Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/46

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Now showing 1 - 20 of 203

Citation - WoS: 17
Citation - Scopus: 20
In Silico Design of Novel and Highly Selective Lysine-Specific Histone Demethylase Inhibitors
(Scientific Technical Research Council Turkey-Tubitak, 2011) Akdoğan, Ebru Demet; Erman, Burak; Yelekçi, Kemal
Histone lysine-specific demethylase (LSD1) is involved in a wide range of epigenetic processes and plays important roles in gene silencing DNA transcription DNA replication DNA repair and heterochromatin formation. Its active site shows a resemblance to those of 2 homologous enzymes monamine oxidase A and B (MAO-A and MAO-B.) In the present work starting from suitable scaffolds and generating thousands of structures from them 10 potential inhibitors were obtained with structural and physicochemical properties selectively suitable for inhibiting LSD1. iLib Diverse software was used to generate the diverse structures and 3 docking tools CDOCKER GOLD and AutoDock were used to find the most probable potential inhibitor based on its binding affinity. The dispositions of the candidate molecules within the organism were checked by ADMET_PSA_2D (polar surface area) versus ADMET_AlogP98 (the logarithm of the partition coefficient between n-octanol and water) and their suitability is discussed. The LSD1 inhibition activities of the candidates were compared with the properties of trans-2-phenylcyclopropylamine (tranylcypromine) and 2-(4-methoxy-phenyl) cyclopropylamine which are the 2 known inhibitors of LSD1.
Citation - WoS: 145
Citation - Scopus: 145
Psychological Correlates of Covid-19 Conspiracy Beliefs and Preventive Measures: Evidence From Turkey
(Springer, 2020) Alper, Sinan; Bayrak, Fatih; Yılmaz, Onurcan
COVID-19 pandemic has led to popular conspiracy theories regarding its origins and widespread concern over the level of compliance with preventive measures. In the current preregistered research, we recruited 1088 Turkish participants and investigated (a) individual differences associated with COVID-19 conspiracy beliefs; (2) whether such conspiracy beliefs are related to the level of preventive measures; and (3) other individual differences that might be related to the preventive measures. Higher faith in intuition, uncertainty avoidance, impulsivity, generic conspiracy beliefs, religiosity, and right-wing ideology, and a lower level of cognitive reflection were associated with a higher level of belief in COVID-19 conspiracy theories. There was no association between COVID-19 conspiracy beliefs and preventive measures while perceived risk was positively and impulsivity negatively correlated with preventive measures. We discuss the implications and directions for future research.
Citation - WoS: 7
Citation - Scopus: 6
Investigation of Pst-Mwcnt Concentration on Epoxyacrylate Photopolymerization and Conductivity of Polymer Films
(Elsevier Science SA, 2013) Doğruyol, Zekeriya; Temel, Gökhan; Doğruyol, Sevnur Keskin; Pekcan, Önder; Arsu, Nergis
Photopolymerization kinetics and conductivity changes of epoxyacrylate composites for various loading modified PSt-MWCNT weight fractions changing from 0.0025 to 0.2 wt.% were evaluated by performing photo differential scanning calorimetry (photo-DSC) and four point conductivity measurements. 0.2% PSt-MWCNT additive polymeric films had their electrical conductivity boosted by 6% more than non-additive polymeric films. (C) 2012 Elsevier B.V. All rights reserved.
