Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://gcris.khas.edu.tr/handle/20.500.12469/46

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Citation - WoS: 58
Citation - Scopus: 57
Docking Studies on Monoamine Oxidase-B Inhibitors: Estimation of Inhibition Constants (k-I) of a Series of Experimentally Tested Compounds
(Pergamon-Elsevier Science Ltd, 2005) Toprakçı, Mustafa; Yelekçi, Kemal; Yelekçi, Kemal; Molecular Biology and Genetics
Monoamine oxidase (EC1.4.3.4
Citation - Scopus: 0
Atomic Collisions and Free Lepton Pair Production
(2005) Güçlü, Mehmet Cem; Yılmaz, Melek
In this work we have calculated the total cross sections of electron-positron pair production for the collisions of fully stripped gold ions for various energies. We have also compared our calculation with other methods.
Citation - WoS: 3
Citation - Scopus: 2
Coulomb Corrections in the Lepton-Pair Production in Ultrarelativistic Nuclear Collisions
(Amer Physical Soc., 2005) Güçlu, Mehmet C.; Kovankaya, G.; Yılmaz, Melek
We solve the perturbative electron-positron pair production exactly by calculating the second-order Feynman diagrams. We compare our result with Born methods that include Coulomb corrections. We find that a small-momentum approximation is not adequate to obtain exact Coulomb corrections and higher-order terms should also be included. We also compare the impact parameter dependence cross sections.
Citation - WoS: 0
Medi 333-Histone Deacetylase Inhibition Activity of Resveratrol and Its Analogs
(Amer Chemical Soc, 2007) Dayangac-Erden, Didem; Yelekçi, Kemal; Ayhan, Peruze; Bora, Gamze; Yelekçi, Kemal; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat; Molecular Biology and Genetics
[Abstract Not Available]
Citation - WoS: 0
Comp 297-Experimental and Molecular Docking Simulation Studies of Histone Deacetylases (hdacs) Enzyme Inhibitors
(Amer Chemical Soc, 2007) Yelekçi, Kemal; Yelekçi, Kemal; Bora, Gamze; Dayangaç-Erden, Didem; Ayhan, Peruze; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat; Molecular Biology and Genetics
[Abstract Not Available]
Citation - WoS: 0
Thermal Rearrangement of 2-Acetoxy Trimethylbicyclo[3.1.0]hexane: Theoretical Elucidation of the Mechanism
(Amer Chemical Soc, 2007) Yelekçi, Kemal; Yelekçi, Kemal; Erdem, Safiye Sağ; Molecular Biology and Genetics
[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; Yelekçi, Kemal; Uyar, Fahriye; Karahan, Özlem; Yelekçi, Kemal; Molecular Biology and Genetics
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: 10
Citation - Scopus: 10
Universality in Gelation of Epoxy Acrylate With Various Photoinitiators: a Photo Differential Scanning Calorimetric Study
(Taylor & Francis Ltd, 2008) Doğruyol, Zekeriya; Pekcan, Mehmet Önder; Karasu, Feyza; Balta, Demet Karaca; Arsu, Nergis; Pekcan, Önder; Molecular Biology and Genetics
Photo-differential scanning calorimetric (Photo-DSC) technique was used to study the gelation of P-3038 (epoxy acrylate (EA) 75% and tripropyleneglycoldiacrylate (TPGDA) 25%) in the presence of various thioxanthone-based initiators namely thioxanthone (TX) 5-thia-naphtacene-12-one (TX-NP) 2-(carboxymethoxy) thioxanthone (TX-OCH(2)COOH) 2-thioxanthone-thioacetic acid (TX-SCH(2)COOH) and 2-mercaptothioxanthone (TX-SH). Photopolymerization reactions were performed under identical conditions of temperature initiator concentration and UV light intensity. Photo-DSC technique allowed us to monitor the gelation without disturbing the system mechanically and to test the universality of the gelation as a function of some kinetic parameters like initiator concentration. During gelation it was observed that all conversion curves present a good sigmoidal behavior by predicting to employ percolation model. Observations around the glass transition point t(g) shows that the gel fraction exponents beta obeyed the percolation picture. On the other hand t(g) was found to be much higher for the crosslinked networks obtained with TX-OCH(2)COOH and TX-SCH(2)COOH initiators than those with the other initiators.
