Researcher:
Kar, Gözde

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PhD Student

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Gözde

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Kar

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Kar, Gözde

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2009 - 200922010 - 20131

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Researcher Of Publications: search.filters.isAuthorOfPublication.3c9d84f8-eb33-48f8-830c-bc8fd7fd2d9a

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    Combining protein-protein interaction networks with structures
    (Cell Press, 2009) Nussinov, Ruth; N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Kar, Gözde; Gürsoy, Attila; Keskin, Özlem; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 8745; 26605
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    Emerging role of the ubiquitin-proteasome system as drug targets
    (Bentham Science Publ Ltd, 2013) Fraternali, Franca; Department of Chemical and Biological Engineering; N/A; Department of Computer Engineering; Keskin, Özlem; Kar, Gözde; Gürsoy, Attila; Faculty Member; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 26605; N/A; 8745
    The ubiquitin-proteosome system (UPS) regulates a wide range of cellular processes including protein degradation, DNA repair, transcription regulation, and cell signaling. Alterations and mutations in UPS components give rise to various human diseases, most prominently cancer and neurodegenerative disorders. Here, we review recent advances in UPS-based drug discovery highlighting the emerging relationships between the UPS and disease and discuss potential future therapeutic interventions. In particular, we focus on recent structural approaches in UPS and explain how the knowledge of protein structural details can guide the design of specifically targeted inhibitors.
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    Human cancer protein-protein interaction network: a structural perspective
    (Public Library of Science, 2009) Department of Computer Engineering; Department of Chemical and Biological Engineering; Kar, Gözde; Gürsoy, Attila; Keskin, Özlem; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Engineering; N/A; 8745; 26605
    Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network). The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%). We illustrate the interface related affinity properties of two cancer-related hub proteins: Erbb3, a multi interface, and Raf1, a single interface hub. The results reveal that affinity of interactions of the multi-interface hub tends to be higher than that of the single-interface hub. These findings might be important in obtaining new targets in cancer as well as finding the details of specific binding regions of putative cancer drug candidates.