Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - Scopus: 4Quasi-Supervised Strategies for Compound-Protein Interaction Prediction(John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.Article Citation - WoS: 8Citation - Scopus: 8Invariants of Bonded Knotoids and Applications To Protein Folding(MDPI, 2022) Güğümcü, Neslihan; Gabrovsek, Bostjan; Kauffman, Louis H.In this paper, we study knotoids with extra graphical structure (bonded knotoids) in the settings of rigid vertex and topological vertex graphs. We construct bonded knotoid invariants by applying tangle insertion and unplugging at bonding sites of a bonded knotoid. We demonstrate that our invariants can be used for the analysis of the topological structure of proteins.Article Citation - WoS: 9Citation - Scopus: 9Rapid Identification of Phosphorus Containing Proteins in Electrophoresis Gel Spots by Laser-Induced Breakdown Spectroscopy, Libs(Royal Society of Chemistry, 2014) Aras, Nadir; Yalçın, ŞerifeA novel method for the rapid in-gel identification of phosphorus containing proteins, specifically casein and ovalbumin, prior to mass spectrometric analysis for the elucidation of phosphorylation sites was developed. After polyacrylamide gel-electrophoretic separation, staining and drying, protein bands were subjected to focused laser pulses at the center or the vicinity of the protein band. Phosphorus containing proteins were recognized from their prominent phosphorus lines in the luminous plasma formed by energetic laser pulses. The LIBS emission intensity of phosphorus lines at 253.5 nm and 255.3 nm has been optimized with respect to laser energy and detector timing parameters by using pure casein in the pellet form. The method was applied to casein, ovalbumin, two commercially available standard protein mixtures and proteins extracted from the canola plant. It was shown that LIBS was capable of identifying phosphorus containing proteins directly in the gel matrix in nanogram amounts. Mass spectrometric analysis of the ovalbumin spot after the in-gel digestion procedure has proved the accuracy of the technique. With the speed and spatial resolution that LIBS offers, this technique shows promise in the micro-local spotting of phosphorus containing proteins in the polyacrylamide gel matrix prior to MS analysis for the determination of the phosphorylation sites. © 2014 The Royal Society of Chemistry.Article Citation - WoS: 55Citation - Scopus: 61Insight Into Serum Protein Interactions With Functionalized Magnetic Nanoparticles in Biological Media(American Chemical Society, 2012) Wiogo, Hilda T. R.; Lim, May; Bulmuş, Volga; Gutie´rrez, Lucía; Woodward, Robert C.; Amal, RoseSurface modification with linear polymethacrylic acid (20 kDa), linear and branched polyethylenimine (25 kDa), and branched oligoethylenimine (800 Da) is commonly used to improve the function of magnetite nanoparticles (MNPs) in many biomedical applications. These polymers were shown herein to have different adsorption capacity and anticipated conformations on the surface of MNPs due to differences in their functional groups, architectures, and molecular weight. This in turn affects the interaction of MNPs surfaces with biological serum proteins (fetal bovine serum). MNPs coated with 25 kDa branched polyethylenimine were found to attract the highest amount of serum protein while MNPs coated with 20 kDa linear polymethacrylic acid adsorbed the least. The type and amount of protein adsorbed, and the surface conformation of the polymer was shown to affect the size stability of the MNPs in a model biological media (RPMI-1640). A moderate reduction in r 2 relaxivity was also observed for MNPs suspended in RPMI-1640 containing serum protein compared to the same particles suspended in water. However, the relaxivities following protein adsorption are still relatively high making the use of these polymer-coated MNPs as Magnetic Resonance Imaging (MRI) contrast agents feasible. This work shows that through judicious selection of functionalization polymers and elucidation of the factors governing the stabilization mechanism, the design of nanoparticles for applications in biologically relevant conditions can be improved. © 2012 American Chemical Society.Article Citation - WoS: 13Citation - Scopus: 18Effect of Corn-Zein Coating on the Mechanical Properties of Polypropylene Packaging Films(John Wiley and Sons Inc., 2011) Tıhmınlıoğlu, Funda; Atik, İsa Doğan; Özen, BanuIn this study, a novel film structure of corn zein coated on polypropylene (PP) synthetic films for food packaging applications was developed, and the