Citation - WoS: 1
Citation - Scopus: 1
The Role of Pyranine in Characterization of Paam-Kappa C Composites by Using Fluorescence Technique
(Springer/Plenum Publishers, 2011) Evingür, Gülşen Akın; Pekcan, Önder
Polyacrylamide (PAAm) doped by kappa-carrageenan (kappa C) gels were prepared with various amounts of kappa C varying in the range between 0 wt.% and 3 wt.%. Steady-state fluorescence (SSF) technique was employed for studying sol-gel transition and swelling of PAAm-kappa C composite gels which were prepared by free-radical crosslinking copolymerization. Pyranine was introduced as a fluorescence probe. Pyranine molecules start to bind to acrylamide polymer chains upon the initiation of the polymerization thus the spectra of the bonded pyranines shift to the shorter wavelengths. Fluorescence spectra from the bonded pyranines allow one to monitor the sol-gel transition and to test the universality of the sol-gel transition as a function of some kinetic parameters like polymer concentration. Observations around the gel point t (c) for PAAm-kappa C composite gels showed that the gel fraction exponent beta obeyed the percolation result for low kappa C (< 2.0 wt. %) however classical results were produced at higher kappa C (> 2.0 wt.%). On the other hand fluorescence intensity of pyranine was measured during in situ swelling process at various amounts of kappa C and it was observed that fluorescence intensity values decreased as swelling is proceeded. Li-Tanaka equation was used to determine the swelling time constants tau and cooperative diffusion coefficients D.
Citation - WoS: 4
Conductivity Percolation of Carbon Nanotubes in Polyacrylamide Gels
(Intech Europe, 2011) Pekcan, Önder; Evingür, Gülşen Akın
[Abstract Not Available]
Citation - WoS: 13
Citation - Scopus: 13
In Situ Steady State Fluorescence (ssf) Technique To Study Drying of Paam Hydrogels Made of Various Cross-Linker Contents
(Elsevier Science, 2009) Evingür, Gülşen Akın; Aktas, Demet Kaya; Pekcan, Önder
Drying experiments of polyacrylamide (PAAm) gels were performed using steady-state fluorescence (SSF) spectrometer. Pyranine (P) was introduced as a fluorescence probe and intensity of P from various crosslinker content gel samples was monitored. It was observed that the intensity of P increased during the in situ drying processes. Gravimetrical and volumetric experiments were also performed. An empirical model was derived and introduced to determine the desorption coefficient D of water molecules from the drying PAAm gels. It is observed that D increased as the cross-linker content was increased. (c) 2008 Elsevier B.V. All rights reserved.
Citation - WoS: 6
Citation - Scopus: 7
Drying of Polyacrylamide Composite Gels Formed With Various Kappa- Carrageenan Content
(Springer/Plenum Publishers, 2011) Evingür, Gülşen Akın; Pekcan, Önder
Drying of polyacrylamide (PAAm)-kappa-carrageenan (kappa C) composite gels were monitored by using steady-state fluorescence technique. Disc shaped gels were formed from acrylamide (AAm) and N N'- methylenebisacrylamide(Bis) with various kappa- carrageenan (kappa C) contents by free radical crosslinking copolymerization in water. Pyranine (P) was doped as a fluorescence probe and scattered light I (sc) and fluorescence intensities I were monitored during drying of these gels. It is observed that fluorescence intensity of pyranine increased as drying time is increased for all samples. The increase in I was modeled using Stern- Volmer equation and diffusion with moving boundary. It is found that desorption coefficient D decreased as kappa C contents were increased. Supporting gravimetrical and volumetric experiments were also carried out during drying of PAAm- kappa C composite gels.