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; Pekcan, Mehmet Önder; Aktas, Demet Kaya; Pekcan, Önder; Molecular Biology and Genetics
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: 3
Citation - Scopus: 5
Oxygen Diffusion Into Polymer-Clay Composite Films as a Function of Clay Content and Temperature
(Wiley-VCH Verlag GmbH, 2009) Uğur, Şaziye; Pekcan, Mehmet Önder; Yargı, Önder; Elaissari, Abdelhamid; Pekcan, Önder; Molecular Biology and Genetics
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: 153
Citation - Scopus: 169
Molecular Modifications on Carboxylic Acid Derivatives as Potent Histone Deacetylase Inhibitors: Activity and Docking Studies
(Pergamon-Elsevier Science Ltd, 2009) Bora-Tatar, Gamze; Yelekçi, Kemal; Dayangac-Erden, Didem; Demir, Ayhan S.; Dalkara, Sevim; Yelekçi, Kemal; Erdem-Yurter, Hayat; Molecular Biology and Genetics
In the light of known HDAC inhibitors 33 carboxylic acid derivatives were tested to understand the structural requirements for HDAC inhibition activity. Several modifications were applied to develop the structure-activity relationships of carboxylic acid HDAC inhibitors. HDAC inhibition activities were investigated in vitro by using HeLa nuclear extract in a fluorimetric assay. Molecular docking was also carried out for the human HDAC8 enzyme in order to predict inhibition activity and the 3D poses of inhibitor-enzyme complexes. Of these compounds caffeic acid derivatives such as chlorogenic acid and curcumin were found to be highly potent compared to sodium butyrate which is a well-known HDAC inhibitor. (C) 2009 Elsevier Ltd. All rights reserved.
Citation - WoS: 39
Citation - Scopus: 41
A Docking Study Using Atomistic Conformers Generated Via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex
(Taylor & Francis Inc, 2009) Akten, Ebru Demet; Akdoğan, Ebru Demet; Cansu, Sertan; Doruker, Pemra; Molecular Biology and Genetics
Anisotropic network model is used to generate a set of distinct conformations for cylophilin A (CypA). The native structure is deformed to different extents along each of the lowest-frequency modes (first 7 modes) both in negative and positive directions. Each node of the elastic network represents either a single atom in the high-resolution model or a single residue in the low-resolution model. Realistic conformations with energies close to or lower than the crystal structure and with satisfactory internal geometry are recovered by energy minimization using implicit solvation model. These conformations are then used for ensemble docking to the ligand cyclosporin A for both a further test of accuracy of generated conformers and exploration of different binding modes. Higher number of correctly docked ligands are obtained for conformations with low deformation factors as a result of lower root mean square distances with respect to crystal structure. Yet Surprisingly the lowest binding energy is obtained for one of the highly deformed conformations as a result of its special contact with arginine side chain oriented towards binding site. Considering the fact that the cyclic ligand's backbone and protein's side chains are held rigid during docking the conformers generated by high- and low-resolution elastic network models are almost equally successful in providing the correct binding mode. The shape of the binding pocket that incorporates crucial interaction sites for hydrogen bond formation is found to be another important determining factor for the success of the dock. Also the small backbone variations of a few angstrom ngstroms in magnitude at the loop regions surrounding the binding pocket can cause amino acids' side chains to be displaced by magnitudes of up to 10 angstrom and therefore have a strong influence on the efficiency of the conformational search during docking.
Citation - WoS: 46
Citation - Scopus: 46
Histone Deacetylase Inhibition Activity and Molecular Docking of (e )-Resveratrol: Its Therapeutic Potential in Spinal Muscular Atrophy
(Wiley, 2009) Dayangac-Erden, Didem; Yelekçi, Kemal; Bora, Gamze; Ayhan, Peruze; Kocaefe, Çetin; Dalkara, Sevim; Yelekçi, Kemal; Demir, Ayhan S.; Erdem-Yurter, Hayat; Molecular Biology and Genetics
Spinal muscular atrophy is an autosomal recessive motor neuron disease that is caused by mutation of the survival motor neuron gene (SMN1) but all patients retain a nearly identical copy SMN2. The disease severity correlates inversely with increased SMN2 copy. Currently the most promising therapeutic strategy for spinal muscular atrophy is induction of SMN2 gene expression by histone deacetylase inhibitors. Polyphenols are known for protection against oxidative stress and degenerative diseases. Among our candidate prodrug library we found that (E )-resveratrol which is one of the polyphenolic compounds inhibited histone deacetylase activity in a concentration-dependent manner and half-maximum inhibition was observed at 650 mu m. Molecular docking studies showed that (E )-resveratrol had more favorable free energy of binding (-9.09 kcal/mol) and inhibition constant values (0.219 mu m) than known inhibitors. To evaluate the effect of (E )-resveratrol on SMN2 expression spinal muscular atrophy type I fibroblast cell lines was treated with (E )-resveratrol. The level of full-length SMN2 mRNA and protein showed 1.2- to 1.3-fold increase after treatment with 100 mu m (E )-resveratrol in only one cell line. These results indicate that response to (E )-resveratrol treatment is variable among cell lines. This data demonstrate a novel activity of (E )-resveratrol and that it could be a promising candidate for the treatment of spinal muscular atrophy.
