To this end, a docking simulation was carried out using predictive docking tools to obtain modeled structures of the actin-actin complex. Following molecular dynamics refinement, hot spots interactions at the protein interface were identified, that were predicted to contribute substantially to the free energy of binding. These provided a detailed prediction of key amino acid interactions at the protein-protein interface. The obtained model can be used for future experimental and computational studies to draw biological and functional conclusions. Also, the identified interactions will be used for designing next studies to understand the occurrence of F-actin structure.Öğe Cross-reacting material 197 (CRM197) affects actin cytoskeleton of endothelial cells(General Physiol And Biophysics, 2017) Edis, Bilge Ozerman; Varol, Basak; Haciosmanoglu, Ebru; Unlu, Ayhan; Bektas, MuhammetCRM197, cross-reacting material 197, is a mutant of diphtheria toxin (DTx). CRM197 is used in pharmacology as a carrier protein. It has been recently shown that CRM197 causes breakdown in actin filaments. In order to show intracellular localization of CRM197 and visualize cell structure via actin cytoskeleton, endothelial cells were cultured and subjected to CRM197 in vitro. To address the interaction between CRM197 and actin both experimental and theoretical studies were carried out. Colocalization of CRM197 with actin filaments was determined by immunofluorescence microscopy. Following 24-hour incubation, the loss of cell-cell contact between cells was prominent. CRM197 was shown to bind to G-actin by gel filtration chromatography, and this binding was confirmed by Western blot analysis of eluted samples obtained following chromatography. Based on crystal structure, docked model of CRM197-actin complex was generated. Molecular dynamics simulation revealed that Lys42, Cys218, Cys233 of CRM197 interacts with Gly197, Arg62 and Ser60 of G-actin, respectively. CRM197 binding to G-actin, colocalization of CRM197 with actin filament, and actin cytoskeleton rearrangement resulting in the loss of cell-cell contact show that actin comes into sight as target molecule for CRM197.Öğe Cytotoxicity of doxrubicin loaded single-walled carbon nanotubes(Springer, 2018) Unlu, Ayhan; Meran, Mehdi; Dinc, Bircan; Karatepe, Nilgun; Bektas, Muhammet; Guner, F. SenihaCarbon nanotube (CNTs) is a new alternative for efficient drug delivery and it has a great potential to change drug delivery system profile in pharmaceutical industry. One of the important advantage of CNTs is their needle-like, cylindrical shape. This shape provides a high surface area for multiple connections and adsorption onto for millions of therapeutic molecules. CNTs can be internalized by cells via endocytosis, passive diffusion and phagocytosis and release the drug with different effects like pH and temperature. The acidic nature of cancer cells and the susceptibility of CNTs to release the drug in the acidic environment have made it a promising area of research in cancer drug delivery. In this research, we investigated cell viability, cytotoxicity and drug delivery in breast cancer cell line by designing non-covalent single walled carbon nanotubes (SWNT)-doxorubicin (DOX) supramolecular complex that can be developed for cancer therapy. Applied high concentrations of DOX loaded SWNTs changed the actin structure of the cells and prevented the proliferation of the cells. It was showed that doxorubicin loaded SWNTs were more effective than free doxorubicin at relatively small concentrations. Once we applied same procedure for short and long (short: 1-1.3 mu m; long: 2.5-4 mu m) SWNTs and compared the results, more disrupted cell structure and reduction in cell proliferation were observed for long CNTs. DOX is bounded more to nanotubes in basic medium, less bound in acidic environment. Cancer cells were also examined for concentration at which they were effective by applying DOX and it was seen that 3.68 mu M doxorubicin kills more than 55% of the cells.