Welcome to the Koç University Institutional Academic Repository
The Koç University Institutional Academic Repository (KUHub Research) is a state-of-the-art academic repository that consolidates all academic outputs—such as articles, conference proceedings, theses, research data, and more—produced by the university since its establishment in 1993.
KUHub Research adheres to the principles of Open Access and FAIR (Findable, Accessible, Interoperable, Reusable), providing access to the bibliographic records, research data, and full texts of research outputs. Equipped with innovative features such as Author Profile pages and enhanced tools, KUHub Research aims to enhance the visibility of researchers both nationally and internationally. KUHub Research aims to preserve and maintain Koç University's valuable academic legacy for future generations while also serving the needs of today’s researchers.
For more information or inquiries please contact openaccess@ku.edu.tr
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Recent Submissions
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2028-01-01) Chretien, Anaïs; Ertem Kuzucu, Fatma Betul; Summers, Jacob; Wranik, Maximilian; 0000-0001-8480-1443; 0000-0002-2144-989x; 0000-0003-3113-0353; 0000-0002-2482-0164
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2027-01-01) Summers, Jacob; Sanctis, Daniele; Vlahakis, Niko; Knight, Victoria; Ertem Kuzucu, Fatma Betul; Chretien, Anaïs; Nurizzo, Didier; 0000-0003-3113-0353; 0000-0003-0391-8290; 0000-0002-5092-0265; 0000-0002-2144-989x; 0000-0001-8480-1443; 0000-0002-7367-5098
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Incidental and Symptomatic Pulmonary Thromboembolism: Clinical Features and Prognostic Comparison
(Springer Science and Business Media LLC, 2026-01-27) Karataş, Ferhan; Dikensoy, Öner; Coşkun Doğan; KUH (Koç University Hospital); KUH (KOÇ UNIVERSITY HOSPITAL)
Background Incidental pulmonary thromboembolism (iPTE) is increasingly being detected owing to the widespread use of computed tomography; however, its clinical significance and prognostic impact compared with symptomatic pulmonary thromboembolism (sPTE) remains controversial. Materials and Methods This retrospective observational study included adult patients with acute pulmonary embolism confirmed using CT pulmonary angiography between January 2022 and January 2025. Patients were classified as having iPTE or sPTE based on the clinical presentation and indications for imaging. Demographic characteristics, comorbidities, clinical findings, laboratory parameters, imaging features, and outcomes were compared between groups. Survival was assessed using Kaplan–Meier analysis, and predictors of mortality were evaluated using Cox regression analysis. Results A total of 306 patients were included, of whom 42 (13.7%) had iPTE and 264 (86.3%) had sPTE. Patients with iPTE had a higher prevalence of malignancy and comorbidities, but showed lower heart rate, higher oxygen saturation, lower cardiac biomarker levels, and less right ventricular dysfunction. Radiologically, iPTE was associated with a less extensive embolic burden and fewer parenchymal complications. The median survival did not differ significantly between the iPTE and sPTE groups (log-rank, p = 0.346). In multivariate analysis, malignancy (hazard ratio [HR] 3.07, p < 0.001) and elevated troponin T (HR 2.70, p = 0.002) were independent predictors of mortality, whereas iPTE status was not. Conclusion Despite a lower hemodynamic and radiological burden, incidental pulmonary thromboembolism was associated with survival comparable to that of symptomatic cases. Mortality was primarily driven by underlying malignancy and myocardial injury rather than by embolism presentation. Trial registration Not applicable (retrospective observational study).
Proximity labeling reveals cell cycle–specific NEK2 interactions and a regulatory axis controlling NUSAP1 stability
(openRxiv, 2026-01-27) to be filled manually; Enes Cicek; Selahattin Can Ozcan; Beste Kanevetci; Batuhan Mert Kalkan; Nazli Ezgi Ozkan; Nurhan Ozlu; Ceyda Acilan; to be filled manually; to be filled manually
ABSTRACT NEK2 is a cell cycle–regulated kinase best known for its role in centrosome separation, yet the phase-specific organization of its interaction network has remained unclear. Here, we combine a doxycycline-inducible TurboID system with mass spectrometry to generate a cell cycle–resolved NEK2 interactome in synchronized U2OS cells. Using generalized additive models (GAMs), we identified different enrichment trajectories of the NEK2 interacting proteins across G1/S, late S, and G2/M, linking NEK2 to chromosome and spindle regulation, RNA–ribonucleoprotein processes, vesicle/lysosome compartments, and ubiquitin-associated pathways. Targeted validations (streptavidin pull-down, co-immunoprecipitation, and immunofluorescence) confirmed the interaction and binding for selected partners. Focusing on NUSAP1, NEK2 induction led to rapid loss of NUSAP1 protein without changes in mRNA levels, and this decrease was blocked by the proteasome inhibitor MG-132. Consistently, NUSAP1 exhibited slower decay in cycloheximide chase assays and reduced ubiquitination in NEK2 knockout cells, indicating NEK2-dependent proteasomal turnover. Global proteomic analysis of NEK2-deficient cells revealed widespread remodeling of protein abundance, including increased NUSAP1 and decreased KIF2C, accompanied by coordinated changes in pathways governing mitotic progression, microtubule organization, and ubiquitin-mediated protein turnover. Together, these findings provide a dynamic map of the NEK2 interactome across the cell cycle and uncover a NEK2–NUSAP1 degradation pathway, offering a framework to study how kinase interactomes are remodeled by cell cycle progression.
Replication materials for: When polarization meets backsliding: Affective polarization and support for undemocratic practices in Turkey
(Koç University, 2026) Irmak, Seda; Karakoç, Büşra Söylemez; Aytaç, Selim Erdem