17 November, 2022 at 10:30 am, Canan Atılgan from Sabancı University is going to be at SABITALKS. The event will take place as hybrid. You can attend the event in person in the SABITA seminar hall.
Location: Istanbul Medipol University Kavacik Nourth Side https://goo.gl/maps/JDDjygVtFLWiPiMJA
*Zoom participation link will be active at the event time.
*Participants from outside SABITA must fill in the participation form.
Our group studies the dynamics of proteins using various modelling and simulation techniques, developing new approaches as the need arises. Over the years, there have been times where our computations have guided us to put forth interesting biological hypotheses which have led us to knock on the doors of colleagues working in the web lab to put to the test (modelers (M) ® experimentalists (E)). At other times, they have come to us seeking reasoning for observations they have not been able to quite explain (E ® M). Sometimes there is collaboration circles between the two sides, offering new questions as one delves deeper into the problem; M « E. In this seminar, I will talk about three such problems we have tackled with over the years. One of them is on the role of allostery and environment on the conformational multiplicity of a bacterial ferric binding protein, based on an idea we came up with when we were developing a new computational tool called perturbation-response scanning [Atilgan & Atilgan, 2009] (M ® E). In this problem, small angle x-ray scattering experiments and molecular dynamics simulations together have informed on how the dynamics are manipulated by ionic strength and an allosteric site. The second problem I will present is centered on the rational design of genetically encoded fluorescent biosensors. These are molecular tools that couple ligand-induced conformational changes to a fluorescence output. Structural determinants of successful biosensors are difficult to predict which makes the development of new biosensors a long trial-and-error process, presenting this E ® M problem. The ferric binding protein that came up in the previous example is selected as a model sensor domain. In this work, we propose a design strategy that combines Alphafold2 with molecular dynamics simulations for predicting structure and dynamics of the composite system [work in progress]. In the last story, I will present our work on the antibiotic resistance problem whereby very rewarding M « E collaborations have led us to explain how point mutations affect evolutionary paths using atomic scale dynamical information [Tamer et al. 2019], how such evolutionary trajectories may be steered using rational design [Manna et al, 2021], and how hidden allosteric sites may be utilized for alternative drug discovery strategies [work in progress].
Sabancı University
Canan Atılgan received her BS degree from the Department of Chemical Engineering at Boğaziçi University in 1991, and her PhD degree from the same institution in 1996. She was a postdoctoral research fellow at the Supercomputer Computations Research Institute of Florida State University through 1999. Since then, she has been a faculty member at the Faculty of Engineering and Natural Sciences of Sabancı University. She is the recipient of Boğaziçi University PhD Thesis (1996), TÜBİTAK Encouragement (2002), Turkish Academy of Sciences Young Scientist (2004), L’Oréal Turkey For Women in Science (2005) Awards. She is an elected member of the Science Academy and is its current President.
Dr. Atılgan’s expertise is on the computational and theoretical investigation of complex molecules. Her focus is on disclosing dynamical features of soft matter systems that lead to unique behaviour identified, but not explained, through experiments. Protein dynamics, manipulation of protein conformations, understanding the antibiotic resistance problem at the scale of the three-dimensional structure of single proteins, prediction and control of nanostructures formed by self-organizing oligomeric systems are areas of current interest for her.
Dr. Atılgan has also contributed to the reflection of the new learning patterns to the teaching of science at the University level. She has been applying and disseminating new paradigms such as student-centered learning and flipped classroom techniques to the courses she teaches at all levels of the University. She is on the editorial board of the Turkish language popular science web site sarkac.org where she is also a regular contributor.