Öğe Evaluation of clinical and laboratory findings with JAK2 V617F mutation as an independent variable in essential thrombocytosis(Springer, 2014) Cetin, Guven; Ozkan, Tuba; Turgut, Seda; Cikrikcioglu, M. Ali; Ar, M. Cem; Ayer, Mesut; Unlu, AyhanEssential thrombocythemia (ET) is an entity of classic Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), characterized by thrombocytosis with megakaryocytic hyperplasia and thrombocytes are increased with abnormal functions. Discovery of the protein tyrosine kinase JAK2 V617F allele contributed to better understanding of the pathogenetic mechanisms of MPNs. Acquired single point mutation in the JAK2 V617F was determined approximately 50-60 % of patients with ET. In this study we aimed to investigate the relationship between JAK2 V617F gene mutation, hematologic, biochemical markers and the complications in the ET patients. A total of 268 patients diagnosed with ET and 219 of those studied for JAK2 gene mutation were followed at the hematology clinics of three major hospitals between 2008 and 2013 were screened retrospectively. Laboratory, clinical and hematologic parameters were compared for JAK2 V617F positive and JAK2 V617F negative patients with ET. 102 (46 %) patients were positive with the JAK2 V617F mutation. The complications were observed in 61 (28 %) patients and 38 (62 %) of them had JAK2 V617F mutation. The levels of white blood cells, neutrophil, basophil, red blood cells, hemoglobin, hematocrit, mean platelet volume, thrombocytes, eosinophil; urea, creatinine were significantly different in patients with the JAK2 V617F mutation (P < 0.05). Presence of the JAK2 V617F mutation supports the diagnosis of ET. It would be useful to investigate the JAK2 V617F mutation and the hematologic and biochemical markers at diagnosis with respect to consider the risk of developing complications and to take the precautions against these complications.Öğe In silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high-affinity PARP-1 inhibitors(Taylor & Francis Ltd, 2016) Salmas, Ramin Ekhteiari; Unlu, Ayhan; Yurtsever, Mine; Noskov, Sergei Y.; Durdagi, SerdarThe rational design of high-affinity inhibitors of poly-ADP-ribose polymerase-1 (PARP-1) is at the heart of modern anti-cancer drug design. While relevance of enzyme to DNA repair processes in cellular environment is firmly established, the structural and functional understanding of the main determinants for high-affinity ligands controlling PARP-1 activity is still lacking. The conserved active site of PARP-1 represents an ideal target for inhibitors and may offer a novel target at the treatment of breast cancer. To fill the gap in the structural knowledge, we report on the combination of molecular dynamics (MD) simulations, principal component analysis (PCA), and conformational analysis that analyzes in great details novel binding mode for a number of inhibitors at the PARP-1. While optimization of the binding affinity for original target is an important goal in the drug design, many of the promising molecules for treatment of the breast cancer are plagued by significant cardiotoxicity. One of the most common side-effects reported for a number of polymerase inhibitors is its off-target interactions with cardiac ion channels and hERG1 channel, in particular. Thus, selected candidate PARP-1 inhibitors were also screened in silico at the central cavities of hERG1 potassium ion channel.Öğe Investigation of Cholera Toxin Interaction Mechanism for StructureBased Drug Design(2022) Unlu, AyhanCholera is a disease that is developed by parasitizing the bacteria called vibrio cholera in the small intestine of people and it causes severe watery diarrhea, if it is left untreated, it can result in death. The bacteria is transmitted to the people through the digestive tract with water and nutrients, starting with vomiting and going on with severe diarrhea. A potent enterotoxin, Cholera Toxin (CT) which is secreted by vibrio cholera is largely responsible for the disease. It first emerged in India and began to spread to the world between 1827-1975. The cause of the disease, Vibrio cholerae bacteria, which has been known since ancient times with high outbreaks and high mortality rates, has less resistance to external influences and dies in 10-15 minutes at 55°C and in 1-2 minutes at boiling temperature. They are not able to resist dryness, sunlight and acids. Gastric acidity inactivates the vibrations in a short time, which protects many people from being caught in cholera. ADP-Ribosylating Toxins (ADPRT), also