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Publication Metadata only Advances in template-based protein docking by utilizing interfaces towards completing structural interactome(Current Biology Ltd, 2015) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Muratçıoğlu, Serena; Maiorov, Emine Güven; Keskin, Özlem; Gürsoy, Attila; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 26605; 8745The increase in the number of structurally determined protein complexes strengthens template-based docking (TBD) methods for modelling protein-protein interactions (PPIs). These methods utilize the known structures of protein complexes as templates to predict the quaternary structure of the target proteins. The templates may be partial or complete structures. Interface based (partial) methods have recently gained interest due in part to the observation that the interface regions are reusable. We describe how available template interfaces can be used to obtain the structural models of protein interactions. Despite the agreement that a majority of the protein complexes can be modelled using the available Protein Data Bank (PDB) structures, a handful of studies argue that we need more template proteins to increase the structural coverage of PPIs. We also discuss the performance of the interface TBD methods at large scale, and the significance of capturing multiple conformations for improving accuracy.Publication Metadata only Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis(2022) Kutnu, Meltem; İşlerel, Elif Tekin; Özcengiz, Gülay; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 245513The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin’s role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein–protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein–protein interactions in B. subtilis.Publication Metadata only Conservation of migratory species(Cell Press, 2018) Horns, Joshua J.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589N/APublication Metadata only Covid-19 under spotlight: a close look at the origin, transmission, diagnosis, and treatment of the 2019-nCoV disease(Wiley, 2020) Sheervalilou, Roghayeh; Shirvaliloo, Milad; Dadashzadeh, Nahid; Shirvalilou, Sakine; Shahraki, Omolbanin; Pilehvar-Soltanahmadi, Younes; Ghaznavi, Habib; Khoei, Samideh; N/A; Nazarlou, Ziba; PhD Student; Graduate School of Sciences and Engineering; N/AMonths after the outbreak of a new flu-like disease in China, the entire world is now in a state of caution. The subsequent less-anticipated propagation of the novel coronavirus disease, formally known as COVID-19, not only made it to headlines by an overwhelmingly high transmission rate and fatality reports, but also raised an alarm for the medical community all around the globe. Since the causative agent, SARS-CoV-2, is a recently discovered species, there is no specific medicine for downright treatment of the infection. This has led to an unprecedented societal fear of the newly born disease, adding a psychological aspect to the physical manifestation of the virus. Herein, the COVID-19 structure, epidemiology, pathogenesis, etiology, diagnosis, and therapy have been reviewed.Publication Metadata only Extracellular glucose level regulates dependence on 78 for cell surface localization of multipass transmembrane proteins in HeLa cells(Wiley, 2018) Toyoda, Yusuke; Sarov, Mihail; Saitoh, Shigeaki; Department of Molecular Biology and Genetics; Akarlar, Büşra; Other; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; N/A; 105301Publication Metadata only Genome-wide chromatin state transitions associated with developmental and environmental cues(CELL PRESS, 2013) Zhu, Jiang; Adli, Mazhar; Zou, James Y.; Verstappen, Griet; Coyne, Michael; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L.; Bennett, David A.; Houmard, Joseph A.; Muoio, Deborah M.; Camahort, Ray; Cowan, Chad A.; Meissner, Alexander; Epstein, Charles B.; Shoresh, Noam; Bernstein, Bradley E.; N/A; Önder, Tamer Tevfik; Faculty Member; School of Medicine; 42946Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming.Publication Metadata only In-depth review: is hepcidin a marker for the heart and the kidney?(Springer, 2021) Afsar, Rengin Elsurer; Ibis, Avsin; Afsar, Baris; N/A; Kanbay, Mehmet; Faculty Member; School of Medicine; 110580Iron is an essential trace element involved in oxidation-reduction reactions, oxygen transport and storage, and energy metabolism. Iron in excess can be toxic for cells, since iron produces reactive oxygen species and is important for survival of pathogenic microbes. There is a fine-tuning in the regulation of serum iron levels, determined by intestinal absorption, macrophage iron recycling, and mobilization of hepatocyte stores versus iron utilization, primarily by erythroid cells in the bone marrow. Hepcidin is the major regulatory hormone of systemic iron homeostasis and is upregulated during inflammation. Hepcidin metabolism is altered in chronic kidney disease. Ferroportin is an iron export protein and mediates iron release into the circulation from duodenal enterocytes, splenic reticuloendothelial macrophages, and hepatocytes. Systemic iron homeostasis is controlled by the hepcidin-ferroportin axis at the sites of iron entry into the circulation. Hepcidin binds to ferroportin, induces its internalization and intracellular degradation, and thus inhibits iron absorption from enterocytes, and iron release from macrophages and hepatocytes. Recent data suggest that hepcidin, by slowing or preventing the mobilization of iron from macrophages, may promote atherosclerosis and may be associated with increased cardiovascular disease risk. This article reviews the current data regarding the molecular and cellular pathways of systemic and autocrine hepcidin production and seeks the answer to the question whether changes in hepcidin translate into clinical outcomes of all-cause and cardiovascular mortality, and cardiovascular and renal end-points.Publication Metadata only Light and electron microscopic examination of the effects of long term-low dose cyclosporina (csa) and its combination with prednisolone on hematopoietic cells(2011) Ercan, F.; Altaner, S.; Aktaş, Ranan Gülhan; Faculty Member; School of Medicine; Koc University Hospital; 137519Publication Metadata only Mechanisms of somatic cell reprogramming(Humana Press Inc, 2013) N/A; N/A; Önder, Tamer Tevfik; Faculty Member; School of Medicine; 42946Generation of induced pluripotent stem cells (iPSCs) from somatic cell types has revolutionized the field of stem cell biology and opened the way for production of disease- and patient-specific stem cells which have tremendous potential for regenerative medicine. Despite the rapid progress and improvement in iPSC-derivation techniques, transcription factor-based reprogramming remains an inefficient and poorly understood process. Successful reprogramming requires the completion of a number of rate-limiting steps that include avoiding senescence, mesenchymal-epithelial transition, and activation of endogenous pluripotency genes. It has also become clear that the global epigenetic landscape of the somatic cell types is completely overhauled during acquisition of pluripotency. The epigenetic state is largely determined by the deposition of chromatin marks which include histone tail modifications and DNA methylation. These marks are not only indicative of a given cell state; they are also functionally important during reprogramming. In this chapter I will review our current understanding of the mechanism of reprogramming and the role chromatin marks and the associated chromatin-modifier proteins play in this process.Publication Metadata only Modeling of biological polymers - discrete and continuum-mechanics formulations(Springer-Verlag Berlin, 1994) Department of Mathematics; Aşkar, Attila; Faculty Member; Department of Mathematics; College of Sciences; 178822N/A