Dynamics
TEAM LEADER
Burak V Kabasakal, PhD
Dr Burak V Kabasakal received his BSc degree in Chemical Engineering from Hacettepe University. After graduate studies in Chemical Engineering, Chemistry and Chemical Biology at Hacettepe University, University of California, Davis and Imperial College London, respectively, he obtained a PhD degree in Dr. James W Murray Lab in Life Sciences from Imperial College London, UK. During his PhD, he studied structural and functional relations of carbon and nitrogen fixation proteins, and he was awarded International Biochemical Society Student Scholarship (2016), European Crystallography Association (ECA) Young Scientist Award (2016), International Crystallography Association (IUCR) Young Scientist Award (2016), and Stanford University Bio-X Award (2015). He then moved to Bristol as a postdoctoral researcher at Professors Christiane Berger-Schaffitzel and Imre Berger Lab in the University of Bristol, Biochemistry Department for about two years. He is now a Principal Investigator at Turkish Accelerator and Radiation Laboratory (TARLA). His research interests are the structure-function relationship and dynamics of proteins, using electron cryo-microscopy, X-ray crystallography, and laser time-resolved absorption spectroscopy. He has nearly fourty protein structures published in the Protein Data Base (PDB).
PhD STUDENTS
Mehmet Çalıseki, MSc
Mehmet received his B.Sc degree from Anadolu University, and in his B.Sc thesis, he carried out artificial chromosome design and chromosome characterization analyses for a single-celled organism called Tetrahymena thermophila. He received his master's degree from Eskişehir Technical University and worked on human growth hormone production using the artificial chromosome vector in Tethrahymena thermophila. Mehmet later started his studies at Sabancı University as a doctoral student, working on autophagy in his first year and on pseudotype virus design for SARS-CoV-2 in his second year. He has been working at Turkish Accelerator & Radiation Laboratory (TARLA) to continue his PhD studies in structural biology.
Contact e-mail: mcaliseki@sabanciuniv.edu
Hatice Akkulak, MSc
Hatice received her BSc degree in Molecular Biology and Genetics from METU in 2021. She completed her internship at Hacettepe University Faculty of Medicine, Department of Child Health and Diseases, Genetics Laboratory in the summer of 2020, gaining skills in cytogenetics and molecular genetics. In October 2020, she joined Q-OmicS Lab as an undergraduate researcher, exploring proteomics and mass spectrometry. She learned to use qualitative and quantitative proteomics software, and she started her master’s degree in the Biochemistry department at METU. Hatice conducted her studies as a member of the Turkish Accelerator & Radiation Laboratory (TARLA) and successfully completed her master's degree in August 2023. Her master's thesis, titled "Structural Proteomics of FtsH Complexes Using Cross-linking Mass Spectrometry," delved into protein structures and interactions. Under the mentorship of Assist. Prof. Dr. Sureyya Ozcan and Dr. Burak V. Kabasakal, she mastered cross-linking software and molecular visualization tools such as UCSF Chimera and PyMOL, developing advanced data analysis skills. Now a Ph.D. student in the Biochemistry department at METU, Hatice focuses on protein purification and structural proteomics. Her journey exemplifies a continuous pursuit of knowledge and expertise in the field. Contact e-mail: hatice.akkulak@metu.edu.tr
Ataollah Nosratinia, MSc
Ataollah received his B.Sc. degree in Cellular and Molecular Biology from Iran. In 2018, he entered the Biotechnology M.Sc. program at METU, where he developed scaffolds for bone tissue engineering purposes gaining experience and skills in handling biomaterials, characterization techniques, and cell culture studies among others. Ataollah continued his academic career in a PhD program at METU joining the Q-OmicS Lab and BvK LaB. He is currently working as a research scholar within the TÜBİTAK 2519 International Collaboration Project with South Korea, involving developing novel peptidomimetic antimicrobial inhibitors targeting bacteria.
MSc STUDENTS
Tuğberk Deniz Karakaş
Tuğberk received their BSc degree in Molecular Biology and Genetics from the Başkent University in 2021. During their senior year, they worked with Asst. Prof. Dr. Özge Erdemli in the project titled “Aptamer modified AuNP-based bacterial biosensor with aloe vera green synthesis method”. During their internship at METU with Asst. Prof. Dr. Çağdaş Devrim Son, they worked on a project about activation and in vitro tests of Arrestinin, which can bind to target proteins independently of receptor phosphorylation, with the help of small molecules. After graduation, they worked at Genenzyme Biotechnology, where they had the chance to improve herself in making RT-PCR test kits for SARS-CoV-2 and gold-nanoparticle based SARS-CoV-2 rapid lateral flow test. They are now a Biotechnology MSc student at METU, and work at TARLA to carry out research focusing on the purification and characterization of sugar beet leaf proteins within the scope of FunTomP project. Contact e-mail: tugba.karakas@metu.edu.tr
Gizem Biter
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Gizem received her BSc degree in Chemistry from Middle East Technical University in 2022. She did her internship as a Quality Control Intern at PharmaVision in İstanbul and got the chance to investigate drug mechanisms on the human body with various types of drugs. In 2021, she joined Q-OmicS Lab and BvK LaB as an undergraduate researcher to learn proteomics and software such as Skyline, MaxQuant, and PyMOL, also structural biology of membrane proteins at the Turkish Accelerator and Radiation Laboratory (TARLA) within the TÜBİTAK STAR program. Currently, she is a Chemistry MSc student at METU and studies on the development of protein-protein interaction inhibitors at TARLA as an MSc student researcher within the TUBİTAK 1001 program. Contact e-mail: gizem.biter@metu.edu.tr
Nurefşan Kuzucu
Nurefşan received her BSc degree in Food Engineering in 2022 and Bioengineering in 2023 from Ege University. She gained knowledge about basic laboratory operations and practices in related fields by doing internships in molecular biology, genetics, and microbiology laboratories. She's been introduced to structural/computational biology by her supervisor Assoc. Prof. Dr. Burcu Kaplan Türköz, and she worked on AlphaFold taste receptor protein structures in her BSc thesis under her mentorship. During her thesis period, she decided to continue her career path by doing academic research in the field of structural biology. She is now a Biotechnology MSc student at Ege University and a member of BKT Lab and BvK Lab, learning to apply and analyze experimental methods in the structural biology field to pursue her career goal.
Contact e-mail: havvanurefsankuzucu@gmail.com