including cholera toxin synthesized by this bacteria, are a large and potentially fatal toxin family. They are secreted by pathogenic bacteria and inhibit the functions of human target proteins. Based on structure-based multiple sequence alignments, the ADPRT family is classified into two groups according to the Nicotinamide Adenine Dinucleotide (NAD) that binds Diphtheria Toxin (DT) and CT. DT group toxins change eukaryotic elongation factor 2 and disrupt protein synthesis in eukaryotic cells. DT, exotoxin A (ETA) and cholix toxin are among the members of this group. CT group toxins target various essential proteins in host organisms. For example, CT and temperature-varying enterotoxin target Arg on Gs-R on G protein. This leads to uncontrolled adenylate cyclase activity. Although ADPRT enzymes exhibit a variety of functions and low sequence identities, they share common structural and functional characteristics. This toxin family has the ability to catalyze NAD by using the same pathway with poly ADP-ribose polymerases. We think that being clarified as a matter of the cholera toxin structure, which is the member of this family, will play an important role in the development of many drug design studies such as being able to interfere in significant proteins structure for cancer cells and the development of various catalysis mechanisms. In this study, we investigated the three-dimensional structure of cholera toxin, which is an important member of the ADPRT family, and the interface which will interact with the other amino acids whose binding energies are higher than other amino acids which are situated in the structure (hot spot) by using theoretical and experimental methods. As a result of our theoretical and experimental studies we think that the 12 amino acid sequence of Cholera toxin, constituting the common structural region that binds to NAD in the ADP-ribosylating toxins family is the sequence of 61- STSISLRSAHLV-72.Öğe Investigation of the three-dimensional structure and interaction mechanism of poly (ADP-ribose) polymerase 4(Taylor & Francis Ltd, 2020) Unlu, Ayhan; Dinc, BircanPoly ADP-ribose polymerases (PARPs) are family of proteins that use nicotinamide adenine dinucleotide (NAD) as substrate. Seventeen putative PARP sequences were determined in the human genome. Although PARPs show a variety of functions and low sequence identities, they share common structural and functional properties. In our study, PARP1 and PARP2 and PARP4 sequences in different species were compared; it was found that active sites of PARP1 for human, rat and mouse have highly conserved sequence. Overall folding of PARP1, PARP2 and PARP4 confirms similarity in catalytic domains but can differ in substrate proteins. The three-dimensional structure of PARP4 was interacted with NAD using the molecular docking method and the interaction sites were determined. When we modeled the three-dimensional structure of PARP4 using MODELLER v9.22 algorithm and examined the interaction with Autodock v4.2 in computer environment, we observed that the enzyme is connected with a common motif similar to PARP1 and PARP2. When PARP1 and PARP2 interact with this common motif with NAD, we experimentally observed that these structures interact directly with NAD in order to undergo catalytic reactions by Thermal-Shift assay. The PARP4-NAD complex with the binding energy -26.73 kJ/mol was further used for molecular dynamics analysis. Root mean square deviation (RMSD) for all backbone atoms, electrostatic energy, van der Waals energy of PARP4-NAD complex were studied in the form of molecular dynamics trajectories to throw light on the medically important PARP family of enzymes.Öğe Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding(Taylor & Francis Inc, 2016) Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Unlu, Ayhan; Yurtsever, Mine; Durdagi, SerdarMutated form (G52E) of diphtheria toxin (DT) CRM197 is an inactive and nontoxic enzyme. Here, we provided a molecular insight using comparative molecular dynamics (MD) simulations to clarify the influence of a single point mutation on overall protein and active-site loop. Post-processing MD analysis (i.e. stability, principal component analysis, hydrogen-bond occupancy, etc.) is carried out on both wild and mutated targets to investigate and to better understand the mechanistic differences of structural and dynamical properties on an atomic scale especially at nicotinamide adenine dinucleotide (NAD) binding site when a single mutation (G52E) happens at the DT. In addition, a docking simulation is performed for wild and mutated forms. The docking scoring analysis and docking poses results revealed that mutant form is not able to properly accommodate the NAD molecule.