Citation - WoS: 0
Citation - Scopus: 0
Polymer-Ceramic Nanocomposites
(Spie-Int Soc Optical Engineering, 2009) Pekcan, Önder; Pekcan, Mehmet Önder; Uğur, Şaziye; Molecular Biology and Genetics
Steady state fluorescence (SSF) and photon transmission (PT) techniques were used for studying film formation from TiO2 and Al2O3 covered polystyrene (PS) latex particles. These films were annealed at elevated temperatures in 10 min time intervals above glass transition (T-g) temperature of polystyrene. Fluorescence emission I-P and transmitted photon I-tr intensities were measured after each annealing step to monitor the stages of film formation. Films present dramatic increase in both I-tr and I-P above the certain onset temperature called minimum film forming temperature T-0. Dissolution of annealed PS film with high TiO2 content presented a nice ordered nano-sized ceramic structure which may predict the construction of nano-layer photonic crystals. It was observed that latex particles are encapsulated above a critical Al2O3 content of 33 wt% which corresponds to the critical occupation probability of p(c)=0.33 at which the film obey the site-percolation model with a critical exponent of 0.45.
Citation - WoS: 2
Citation - Scopus: 2
Critical Exponents of Thermal Phase Transitions of Kappa-Carrageenan in Various Salt Solutions
(Wiley-VCH Verlag GmbH, 2009) Tarı, Özlem; Pekcan, Mehmet Önder; Pekcan, Önder; Molecular Biology and Genetics
The steady state fluorescence (SSF) technique was employed to study the phase transitions Of kappa-carrageenan in NaCl and KCl solutions. Pyranine was used as a fluorescence probe for monitoring these transitions. Scattered light I(sc) and fluorescence intensity 1 was monitored against temperature to determine transition temperatures and exponents. It was observed that transition temperatures are strongly correlated with the NaCl and KCl contents. The weight-average degree of polymerization DP(w) and gel fraction G exponents (gamma and beta) were measured and found to be in accord with the classical Flory-Stockmayer model.
Citation - WoS: 21
Citation - Scopus: 20
Critical Exponents of Kappa Carrageenan in the Coil-Helix and Helix-Coil Hysteresis Loops
(Taylor & Francis Inc, 2009) Tarı, Özlem; Pekcan, Mehmet Önder; Kara, Selim; Pekcan, Önder; Molecular Biology and Genetics
The steady-state fluorescence technique was used to study coil-helix (sol-gel) and helix-coil (gel-sol) transitions of the kappa carrageenan-water system with various carrageenan contents. Fluorescence (I) and scattered light (I-sc) intensities were measured against temperature to determine critical phase transition temperatures and exponents. It was observed that the coil-helix transition temperatures T-ch were much lower than the helix-coil (T-hc) transition temperatures due to the hysteresis of the phase transition loops. The gel fraction exponent (beta) was measured and found to be in accord with the classical Flory-Stockmayer model.
Citation - WoS: 10
Citation - Scopus: 10
Oxygen diffusion into polystyrene-bentonite films
(Elsevier, 2009) Pekcan, Mehmet Önder; Yargı, Önder; Pekcan, Önder; Molecular Biology and Genetics
A simple fluorescence technique is proposed for the measurement of the diffusion coefficient of oxygen into polystyrene-clay composite films. The composite films were prepared from the mixture of surfactant-free pyrene (P)-labeled polystyrene latexes (PS) and modified bentonite (MNaLB) at various compositions at room temperature. These films were annealed at 200 degrees C above the glass transition (T-g) temperature of polystyrene for 10 min. Oxygen diffusion into the films was monitored with steady state fluorescence (SSF) measurements. Measurements were performed at room temperature for different film compositions (0 510 2030 50 and 60 mass% modified bentonite) films to evaluate the effect of MNaLB content on oxygen diffusion. The diffusion coefficient D of oxygen was determined by the fluorescence quenching method by assuming Fickian transport and increased from 7.4 x 10(-10) to 26.9 x 10(-10) cm(2) s(-1) with increasing MNaLB content. This increase in D value was explained by formation of microvoids in the film. These voids are large enough to contribute to the penetration of oxygen molecules through the films. The montmorillonite content did not affect the quenching rate constant k(q) and mutual diffusion coefficient D-m values. (C) 2008 Elsevier B.V. All rights reserved
Citation - WoS: 16
Citation - Scopus: 16
Critical Exponents of Photoinitiated Gelation at Different Light Intensities
(Taylor & Francis Inc, 2009) Doğruyol, Zekeriya; Pekcan, Mehmet Önder; Arsu, Nergis; Pekcan, Önder; Molecular Biology and Genetics
A photo-differential scanning calorimetric (Photo-DSC) technique was used to study the photoinitiated radical polymerization of a 75% epoxy diacrylate (EA) and 25% tripropyleneglycoldiacrylate (TPGDA) mixture with 2-mercaptothioxanthone (TX-SH) as photoinitiator by using different light intensities. Photopolymerization reactions were carried out under identical conditions of temperature and initiator concentration. It was observed that all conversion curves during gelation at various Might intensities present good sigmoidal behavior as predicted by the percolation model. Observations around the critical time called the glass transition point (t(g)) taken for polymerization to reach the maximum rate (R-pmax) show that the gel fraction exponents beta obeyed the universal percolation picture. On the other hand R-pmax t(g) and final conversion values were found to be dependent on the UV light intensity.