Citation - WoS: 54
Citation - Scopus: 66
Synthesis Molecular Modeling in Vivo Study and Anticancer Activity of 124-Triazole Containing Hydrazide-Hydrazones Derived From (s)-Naproxen
(Wiley-VCH Verlag GmbH, 2019) Han, Muhammed İhsan; Bekçi, Hatice; Uba, Abdullahi İbrahim; Yıldırım, Yeliz; Karasulu, Ercüment; Cumaoğlu, Ahmet; Karasulu, Hatice Y.; Yelekçi, Kemal; Yılmaz, Ozguer; Küçükgüzel, Şükriye Güniz
A new series of 124-triazole containing hydrazide-hydrazones derived from (S)-naproxen (7a-m) was synthesized in this study. The structures of these compounds were characterized by spectral (Fourier-transform infrared spectroscopy H-1-nuclear magnetic resonance (NMR) C-13-NMR and high-resolution electron ionization mass spectrometry) methods. Furthermore molecular modeling of these compounds was studied on human methionine aminopeptidase-2. All synthesized compounds were screened for anticancer activity against three prostate cancer cell lines (PC3 DU-145 and LNCaP) using the 3-(45-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium colorimetric method. Compound 7a showed the best activity against the PC3 DU-145 and LNCaP cancer cell lines with IC50 values of 26.0 34.5 and 48.8 mu M respectively. Compounds 7b 7k and 7m showed anticancer activity against cancer cell lines PC3 and DU-145 with IC50 values of 43.0 36.5 29.3 mu M and 49.8 49.1 31.6 mu M respectively. Compounds 7f and 7g showed anticancer activity against PC3 cells with IC50 values of 43.4 and 34.5 mu M respectively. To assess the biodistribution in mice of IRDye800 dye-labeled compound 7a or 100 mu M of free dye was injected intravenously into the mice's tail. In vivo images were taken with in vivo imaging system spectrum device at 60 120 180 240 300 and 360 min after injection. At the end of 360 min ex vivo studies were carried out to determine in which organs the dye was accumulated in the urogenital system. Ex vivo studies showed that the accumulation of compound 7a in the prostate is greater than that of the free dye and it is concluded that compound 7a may be promising for the treatment of prostate cancer..
Citation - WoS: 10
Citation - Scopus: 10
Ligand-Binding Affinity of Alternative Conformers of Human Beta(2)-Adrenergic Receptor in the Presence of Intracellular Loop 3 (icl3) and Their Potential Use in Virtual Screening Studies
(Wiley, 2019) Dilcan, Gonca; Doruker, Pemra; Akten, Ebru Demet
This study investigates the structural distinctiveness of orthosteric ligand-binding sites of several human beta(2) adrenergic receptor (beta(2)-AR) conformations that have been obtained from a set of independent molecular dynamics (MD) simulations in the presence of intracellular loop 3 (ICL3). A docking protocol was established in order to classify each receptor conformation via its binding affinity to selected ligands with known efficacy. This work's main goal was to reveal many subtle features of the ligand-binding site presenting alternative conformations which might be considered as either active- or inactive-like but mostly specific for that ligand. Agonists inverse agonists and antagonists were docked to each MD conformer with distinct binding pockets using different docking tools and scoring functions. Mostly favored receptor conformation persistently observed in all docking/scoring evaluations was classified as active or inactive based on the type of ligand's biological effect. Classified MD conformers were further tested for their ability to discriminate agonists from inverse agonists/antagonists and several conformers were proposed as important targets to be used in virtual screening experiments that were often limited to a single X-ray structure.
Citation - WoS: 3
Citation - Scopus: 3
The Neural Gamma(2)alpha(1)beta(2)alpha(1)beta(2) Gamma Amino Butyric Acid Ion Channel Receptor: Structural Analysis of the Effects of the Ivermectin Molecule and Disulfide Bridges
(Springer, 2018) Ayan, Meral; Eşsiz, Şebnem
While similar to 30% of the human genome encodes membrane proteins only a handful of structures of membrane proteins have been resolved to high resolution. Here we studied the structure of a member of the Cys-loop ligand gated ion channel protein superfamily of receptors human type A gamma(2)alpha(1)beta(2)alpha(1)beta(2) gamma amino butyric acid receptor complex in a lipid bilayer environment. Studying the correlation between the structure and function of the gamma amino butyric acid receptor may enhance our understanding of the molecular basis of ion channel dysfunctions linked with epilepsy ataxia migraine schizophrenia and other neurodegenerative diseases. The structure of human gamma(2)alpha(1)beta(2)alpha(1)beta(2) has been modeled based on the X-ray structure of the Caenorhabditis elegans glutamate-gated chloride channel via homology modeling. The template provided the first inhibitory channel structure for the Cys-loop superfamily of ligand-gated ion channels. The only available template structure before this glutamate-gated chloride channel was a cation selective channel which had very low sequence identity with gamma aminobutyric acid receptor. Here our aim was