Researcher:
Kamacıoğlu, Altuğ

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Master Student

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Altuğ

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Kamacıoğlu

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Kamacıoğlu, Altuğ

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2020 - 20234

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Researcher Of Publications: search.filters.isAuthorOfPublication.392b8be9-d2e4-42b7-b1c5-0659695f0082

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Now showing 1 - 4 of 4
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    Structural analysis of mammalian protein phosphorylation at a proteome level
    (Cell Press, 2021) N/A; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Kamacıoğlu, Altuğ; Tunçbağ, Nurcan; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; 245513; 105301
    Phosphorylation is an essential post-translational modification for almost all cellular processes. Several global phosphoproteomics analyses have revealed phosphorylation profiles under different conditions. Beyond identification of phospho-sites, protein structures add another layer of information about their functionality. In this study, we systematically characterize phospho-sites based on their 3D locations in the protein and establish a location map for phospho-sites. More than 250,000 phospho-sites have been analyzed, of which 8,686 sites match at least one structure and are stratified based on their respective 3D positions. Core phospho-sites possess two distinct groups based on their dynamicity. Dynamic core phosphorylations are significantly more functional compared with static ones. The dynamic core and the interface phosphosites are the most functional among all 3D phosphorylation groups. Our analysis provides global characterization and stratification of phospho-sites from a structural perspective that can be utilized for predicting functional relevance and filtering out false positives in phosphoproteomic studies.
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    Proximal biotinylation-based combinatory approach for isolating integral plasma membrane proteins
    (Amer Chemical Soc, 2020) N/A; Department of Molecular Biology and Genetics; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Akdağ, Mehmet; Yunt, Zeynep Sabahat; Kamacıoğlu, Altuğ; Qureshi, Mohammad Haroon; Akarlar, Büşra; Master Student; Teaching Faculty; Master Student; PhD Student; Other; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; College of Sciences; N/A; 116178; N/A; N/A; N/A; 105301
    Comprehensive profiling of the cell-surface proteome has been challenging due to the lack of tools for an effective and reproducible way to isolate plasma membrane proteins from mammalian cells. Here we employ a proximity-dependent biotinylation approach to label and isolate plasma membrane proteins without an extra in vitro labeling step, which we call Plasma Membrane-BiolD. The lipid-modified BirA* enzyme (MyrPalm BirA*) was targeted to the inner leaflet of the plasma membrane, where it effectively biotinylated plasma membrane proteins. Biotinylated proteins were then affinity-purified and analyzed by mass spectrometry. Our analysis demonstrates that combining conventional sucrose density gradient centrifugation and Plasma Membrane-BioID is ideal to overcome the inherent limitations of the identification of integral membrane proteins, and it yields highly pure plasma components for downstream proteomic analysis.
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    Roles of developmentally regulated KIF2A alternative isoforms in cortical neuron migration and differentiation
    (The Company of Biologists, 2021) N/A; N/A; N/A; N/A; N/A; N/A; N/A; Department of Molecular Biology and Genetics; N/A; Akkaya, Cansu; Atak, Dila; Kamacıoğlu, Altuğ; Akarlar, Büşra; Güner, Gökhan; Bayam, Efil; Taşkın, Ali Cihan; Dunn, Gülayşe İnce; PhD Student; PhD Student; Master Student; Other; Master Student; Researcher; Other; Faculty Member; Other; Department of Molecular Biology and Genetics; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; N/A; N/A; College of Sciences; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 291296; 105301; N/A
    KIF2A is a kinesin motor protein with essential roles in neural progenitor division and axonal pruning during brain development. However, how different KIF2A alternative isoforms function during development of the cerebral cortex is not known. Here, we focus on three Kif2a isoforms expressed in the developing cortex. We show that Kif2a is essential for dendritic arborization in mice and that the functions of all three isoforms are sufficient for this process. Interestingly, only two of the isoforms can sustain radial migration of cortical neurons; a third isoform, lacking a key N-terminal region, is ineffective. By proximity-based interactome mapping for individual isoforms, we identify previously known KIF2A interactors, proteins localized to the mitotic spindle poles and, unexpectedly, also translation factors, ribonucleoproteins and proteins that are targeted to organelles, prominently to the mitochondria. In addition, we show that a KIF2A mutation, which causes brain malformations in humans, has extensive changes to its proximity-based interactome, with depletion of mitochondrial proteins identified in the wild-type KIF2A interactome. Our data raises new insights about the importance of alternative splice variants during brain development.
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    Cell cycle-dependent palmitoylation of protocadherin 7 by ZDHHC5 promotes successful cytokinesis
    (Company of Biologists Ltd, 2023) N/A; Department of Molecular Biology and Genetics; Department of Physics; N/A; N/A; Kiraz, Alper; Bavili, Nima; Kamacıoğlu, Altuğ; Küçük, Nazlı Ezgi Özkan; Qureshi, Mohammad Haroon; Yapıcı, Gamze Nur; Yiğit, Berfu Nur; Değirmenci, Beste Senem; Faculty Member; Faculty Member; PhD Student; Master Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Department of Molecular Biology and Genetics; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 105301; 22542; N/A; N/A; N/A; N/A; N/A; N/A; N/A
    Cell division requires dramatic reorganization of the cell cortex, which is primarily driven by the actomyosin network. We previously reported that protocadherin 7 (PCDH7) gets enriched at the cell surface during mitosis, which is required to build up the full mitotic rounding pressure. Here, we report that PCDH7 interacts with and is palmitoylated by the palmitoyltransferase, ZDHHC5. PCDH7 and ZDHHC5 colocalize at the mitotic cell surface and translocate to the cleavage furrow during cytokinesis. The localization of PCDH7 depends on the palmitoylation activity of ZDHHC5. Silencing PCDH7 increases the percentage of multinucleated cells and the duration of mitosis. Loss of PCDH7 expression correlates with reduced levels of active RhoA and phospho-myosin at the cleavage furrow. This work uncovers a palmitoylation-dependent translocation mechanism for PCDH7, which contributes to the reorganization of the cortical cytoskeleton during cell division.