Biyoinformatik ve Genetik Bölümü Koleksiyonu

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

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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: 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: 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.
Citation - WoS: 4
Citation - Scopus: 3
Drying of Polyacrylamide-Multiwalled Carbon Nanotube (mwnt) Composites With Various Mwnts Contents: a Fluorescence Study
(Walter De Gruyter Gmbh, 2013) Evingür, Gülşen Akin; Pekcan, Önder
We studied the drying of polyacrylamide (PAAm)-multiwalled carbon nanotube (MWNT) composites prepared by free radical crosslinking copolymerization in water with a steady state fluorescence technique. Composite gels were prepared at room temperature with pyranine (Py) doped as a fluorescence probe. Drying experiments were performed in air at various MWNT contents by real time monitoring of the Py fluorescence intensity (I) which increased as the drying proceeded. The Stern-Volmer equation combined with the moving boundary diffusion model was used to explain the behavior of I during drying. It was observed that the desorption coefficient (D) increased as the temperature increased. Drying energies (Delta E) were measured for the drying processes for each MWNT content gel by using fluorescence gravimetrical and volumetric methods. It is understood that Delta E values decrease by increasing MWNT content until 1 wt % MWNT and then increase above the level of this threshold value. The energy of drying is strongly correlated with the MWNT content in the composite. Delta E drops to its lowest value at which conducting cluster starts to appear.
Citation - WoS: 25
Citation - Scopus: 26
How an Inhibitor Bound To Subunit Interface Alters Triosephosphate Isomerase Dynamics
(Cell Press, 2015) Kürkçüoğlu, Zeynep; Fındık, Doğa; Akdoğan, Ebru Demet; Doruker, Pemra
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface distant from its catalytic site is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor named bt10. Within the time frame of our MD simulations we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10 which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54000 MD snapshots. Using this computationally efficient technique we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly we observed allosteric changes in the catalytic loop's dynamics flexibility and correlations as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
Citation - WoS: 17
Citation - Scopus: 16
Cation Effect on Slow Release From Alginate Beads: a Fluorescence Study
(Springer/Plenum Publishers, 2014) Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder; Evingür, Gülşen Akin
In this study spherical alginate beads containing pyranine (P-y) as a fluorescence probe were prepared by ionotropic gelation of a sodium alginate solution. The steady state fluorescence technique was used to study pyranine release from the alginate beads crosslinked with calcium barium and aluminum ions respectively. The slow release of P-y was observed with the time drive mode of the spectrophotometer at 512 nm. Fluorescence emission intensity (I-p) from P-y was monitored during the release process and the encapsulation efficiency (EE) of pyranine from the alginate beads was calculated. The Fickian Diffusion model was used to measure the release coefficients D-sl. It was seen that the slow release coefficients of pyranine from the alginate beads crosslinked with Ca2+ Ba2+ and Al3+ ions increased in the following order: D-sl (Al3+)> D-sl (Ca2+)> D-sl (Ba2+). In contrast the initial amount of pyranine and EE into the beads showed the reverse behavior.