to study the effect of structural corrections originating from modeling on a more reliable template structure. The homology model was analyzed for structural properties via a 100 ns molecular dynamics (MD) study. Due to the structural shifts and the removal of an open channel potentiator molecule ivermectin from the template structure helical packing changes were observed in the transmembrane segment. Namely removal of ivermectin molecule caused a closure around the Leu 9 position along the ion channel. In terms of the structural shifts there are three potential disulfide bridges between the M1 and M3 helices of the gamma(2) and 2 alpha(1) subunits in the model. The effect of these disulfide bridges was investigated via monitoring the differences in root mean square fluctuations (RMSF) of individual amino acids and principal component analysis of the MD trajectory of the two homology models-one with the disulfide bridge and one with protonated Cys residues. In all subunit types RMSF of the transmembrane domain helices are reduced in the presence of disulfide bridges. Additionally loop A loop F and loop C fluctuations were affected in the extracellular domain. In cross-correlation analysis of the trajectory the two model structures displayed different coupling in between the M2-M3 linker region protruding from the membrane and the beta 1-beta 2/D loop and cys-loop regions in the extracellular domain. Correlations of the C loop which collapses directly over the bound ligand molecule were also affected by differences in the packing of transmembrane helices. Finally more localized correlations were observed in the transmembrane helices when disulfide bridges were present in the model. The differences observed in this study suggest that dynamic coupling at the interface of extracellular and ion channel domains differs from the coupling introduced by disulfide bridges in the transmembrane region. We hope that this hypothesis will be tested experimentally in the near future.
Citation - Scopus: 23
The Drosophila Fragile X Mental Retardation Protein Participates in the Pirna Pathway
(Company of Biologists Ltd, 2015) Bozzetti, Maria Pia; Specchia, Valeria; Cattenoz, Pierre B.; Laneve, Pietro; Geusa, Annamaria; Şahin, H. Bahar; Di Tommaso, Silvia D.; Friscini, Antonella; Massari, Serafina; Diebold, Celine; Giangrande, Angela
RNA metabolism controls multiple biological processes and a specific class of small RNAs called piRNAs act as genome guardians by silencing the expression of transposons and repetitive sequences in the gonads. Defects in the piRNA pathway affect genome integrity and fertility. The possible implications in physiopathological mechanisms of human diseases have made the piRNA pathway the object of intense investigation and recent work suggests that there is a role for this pathway in somatic processes including synaptic plasticity. The RNA-binding fragile X mental retardation protein (FMRP also known as FMR1) controls translation and its loss triggers the most frequent syndromic form of mental retardation as well as gonadal defects in humans. Here we demonstrate for the first time that germline as well as somatic expression of Drosophila Fmr1 (denoted dFmr1) the Drosophila ortholog of FMRP are necessary in a pathway mediated by piRNAs. Moreover dFmr1 interacts genetically and biochemically with Aubergine an Argonaute protein and a key player in this pathway. Our data provide novel perspectives for understanding the phenotypes observed in Fragile X patients and support the view that piRNAs might be at work in the nervous system. © 2015.
Citation - WoS: 8
Citation - Scopus: 9
Human Dopamine Transporter: the First Implementation of a Combined in Silico/In Vitro Approach Revealing the Substrate and Inhibitor Specificities
(Taylor & Francis Inc, 2019) Djikic, Teodora; Marti, Yasmina; Spyrakis, Francesca; Lau, Thorsten; Benedetti, Paolo; Davey, Gavin; Schloss, Patrick; Yelekçi, Kemal
Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the human dopamine transporter (hDAT) could represent a viable strategy for establishing selective neuroprotection. Molecules able to increase the bioactive amount of extracellular dopamine thereby enhancing and compensating a loss of dopaminergic neurotransmission and to exert neuroprotective response because of their accumulation in the cytoplasm are required. By means of homology modeling molecular docking and molecular dynamics simulations we have generated 3D structure models of hDAT in complex with substrate and inhibitors. Our results clearly reveal differences in binding affinity of these compounds to the hDAT in the open and closed conformations critical for future drug design. The established in silico approach allowed the identification of promising substrate compounds that were subsequently analyzed for their efficiency in inhibiting hDAT-dependent fluorescent substrate uptake through in vitro live cell imaging experiments. Taken together our work presents the first implementation of a combined in silico/in vitro approach enabling the selection of promising dopaminergic neuron-specific substrates.
