6 results on '"Gümüş, Zeynep Hülya"'
Search Results
2. Identification of SERPINE1 as a regulator of glioblastoma cell dispersal with transcriptome profiling
- Author
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Şeker, Fidan; Cingöz, Ahmet; Sur Erdem, İlknur; Ergüder, Nazlı; Erkent, Alp; Önder, Tuğba Bağcı (ORCID 0000-0003-3646-2613 & YÖK ID 184359); Gönen, Mehmet (ORCID 0000-0002-2483-075X & YÖK ID 237468), Uyulur, Fırat; Selvan, Myvizhi Esa; Gümüş, Zeynep Hülya; Bayraktar, Halil; Wakimoto, Hiroaki, Graduate School of Sciences and Engineering; College of Engineering, Department of Industrial Engineering, Şeker, Fidan; Cingöz, Ahmet; Sur Erdem, İlknur; Ergüder, Nazlı; Erkent, Alp; Önder, Tuğba Bağcı (ORCID 0000-0003-3646-2613 & YÖK ID 184359); Gönen, Mehmet (ORCID 0000-0002-2483-075X & YÖK ID 237468), Uyulur, Fırat; Selvan, Myvizhi Esa; Gümüş, Zeynep Hülya; Bayraktar, Halil; Wakimoto, Hiroaki, Graduate School of Sciences and Engineering; College of Engineering, and Department of Industrial Engineering
- Abstract
Scientific and Technological Research Council of Turkey (TÜBİTAK); Koç University; Turkish Academy of Sciences (TÜBA), TÜBA-Gedip The Young Scientist Award Program) and the Science Academy of Turkey (BAGEP; The Young Scientist Award Program); LUNGevity foundation
- Published
- 2019
3. Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
- Author
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Erman, Burak (ORCID 0000-0002-2496-6059 & YÖK ID 179997), Vatansever, Sezen; Gümüş, Zeynep Hülya, College of Engineering, Department of Chemical and Biological Engineering, Erman, Burak (ORCID 0000-0002-2496-6059 & YÖK ID 179997), Vatansever, Sezen; Gümüş, Zeynep Hülya, College of Engineering, and Department of Chemical and Biological Engineering
- Abstract
K-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to understand how it alters the regulation of its dynamics. Here, we present local changes in K-Ras structure, conformation and dynamics upon G12D mutation, from long-timescale Molecular dynamics simulations of active (GTP-bound) and inactive (GDP-bound) forms of wild-type and mutant K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and correlated residue motions. Our results reveal that the local changes in K-Ras are specific to bound nucleotide (GTP or GDP), and we provide a structural basis for this. Specifically, we show that G12D mutation causes a shift in the population of local conformational states of K-Ras, especially in Switch-II (SII) and alpha 3-helix regions, in favor of a conformation that is associated with a catalytically impaired state through structural changes; it also causes SII motions to anti-correlate with other regions. This detailed picture of G12D mutation effects on the local dynamic characteristics of both active and inactive protein helps enhance our understanding of local K-Ras dynamics, and can inform studies on the development of direct inhibitors towards the treatment of K-Ras(G12D)-driven cancers., LUNGevity Foundation; Icahn Institute at Icahn School of Medicine at Mount Sinai
- Published
- 2019
4. ANGI-08. IDENTIFICATION OF NOVEL MOLECULAR PLAYERS OF GBM CELL DISPERSAL THROUGH AN IN VITRO PROFILING APPROACH
- Author
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Seker, Fidan, primary, Erkent, Alp, additional, Ergüder, Nazlı, additional, Sevinç, Kenan, additional, Gönen, Mehmet, additional, Gümüş, Zeynep Hülya, additional, and Bagci-Onder, Tugba, additional
- Published
- 2016
- Full Text
- View/download PDF
5. Identification of SERPINE1 as a regulator of glioblastoma cell dispersal with transcriptome profiling
- Author
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Ahmet Cingoz, Alp Erkent, Fırat Uyulur, Fidan Seker, Zeynep H. Gümüş, Myvizhi Esai Selvan, Ilknur Sur-Erdem, Halil Bayraktar, Mehmet Gönen, Tugba Bagci-Onder, Hiroaki Wakimoto, Nazli Erguder, Şeker, Fidan, Cingöz, Ahmet, Sur Erdem, İlknur, Ergüder, Nazlı, Erkent, Alp, Önder, Tuğba Bağcı (ORCID 0000-0003-3646-2613 & YÖK ID 184359), Gönen, Mehmet (ORCID 0000-0002-2483-075X & YÖK ID 237468), Uyulur, Fırat, Selvan, Myvizhi Esa, Gümüş, Zeynep Hülya, Bayraktar, Halil, Wakimoto, Hiroaki, Graduate School of Sciences and Engineering, College of Engineering, and Department of Industrial Engineering
- Subjects