Citation - WoS: 4
Citation - Scopus: 4
Temperature Dependence of Oxygen Diffusion Into Polymer/Carbon Nanotube Composite Films
(Wiley-Blackwell, 2012) Yargı, Önder; Uğur, Şaziye; Pekcan, Önder
This study examines the transport properties of polystyrene (PS)/multiwalled carbon nanotube (MWNT) composite films taking into consideration both MWNT composition and temperature via fluorescence technique. Three different (3 15 and 40 wt%) MWNT content films were prepared from PS/MWNT mixtures by annealing them at 170 degrees C above the glass transition temperature of PS for 10 min. The diffusivity of the PS/MWNT composite was determined by performing oxygen (O2) diffusion measurements within a temperature range of 24 to 70 degrees C for each film and pyrene (P) was used as the fluorescent probe. The diffusion coefficients (D) of oxygen were determined by the fluorescence quenching method assuming Fickian transport. Results indicated that D values are strongly dependent on both temperature and the MWNT content in the film and it was also observed that D coefficients obey Arrhenius behavior from which diffusion energies were produced and increased along with increases of MWNT content. POLYM. ENG. SCI. 2012. (C) 2011 Society of Plastics Engineers
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]
Citation - WoS: 6
Citation - Scopus: 6
Temperature Effect on the Swelling of Paam-Kappa Composites
(Wiley-Blackwell, 2012) Evingür, Gülşen Akin; Pekcan, Önder
The steady-state fluorescence (SSF) technique was used for studying swelling of disc-shaped polyacrylamide (PAAm)-kappa-carrageenan (kappa C) composites which were prepared by free-radical crosslinking copolymerization at 80 degrees C. Pyranine was introduced as a fluorescence probe during polymerization. Swelling experiments were performed in water at various temperatures by real-time monitoring of the pyranine (Py) fluorescence intensity I which decreased as swelling proceeded. Stern-Volmer equation is modified for low quenching efficiencies to interpret the behavior of Py intensity during the swelling of PAAm-kappa C composites. The Li-Tanaka equation was used to determine the swelling time constants tau(1) and cooperative diffusion coefficients D(0) from fluorescence intensity weight and volume variations of the composites at various temperatures. It was observed that tau(1) first decreased up to 40 degrees C and then increased
The Association of Gvhd With Hla Dr Alleles, Ifn-Gamma, Tgf-Beta, and Mbl2 Gene Polymorphism
(Wiley, 2019) Oğuz, Rusdu; Çiftçi, Hayriye Şentürk; Gökçe, Muge; Öğret, Yeliz; Karadeniz, Sedat Tanju; Pehlivan, Sacide; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 4
Citation - Scopus: 4
Thermal Rearrangement of 2-Acetoxy Theoretical Elucidation of the Mechanism
(Elsevier Science, 2007) Erdem, Safiye Sağ; Uyar, Fahriye; Karahan, Özlem; Yelekçi, Kemal
Bicyclohexenes are believed to be the immediate precursors of aromatic compounds. As a part of the exploratory study of thermal aromatization reactions 266-trimethylbicyclo[3.1.0]hexan-2-ol and its ester derivative 2-acetoxy-266-trimethylbicyclo[3.1.0]hexane were synthesized. Pyrolysis of 2-acetoxy-266-trimethylbicyclo[3.1.0]hexane at 350 degrees C gave 133-trimethyl-14-cyclohexadiene instead of the expected product 266-trimethylbicyclo[3.1.0]hex-2-ene. Computational methods such as PM3 31G]* were employed in order to elucidate the mechanism of this reaction. The Gibbs free energy of activation and the reaction energy were calculated for the proposed polar and biradical mechanisms. The results showed that a two-step mechanism is plausible at 350 degrees C in which the expected product 266-trimetliylbicyclo[3.1.0]hex2-ene is the intermediate. The first step is the 12-elimination of the ester leading to 266-trimethylbicyclo [3. 1. 0]hex-2-ene. The second step is the sigmatropic rearrangement of 266-trimethylbicyclo[3.1.0]hex-2-ene via concerted homodienyl 15-hydrogen shift which is also the rate-determining step. UB3LYP/6-31G* calculations reveal that the cyclopropyl moiety of bicyclo[3.1.0]hex-2-ene can undergo homolytic bond cleavage to give an allylically stabilized biradical intermediate. However the formation of 14-cyclohexadiene from such an intermediate through a biradical transition state involving 12-hydrogen migration does not seem to be plausible. (c) 2007 Elsevier B.V. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 7
Molecular Docking Study Based on Pharmacophore Modeling for Novel Phosphodiesteraseiv Inhibitors
(Wiley-VCH Verlag GmbH, 2012) Cifci, Gulsah; Aviyente, Viktorya; Akten, Ebru Demet