Citation - WoS: 33
Citation - Scopus: 33
Cis-Cyclopropylamines as Mechanism-Based Inhibitors of Monoamine Oxidases
(Wiley-Blackwell, 2015) Malcomson, Thomas; Yelekçi, Kemal; Borrello, Maria Teresa; Ganesan, A.; Semina, Elena; De Kimpe, Norbert; Mangelinckx, Sven; Ramsay, Rona R.
Cyclopropylamines inhibitors of monoamine oxidases (MAO) and lysine-specific demethylase (LSD1) provide a useful structural scaffold for the design of mechanism-based inhibitors for treatment of depression and cancer. For new compounds with the less common cis relationship and with an alkoxy substituent at the 2-position of the cyclopropyl ring the apparent affinity determined from docking experiments revealed little difference between the enantiomers. Using the racemate kinetic parameters for the reversible and irreversible inhibition of MAO were determined. No inhibition of LSD1 was observed. For reversible inhibition most compounds gave high IC50 values with MAO A but sub-micromolar values with MAO B. After pre-incubation of the cyclopropylamine with the enzyme the inhibition was irreversible for both MAOA and MAOB and the activity was not restored by dilution. Spectral changes during inactivation of MAOA included bleaching at 456nm and an increased absorbance at 400nm consistent with flavin modification. These derivatives are MAOB-selective irreversible inhibitors that do not show inhibition of LSD1. The best inhibitor was cis-N-benzyl-2-methoxycyclopropylamine with an IC50 of 5nm for MAOB and 170nm for MAOA after 30min pre-incubation. This cis-cyclopropylamine is over 20-fold more effective than tranylcypromine so may be studied as a lead for selective inhibitors of MAOB that do not inhibit LSD1.
Citation - WoS: 1
Citation - Scopus: 1
Evaluation of the Fractal Dimension of Polyacrylamide During Gelation and Swelling
(Elsevier, 2021) Arda, Ertan; Kara, Selim; Pekcan, Önder; Gülşen, Akın-Evingür
[Abstract Not Available]
Citation - WoS: 4
Citation - Scopus: 6
Oxygen Diffusion Into Polymer-Clay Composite Films as a Function of Clay Content and Temperature
(Wiley-VCH Verlag GmbH, 2009) Uğur, Şaziye; Yargı, Önder; Elaissari, Abdelhamid; Pekcan, Önder
A simple fluorescence technique is proposed for the measurement of the diffusion coefficient of oxygen into polystyrene-clay composite films as a function of clay content and temperature. The composite films were prepared from a mixture of surfactant-free pyrene-labeled polystyrene latexes and modified Na-montmorillonite clay of various compositions at room temperature. Diffusion measurements were performed with films at room temperature for seven different clay contents (0 5 10 20 30 50 and 60 wt.%). The diffusion coefficients of oxygen increased from 7.4 x 10(-10) to 26.9 x 10(-10) cm(2)s(-1) with increasing clay content. On the other hand diffusion measurements were performed over a temperature range Of 25-70 degrees C for 0 5 and 20 wt.% clay content films. The calculated diffusion activation energies decreased from 2.44 to 0.44 kcal/mol with increasing clay content. No clay content and temperature effects were observed on quenching rate constant and mutual diffusion coefficient values. The results showed that the diffusion coefficients are strongly dependent on both the temperature and clay content in the film.
