Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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: 7Citation - Scopus: 9Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences(Public Library of Science, 2013) Doğan, Tunca; Karaçalı, BilgeIdentifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.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: 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.