In this study pharmacophore modelling was carried out for novel PhosphodiesteraseIV (PDEIV) inhibitors. A pharmacophore-based virtual screening which resulted in 1959 hit compounds was performed with six chemical databases. The pharmacophore screening was proven to be successful in discriminating active and inactive inhibitors using a set of compounds with known activity obtained from ChEMBL database. Furthermore the Lipinskis rule of five was applied for physicochemical filtering of the hit molecules and this yielded 1840 compounds. Three docking software tools AutoDock 4.0 AutoDock Vina and Gold v5.1 were used for the docking process. All 1840 compounds and the known selective inhibitor rolipram were docked into the active site of the target protein. A total of 234 compounds with all three scoring values higher than those of rolipram were determined with the three docking tools. The interaction maps of 14 potent inhibitors complexed with PDEIV B and D isoforms have been analyzed and seven key residues (Asn 395 Gln 443 Tyr 233 Ile 410 Phe 446 Asp 392 Thr 407) were found to interact with more than 80?% of the potent inhibitors. For each one of the 234 hit compounds using the bound conformation with the highest AutoDock score the interacting residues were determined. 117 out of 234 compounds are found to interact with at least five of the seven key residues and these were selected for further evaluation. The conformation with the highest AutoDock score for each 117 compounds were rescored using the DSX scoring function. This yielded a total of 101 compounds with better score values than the natural ligand rolipram. For ADME/TOX calculations the FAF-Drugs2 server was used and 32 out of 101 compounds were found to be non-toxic.
Citation - WoS: 6
Citation - Scopus: 6
Study of Thermal Phase Transitions in Iota Carrageenan Gels Via Fluorescence Technique
(Wiley-Blackwell, 2011) Tari, Ozlem; Kara, Selim; Pekcan, Önder
The effect of carrageenan concentration on thermal phase transitions of the iota carrageenan gels was investigated by using fluorescence technique. During heating and cooling processes scattered light I(sc) and fluorescence intensity I(p) were monitored against temperature to investigate phase transitions. Transition temperatures from the derivative of the transition paths were determined. Two regions were observed during the heating and cooling processes. At the first step of the heating dimers were converted into double helix by undergoing dimer to double helix (d-h) transition. At the higher temperature region double helix to coil (h-c) transition took place. During the cooling process these transitions are arranged in the order of coil to double helix (c-h) and double helix to dimer (h-d). A hysteresis was observed between (h-d) and (d-h) transitions. The critical gel fraction exponents beta were found to be independent of the system by indicating that they all fall into the same universality class. (C) 2011 Wiley Periodicals Inc. J Appl Polym Sci 121: 2652-2661 2011
Citation - WoS: 11
Citation - Scopus: 14
Effect of Multiwalled Carbon Nanotube (mwnt) on the Behavior of Swelling of Polyacrylamide-Mwnt Composites
(Sage Publications Ltd, 2014) Evingür, Gülşen Akin; Pekcan, Önder
The purpose of this paper is to discuss the role of multiwalled carbon nanotube in the swelling of polyacrylamide-multiwalled carbon nanotube composites. Swelling experiments were performed in water at various temperatures by real-time monitoring of the decrease in pyranine (Py) and emission light intensity (I-em). The Stern-Volmer equation is modified for low-quenching efficiencies to interpret the behavior of pyranine intensity during the swelling of polyacrylamide-multiwalled carbon nanotube composites. The Li-Tanaka equation was used to determine the swelling time constants tau and cooperative diffusion coefficients D from fluorescence intensity weight and volume variations of the composite at various temperatures. It was observed that when tau decreased naturally D increased by increasing temperatures.
Collective Enhancement of Nuclear State Densities by the Shell Model Monte Carlo Approach
(IOP Publishing Ltd, 2015) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
The shell model Monte Carlo (SMMC) approach allows for the microscopic calculation of statistical and collective properties of heavy nuclei using the framework of the configuration-interaction shell model in very large model spaces. We present recent applications of the SMMC method to the calculation of state densities and their collective enhancement factors in rare-earth nuclei.

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