Citation - WoS: 51
Citation - Scopus: 55
Crossover From Vibrational To Rotational Collectivity in Heavy Nuclei in the Shell-Model Monte Carlo Approach
(Amer Physical Soc., 2013) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
Heavy nuclei exhibit a crossover from vibrational to rotational collectivity as the number of neutrons or protons increases from shell closure towards midshell but the microscopic description of this crossover has been a major challenge. We apply the shell model Monte Carlo approach to families of even-even samarium and neodymium isotopes and identify a microscopic signature of the crossover from vibrational to rotational collectivity in the low-temperature behavior of < J(2)>(T) where J is the total spin and T is the temperature. This signature agrees well with its values extracted from experimental data. We also calculate the state densities of these nuclei and find them to be in very good agreement with experimental data. Finally we define a collective enhancement factor from the ratio of the total state density to the intrinsic state density as calculated in the finite-temperature Hartree-Fock-Bogoliubov approximation. The decay of this enhancement factor with excitation energy is found to correlate with the pairing and shape phase transitions in these nuclei. DOI: 10.1103/PhysRevLett.110.042502
Citation - WoS: 13
Citation - Scopus: 14
Superelastic Percolation Network of Polyacrylamide (paam)-Kappa Carrageenan (kappa C) Composite
(Springer, 2013) Evingür, Gülşen Akin; Pekcan, Önder
The elasticity of the polyacrylamide (PAAm)-kappa carrageenan (kappa C) composite was determined as a function of (w/v-%) kappa C content at 40 A degrees C. The gel composites studied contained various percentages (w/v-%) of kappa C. The elasticity of the swollen PAAm-kappa C composite was characterized by using the tensile testing technique. This study investigated the elasticity and the percolation threshold of PAAm-kappa C composite as a function of kappa C content. It is understood that the compressive elastic modulus decreases up to 1 (w/v-%) of kappa C and then increases at contents above 1(w/v-%) of kappa C. The critical exponent of elasticity y was determined between 1 and 1.6 (w/v-%) of kappa C and found to be 0.68. The observed elastic percolation threshold is consistent with the suggested values of the superelastic percolation network.
Design and Synthesis of Novel 2-Pyrazoline Analogues and Their Hmao Inhibitory Activities
(Wiley-Blackwell, 2015) Uçar, Gülberk; Evranos-Aksoz, Begum; Yabanoglu-Çiftçi, Samiye; Yelekçi, Kemal
[Abstract Not Available]
Drying process in vapor swollen heterogels
(Springer, 2010) Erdogan, Matem; Pekcan, Önder
Disk-shaped heterogels were prepared by combining methyl methacrylate (MMA) and styrene (S) with ethylene glycol dimethacrylate (EGDM) as a crosslinker agent in the presence of 22'-azobisisobutyronitrile (AIBN). Swelling experiments were performed under chloroform vapor and the swollen gels are then allowed to dry under room temperature. Gravimetric technique was used to study drying processes. It is observed that two different regimes are present in the drying processes of these heterogels. Fickian diffusion model was used to determine desorption coefficients for each drying step in both regimes. Desorption coefficients D (d) of heterogels were found to be strongly correlated with the mixture composition of polymeric materials in the heterogel system for both regimes. Heterogels with high S content dry much slower than the heterogels with low S content.
Citation - WoS: 8
Citation - Scopus: 8
Elastic Properties of a Swollen Paam-Nipa Copolymer With Various Nipa Contents
(Taylor & Francis, 2014) Evingür, Gülşen Akin; Pekcan, Önder
Copolymer based on cross-linked polyacrylamide (PAAm) having N-isopropylacrylamide (NIPA) was prepared and their elastic properties were studied as a function of NIPA contents. NIPA content dependency of the shear modulus S of the PAAm-NIPA copolymers due to volume phase transition was measured using tensile testing technique at 30 degrees C. It was observed that its shear modulus and toughness were found to be strongly dependent on NIPA content. It is understood that the shear modulus was found to increase with NIPA contents keeping constant temperature at 30 degrees C. Elastic properties of the PAAm-NIPA copolymers show compositional dependence.

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