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Quartile: search.filters.quartile.Q3Subject: search.filters.subject.Molecular biology

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Now showing 1 - 10 of 27
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    A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons
    (Springer, 2014) Sutay, Berkay; Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129
    In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I-2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol(-1) more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I-2+naphtalene dimer interaction is almost twice of that of I-2+naphtalene, showing the long range character of the interaction.
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    Anharmonicity, mode-coupling and entropy in a fluctuating native protein
    (Iop Publishing Ltd, 2010) N/A; Department of Physics; Department of Computer Engineering; N/A; Department of Chemical and Biological Engineering; Kabakçıoğlu, Alkan; Yüret, Deniz; Gür, Mert; Erman, Burak; Faculty Member; Faculty Member; PhD Student; Faculty Member; Department of Physics; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 49854; 179996; 216930; 179997
    We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. the effect of anharmonicity and mode-coupling on the fluctuational entropy is in the order of a few percent.
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    Application of exosomes for the alleviation of COVID-19-related pathologies
    (Wiley, 2022) Rezabakhsh, Aysa; Mahdipour, Mahdi; Nourazarian, Alireza; Habibollahi, Paria; Avcı, Çığır Biray; Rahbarghazi, Reza; Sokullu, Emel; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; 163024
    The pandemic of COVID-19 caused worldwide concern. Due to the lack of appropriate medications and the inefficiency of commercially available vaccines, lots of efforts are being made to develop de novo therapeutic modalities. Besides this, the possibility of several genetic mutations in the viral genome has led to the generation of resistant strains such as Omicron against neutralizing antibodies and vaccines, leading to worsening public health status. Exosomes (Exo), nanosized vesicles, possess several therapeutic properties that participate in intercellular communication. The discovery and application of Exo in regenerative medicine have paved the way for the alleviation of several pathologies. These nanosized particles act as natural bioshuttles and transfer several biomolecules and anti-inflammatory cytokines. To date, several approaches are available for the administration of Exo into the targeted site inside the body, although the establishment of standard administration routes remains unclear. As severe acute respiratory syndrome coronavirus 2 primarily affects the respiratory system, we here tried to highlight the transplantation of Exo in the alleviation of COVID-19 pathologies.
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    Binding stability of peptides on major histocompatibility complex class I proteins: role of entropy and dynamics
    (Institute of Physics (IOP) Publishing, 2018) Gul, Ahmet; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper draws attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme that allows for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining the right peptides for personal immunotherapy.
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    Characterization and comparison of insulinoma tumor model and pancreatic damage caused by the tumor, and identification of possible markers
    (Springer Science and Business Media B.V., 2024) Karatug Kacar, Ayse; Aylar, Dilara; Celikten, Mert; Bolkent, Sehnaz; Bulutay, Pınar; School of Medicine
    Insulinoma is a neuroendocrine tumor. It arises from the uncontrolled proliferation of pancreatic β cells. In this study, we created an insulinoma tumor model in nude mice. INS-1 cells were injected in two different ways, subcutaneously (S.C.) or intraperitoneally (I.P.). Body weight, tumor weight, and size were measured. ELISA kits were used analyze to Glucose, insulin, and CA19-9 levels in serum, pancreas, and tumor tissues. KCNN4, KCNK1, GLUT2, IR, HSP70, HSF1, and HSP90 levels were analyzed by western blotting of membrane and/or cytosolic fractions of tumor and pancreas tissue. Tumor formation occurred in nude mice, but it did not occur in Wistar albino rats. The tumor has neuroendocrine cell morphology. Insulin and CA19-9 levels increased in pancreas tissue. In tumor tissue, KCNN4 levels were higher in both membrane and cytosolic fractions, while KCNK1 levels were lower in the membrane fraction of the S.C. group. HSP70 levels were also lower in the S.C. group. In pancreas tissue, KCNK1 levels were lower in the membrane fraction of the S.C. and I.P. groups. GLUT2 levels increased in both groups according to the control group, while IR levels decreased in the S.C. group compared to the control group. However, HSF1 levels increased in the I.P. group, while HSP90 decreased in the S.C. group in pancreatic tissues. The S.C. group is a more suitable insulinoma tumor model. KCNN4, KCNK1, and HSP70 proteins may be important biomarkers in the diagnosis and treatment of insulinoma.