Citation - WoS: 34
Citation - Scopus: 37
Synthesis and Molecular Modeling of Some Novel Hexahydroindazole Derivatives as Potent Monoamine Oxidase Inhibitors
(Pergamon-Elsevier Science Ltd, 2009) Gökhan-Kelekçi, Nesrin; Yelekçi, Kemal; Şimşek, O. Özgün; Ercan, Ayşe; Yelekçi, Kemal; Şahin, Z. Sibel; Işık, Şamil; Uçar, Gülberk; Bilgin, Abdullah Altan; Molecular Biology and Genetics
A novel series of 2-thiocarbamoyl-234567-hexahydro-1H-indazole and 2-substituted thiocarbamoyl-33a 4567-hexahydro-2H-indazoles derivatives were synthesized and investigated for the ability to inhibit the activity of the A and B isoforms of monoamine oxidase (MAO). The target molecules were identified on the basis of satisfactory analytical and spectra data (IR H-1 NMR C-13 NMR D-2 NMR DEPT EI-MASS techniques and elemental analysis). Synthesized compounds showed high activity against both the MAO-A (compounds 1d 1e 2c 2d 2e) and the MAO-B (compounds 1a 1b 1c 2a 2b) isoforms. In the discussion of the results the influence of the structure on the biological activity of the prepared compounds was delineated. It was suggested that non-substituted and N-methyl/ethyl bearing compounds (except 2c) increased the inhibitory effect and selectivity toward MAO-B. The rest of the compounds carrying N-allyl and N-phenyl appeared to select the MAO-A isoform. The inhibition pro. le was found to be competitive and reversible for all compounds. A series of experimentally tested (1a-2e) compounds was docked computationally to the active site of the MAO-A and MAO-B isoenzyme. The AUTODOCK 4.01 program was employed to perform automated molecular docking. In order to see the detailed interactions of the docked poses of the model inhibitors compounds 1a 1d 1e and 2e were chosen because of their ability to reversibly inhibit the MAO-B and MAO-A and the availability of experimental inhibition data. The differences in the intermolecular hydrophobic and H-bonding of ligands to the active site of each MAO isoform were correlated to their biological data. Observation of the docked positions of these ligands revealed interactions with many residues previously reported to have an effect on the inhibition of the enzyme. Excellent to good correlations between the calculated and experimental K-i values were obtained. In the docking of the MAO-A complex the trans configuration of compound 1e made various very close interactions with the residues lining the active site cavity these interactions were much better than those of the other compounds tested in this study. This tight binding observation may be responsible for the nanomolar inhibition of form of MAOA. However it binds slightly weaker (experimental K-i = 1.23 mu M) to MAO-B than to MAO-A (experimental K-i = 4.22 nM). (C) 2009 Elsevier Ltd. All rights reserved.
Citation - WoS: 11
Citation - Scopus: 11
Steady State Fluorescence Technique for Studying Phase Transitions in Paam-Pnipa Mixture
(Taylor & Francis, 2009) Evingür, Gülşen Akın; Pekcan, Mehmet Önder; Aktaş, Demet Kaya; Pekcan, Önder; Molecular Biology and Genetics
The steady state fluorescence (SSF) technique was used to study the sol-gel phase transition during free radical crosslinking copolymerisation of various amounts of acrylamide (AAm) and N-isopropylacrylamide (NIPA) mixtures. NN'-methylenebis (acrylamide) (BIS) and ammonium persulfate (APS) were used as crosslinker and an initiator respectively. Pyranine (8-hydroxypyrene-1 3 6-trisulfonic acid trisodium salt HPTS) was added as a fluoroprobe for monitoring the polymerisation. It was observed that pyranine molecules bind to AAm and NIPA chains upon the initiation of the polymerisation thus the fluorescence spectra of the bonded pyranines shift to the shorter wavelengths. Fluorescence spectra from the bonded pyranines allowed us to monitor the sol-gel phase transition without disturbing the system mechanically and to test the universality of the sol-gel transition as a function of polymer concentration ratios. Observations around the gel point of PAAm-PNIPA mixtures show that the gel fraction exponent obeyed the percolation result.

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