0301 basic medicine ,Cancer Research ,Cell ,Regulator ,Biology ,urologic and male genital diseases ,lcsh:RC254-282 ,Transcriptome ,03 medical and health sciences ,transcriptome analysis ,0302 clinical medicine ,Glioma ,medicine ,dispersal ,Cell adhesion ,Dispersal ,GBM ,Transcriptome analysis ,urogenital system ,Mesenchymal stem cell ,Spheroid ,gbm ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.disease ,nervous system diseases ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Biological dispersal - Abstract
High mortality rates of glioblastoma (GBM) patients are partly attributed to the invasive behavior of tumor cells that exhibit extensive infiltration into adjacent brain tissue, leading to rapid, inevitable, and therapy-resistant recurrence. In this study, we analyzed transcriptome of motile (dispersive) and non-motile (core) GBM cells using an in vitro spheroid dispersal model and identified SERPINE1 as a modulator of GBM cell dispersal. Genetic or pharmacological inhibition of SERPINE1 reduced spheroid dispersal and cell adhesion by regulating cell-substrate adhesion. We examined TGFβ as a potential upstream regulator of SERPINE1 expression. We also assessed the significance of SERPINE1 in GBM growth and invasion using TCGA glioma datasets and a patient-derived orthotopic GBM model. SERPINE1 expression was associated with poor prognosis and mesenchymal GBM in patients. SERPINE1 knock-down in primary GBM cells suppressed tumor growth and invasiveness in the brain. Together, our results indicate that SERPINE1 is a key player in GBM dispersal and provide insights for future anti-invasive therapy design., Scientific and Technological Research Council of Turkey (TÜBİTAK); Koç University; Turkish Academy of Sciences (TÜBA), TÜBA-Gedip The Young Scientist Award Program) and the Science Academy of Turkey (BAGEP; The Young Scientist Award Program); LUNGevity foundation
- Published
- 2019
6. Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
- Author
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Burak Erman, Zeynep H. Gümüş, Sezen Vatansever, Erman, Burak (ORCID 0000-0002-2496-6059 & YÖK ID 179997), Vatansever, Sezen, Gümüş, Zeynep Hülya, College of Engineering, and Department of Chemical and Biological Engineering
- Subjects
0301 basic medicine ,Models, Molecular ,GTP' ,Protein Conformation ,Population ,Mutant ,lcsh:Medicine ,Plasma protein binding ,Article ,Proto-Oncogene Proteins p21(ras) ,03 medical and health sciences ,Molecular dynamics ,Structure-Activity Relationship ,Computational biophysics ,0302 clinical medicine ,Protein structure ,Humans ,Nucleotide ,lcsh:Science ,education ,Science and technology ,chemistry.chemical_classification ,education.field_of_study ,Multidisciplinary ,Molecular-dynamics ,Signal-Transduction ,Gtpase ,Inhibitors ,Binding ,Protein ,Kras ,Communication ,Switch ,lcsh:R ,Dynamics (mechanics) ,Hydrogen Bonding ,030104 developmental biology ,chemistry ,Amino Acid Substitution ,Mutation (genetic algorithm) ,Mutation ,Biophysics ,lcsh:Q ,Molecular modelling ,030217 neurology & neurosurgery ,Function (biology) ,Algorithms ,Protein Binding - Abstract
K-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to understand how it alters the regulation of its dynamics. Here, we present local changes in K-Ras structure, conformation and dynamics upon G12D mutation, from long-timescale Molecular dynamics simulations of active (GTP-bound) and inactive (GDP-bound) forms of wild-type and mutant K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and correlated residue motions. Our results reveal that the local changes in K-Ras are specific to bound nucleotide (GTP or GDP), and we provide a structural basis for this. Specifically, we show that G12D mutation causes a shift in the population of local conformational states of K-Ras, especially in Switch-II (SII) and alpha 3-helix regions, in favor of a conformation that is associated with a catalytically impaired state through structural changes; it also causes SII motions to anti-correlate with other regions. This detailed picture of G12D mutation effects on the local dynamic characteristics of both active and inactive protein helps enhance our understanding of local K-Ras dynamics, and can inform studies on the development of direct inhibitors towards the treatment of K-Ras(G12D)-driven cancers., LUNGevity Foundation; Icahn Institute at Icahn School of Medicine at Mount Sinai
- Published
- 2017
- Full Text
- View/download PDF
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