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    Characterization and prediction of protein interfaces to infer protein-protein interaction networks
    (Bentham Science Publ Ltd, 2008) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Tunçbağ, Nurcan; Gürsoy, Attila; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; College of Engineering; College of Engineering; College of Engineering; 26605; 245513; 8745
    Complex protein-protein interaction networks govern biological processes in cells. Protein interfaces are the sites where proteins physically interact. Identification and characterization of protein interfaces will lead to understanding how proteins interact with each other and how they are involved in protein-protein interaction networks. What makes a given interface bind to different proteins; how similar/different the interactions in proteins are some key questions to be answered. Enormous amount of protein structures and experimental protein-protein interactions data necessitate advanced computational methods for analyzing and inferring new knowledge. Interface prediction methods use a wide range of sequence, structural and physico-chemical characteristics that distinguish interface residues from non-interface surface residues. Here, we present a review focusing on the characteristics of interfaces and the current status of interface prediction methods.
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    Coherent regulation in yeast's cell-cycle network
    (Iop Publishing Ltd, 2015) N/A; Department of Physics; Aral, Neşe; Kabakçıoğlu, Alkan; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854
    We define a measure of coherent activity for gene regulatory networks, A property that reflects the unity of purpose between the regulatory agents with a common target. We propose that such harmonious regulatory action is desirable under a demand for energy efficiency and may be selected for under evolutionary pressures. We consider two recent models of the cell-cycle regulatory network of the yeast, Saccharomyces cerevisiae as a case study and calculate their degree of coherence. a comparison with random networks of similar size and composition reveals that the yeast's cell-cycle regulation is wired to yield an exceptionally high level of coherent regulatory activity. We also investigate the mean degree of coherence as a function of the network size, connectivity and the fraction of repressory/activatory interactions.
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    Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs
    (Wiley-Blackwell, 2013) Marusic, Maja; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Azizoğlu, Selimcan; Kızılel, Rıza; Kavaklı, İbrahim Halil; Erman, Burak; Kızılel, Seda; Master Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 114475; 40319; 179997; 28376
    This paper reports the previously unknown interactions between eight low molecular weight commercially available drugs (130800Da) and DNA repair protein photolyase using computational docking simulations and surface plasmon resonance (SPR) experiments. Theoretical dissociation constants, Kd, obtained from molecular docking simulations were compared with the values found from SPR experiments. Among the eight drugs analyzed, computational and experimental values showed similar binding affinities between selected drug and protein pairs. We found no significant differences in binding interactions between pure and commercial forms of the drug lornoxicam and DNA photolyase. Among the eight drugs studied, prednisone, desloratadine, and azelastine exhibited the highest binding affinity (Kd=1.65, 2.05, and 8.47M, respectively) toward DNA photolyase. Results obtained in this study are promising for use in the prediction of unknown interactions of common drugs with specific proteins such as human clock protein cryptochrome. Copyright (c) 2013 John Wiley & Sons, Ltd.
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    Computational approaches leveraging integrated connections of multi-omic data toward clinical applications
    (Royal Society of Chemistry (RSC), 2022) Demirel, Habibe Cansu; Arıcı, Müslüm Kaan; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 245513
    In line with the advances in high-throughput technologies, multiple omic datasets have accumulated to study biological systems and diseases coherently. No single omics data type is capable of fully representing cellular activity. The complexity of the biological processes arises from the interactions between omic entities such as genes, proteins, and metabolites. Therefore, multi-omic data integration is crucial but challenging. The impact of the molecular alterations in multi-omic data is not local in the neighborhood of the altered gene or protein; rather, the impact diffuses in the network and changes the functionality of multiple signaling pathways and regulation of the gene expression. Additionally, multi-omic data is high-dimensional and has background noise. Several integrative approaches have been developed to accurately interpret the multi-omic datasets, including machine learning, network-based methods, and their combination. In this review, we overview the most recent integrative approaches and tools with a focus on network-based methods. We then discuss these approaches according to their specific applications, from disease-network and biomarker identification to patient stratification, drug discovery, and repurposing.
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    Design of bioartificial pancreas with functional micro/nano-based encapsulation of islets
    (Bentham Science Publ Ltd, 2014) N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Kepsütlü, Burcu; Nazlı, Caner; Bal, Tuğba; Kızılel, Seda; Master Student; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 353534; 28376
    Type I diabetes mellitus (TIDM), a devastating health issue in all over the world, has been treated by successful transplantation of insulin secreting pancreatic islets. However, serious limitations such as the requirement of immunosuppressive drugs for recipient patients, side effects as a result of long-term use of drugs, and reduced functionality of islets at the transplantation site remain. Bioartificial pancreas that includes islets encapsulated within semi-permeable membrane has been considered as a promising approach to address these requirements. Many studies have focused on micro or nano-based islet immunoisolation systems and tested the efficacy of encapsulated islets using in vitro and in vivo platforms. In this review, we address current progress and obstacles for the development of a bioartificial pancreas using micro/nano-based systems for encapsulation of islets.