Öğe Noncovalent Pyrene-Polyethylene Glycol Coatings of Carbon Nanotubes Achieve in Vitro Biocompatibility(AMER CHEMICAL SOC, 2018) Meran, Mehdi; Akkus, Pelin Deniz; Kurkcuoglu, Ozge; Baysak, Elif; Hizal, Gurkan; Haciosmanoglu, Ebru; Unlu, Ayhan; Karatepe, Nilgun; Guner, F. SenihaSingle-walled carbon nanotubes (SWNTs) have become increasingly exploited in biological applications, such as imaging and drug delivery. The application of SWNTs in biological settings requires the surface chemistry to remain through the low solubility in aqueous media. In this research, a facile approach for the preparation of a polyethylene glycol (PEG)-coated SWNT-based nanocarrier was reported. We focused on the effect of PEG chain length and SWNT size on the cytotoxicity of PEG coated SWNTs as a superior drug delivery nanovector. First, all-atom molecular dynamics (MD) simulations were employed to explore the stability and behavior of SWNT/pyrene-PEG (SWNT/Pyr-PEG) structures at a molecular level that is not attainable with experiments. The MD studies revealed that (i) a pi-pi stacking interactions between the pyrene bearing PEG molecules and SWNTs are maintained in bulky situations, regardless of PEG molecular weight or SWNT size; (ii) pyrene molecules diffuse over the SWNT surface without detaching; and (iii) both short and long dynamic Pyr-PEG chains have the capability of effectively coating the SWNT surface. In light of the simulations, noncovalent (pi-pi stacking) assemblies of SWNT/Pyr-PEG with different molecular weights of PEG (M-W = 2000, 5000, and 12000) were successfully fabricated and characterized. For longer PEG chains, more effective coating of SWNTs was obtained, resulting in more biocompatible SWNT/Pyr-PEG nanomaterials. The number of SWNTs coated by Pyr-PEG was highly dependent on the length of pyrene bearing PEG polymers. Moreover, the short SWNTs showed a higher amount of PEG coating with respect to the long SWNTs. Cell viability results demonstrated a dose-dependent cytotoxicity of coated SWNTs. Short SWNTs coated with longer PEG chains have low cytotoxicity to be used in in vivo studies.Öğe Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies(Taylor & Francis Inc, 2017) Salmas, Ramin Ekhteiari; Unlu, Ayhan; Bektas, Muhammet; Yurtsever, Mine; Mestanoglu, Mert; Durdagi, SerdarPoly(ADP-ribose) polymerase-1 (PARP-1) enzyme has critical roles in DNA replication repair and recombination. Thus, PARP-1 inhibitors play an important role in the cancer therapy. In the current study, we have performed combination of in silico and in vitro studies in order to discover novel inhibitors against PARP-1 target. Structure-based virtual screening was carried out for an available small molecules database. A total of 257,951 ligands from Otava database were screened at the binding pocket of PARP-1 using high-throughput virtual screening techniques. Filtered structures based on predicted binding energy results were then used in more sophisticated molecular docking simulations (i.e. Glide/standard precision, Glide/XP, induced fit docking - IFD, and quantum mechanics polarized ligand docking - QPLD). Potential high binding affinity compounds that are predicted by molecular simulations were then tested by in vitro methods. Computationally proposed compounds as PARP-1 inhibitors (Otava Compound Codes: 7111620047 and 7119980926) were confirmed by in vitro studies. In vitro results showed that compounds 7111620047 and 7119980926 have IC50 values of 0.56 and 63M against PARP-1 target, respectively. The molecular mechanism analysis, free energy perturbation calculations using long multiple molecular dynamics simulations for the discovered compounds which showed high binding affinity against PARP-1 enzyme, as well as structure-based pharmacophore development (E-pharmacophore) studies were also studied.