mechanical properties of the resulting coated film, as affected by the coating formulation, were investigated. Composite structures of PP films coated with corn zein were obtained through a simple solvent casting method. Different amounts of corn zein (5 and 15%) were dissolved in 70 and 95% aqueous ethanol solution at 50 C. Solutions of corn zein plasticized with poly(ethylene glycol) and glycerol (GLY) at various levels (20 and 50%) were applied on corona-discharge-treated PP. A statistical analysis based on full factorial design was performed to examine the influence of the coating formulation on the final properties of the corn-zein-coated PP films. A significant (p < 0.05) improvement in the coated film’s mechanical properties was observed compared to those of the uncoated PP. The effect of the plasticization of the coating solutions was also quite significant. In general, GLY provided better improvements in the mechanical properties of the corn-zein-coated PP films. The statistical analysis of the results showed that the corn-zein and plasticizer concentrations and plasticizer type used in the coating formulations were more effective parameters and had significant effects on the mechanical behavior of the coated PP films. In conclusion, corn-zein coatings could have potential as alternatives to conventional synthetic polymers used in composite multilayer structures for food packaging applications.Article Citation - WoS: 8Citation - Scopus: 8Genetic Multivariate Calibration for Near Infrared Spectroscopic Determination of Protein, Moisture, Dry Mass, Hardness and Other Residues of Wheat(John Wiley and Sons Inc., 2006) Özdemir, DurmuşDetermination of wheat flour quality parameters, such as protein, moisture, dry mass by wet chemistry analyses takes long time. Near infrared spectroscopy (NIR) coupled with multivariate calibration offers a fast and nondestructive alternative to obtain reliable results. However, due to the complexity of the spectra obtained from NIR, some wavelength selection is generally required to improve the predictive ability of multivariate calibration methods. In this study, two different wheat data sets are investigated with the aim of establishing successful calibration models using NIR spectra of wheat samples. The first data set (material 1) was obtained from the ftp address (ftp://ftp.clarkson.edu/pub/hopkepk/Chemdata/) and contained 100 NIR spectra of wheat of which wet chemical analysis of protein and moisture content were done with reference methods. The second data set (material 2) contained 176 spectra and was downloaded from http://www.spectroscopynow.com/Spy/basehtml/SpyH/1,1181, 2-1-2-0-0-newsdetail-0-74,00.html. This wheat data set was given with the quality parameters, such as protein content, moisture content, other residues, dry mass, protein content in dry mass and hardness that were determined previously. Multivariate calibration models generated with genetic inverse least squares method demonstrated very good prediction results for the parameter mentioned here. Overall, the average per cent recoveries (APR) ranged between 99.23% and 100.34% with a standard deviation (SD) ranging from 0.34 to 3.15 for all the parameters investigated, except hardness. The APR value of hardness was 103.32 with the SD of 14.97.Article Citation - WoS: 90Citation - Scopus: 93Purification and Characterization of Three Members of the Photolyase/Cryptochrome Family Blue-Light Photoreceptors From Vibrio Cholerae(American Society for Biochemistry and Molecular Biology, 2003) Worthington, Erin N.; Kavaklı, İ. Halil; Berrocal-Tito, Gloria M.; Bondo, Bruce; Sancar, AzizThe sequence of Vibrio cholerae genome revealed three genes belonging to the photolyase/cryptochrome blue-light photoreceptor family. The proteins encoded by the three genes were purified and characterized. All three proteins contain folate and flavin cofactors and have absorption peaks in the range of 350-500 nm. Only one of the three, VcPhr, is a photolyase specific for cyclobutane pyrimidine dimers. The other two are cryptochromes and were designated VcCry1 and VcCry2, respectively. Mutation of phr abolishes photoreactivation of UV-induced killing, whereas mutations in cry1 and cry2 do not affect photorepair activity. VcCry1 exhibits some unique features. Of all cryptochromes characterized to date, it is the only one that contains stoichiometric amounts of both chromophores and retains its flavin cofactor in the two-electron reduced FADH2 form. In addition, VcCry1 exhibits RNA binding activity and copurifies with an RNA of 60-70 nucleotides in length.