Language: English
Organisers: Sabancı University & TÜBİTAK ULAKBİM
Format: In-person
Level: Intermediate
Prerequisites: Participants are expected to have a knowledge of protein structure and experience with molecular dynamics simulations.
Topic: Computational Biology
General Information: In the theory session, we will introduce the fundamentals of molecular dynamics (MD) simulations of membrane proteins and focus on the principles of steered molecular dynamics (SMD), including how external forces are applied to explore conformational changes or molecular transport through biological channels. We will discuss how to set up protein–membrane systems and how to interpret SMD force profiles and potential of mean force (PMF) results. In the hands-on session, we will perform MD and SMD simulations of a membrane-embedded protein to observe the passage of a small molecule through the pore. The exercises will include system building, equilibration, and analysis using CHARMM-GUI, NAMD, and VMD software.
Trainer: Işık Kantarcioglu finished her B.Sc. in Genetics and Bioengineering at Istanbul Bilgi University in 2015. She then pursued an M.Sc. in Bioengineering at Bahcesehir University, graduating in 2018, with a thesis focused on computational approaches to discover novel inhibitors. In 2024, Işık earned her Ph.D. from Sabanci University, where her research centered on the TolC transmembrane efflux protein. She utilized both computational and experimental methods to reveal how TolC’s structural shifts enhance its ability to expel β-lactam antibiotics, aiming to understand the resistance mechanisms. Işık conducted her experiments at UTSW Medical Center in collaboration with Toprak Lab, supported by TÜBİTAK funding for a year. As a postdoctoral researcher at MIDST Lab, she plans to expand her research to investigate other efflux pumps and their roles in antibiotic resistance, advancing our understanding of bacterial defense mechanisms against a broader spectrum of antibiotics.
Contact: ncc@ulakbim.gov.tr
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