Abstract: Proteins possess exceptional conformational flexibility, allowing for precise functional regulation through allostery. This property is central to the design of protein-based biosensors, which detect environmental cues such as ligand binding and transduce them into measurable signals, typically fluorescence. However, optimizing their design remains a significant challenge and is often pursued through extensive experimental screening. In this talk, I will summarize our findings that guide the rational design of genetically encoded fluorescent biosensors. These will include selection of fluorescent protein (FP) insertion sites on the sensory domain (SD) via our recently developed novel approach [1], Multiply Perturbed Response; prediction of the three-dimensional structures of the full constructs in both apo and holo forms via AlphaFold [2]; and precise quantification of biosensor performance by measuring chromophore accessibility obtained from affordable lengths of molecular dynamics simulations [3]. I will also discuss the allosteric mechanisms that control the dynamic interplay between the SD and the FP, exploring how structural interfaces affect fluorescence modulation upon ligand binding. Throughout the talk, I will provide cues on how physics-based collective variables may be utilized for mapping protein conformational transitions, a concept that has multitude of applications that extend far beyond nanobiosensor design. [Supported by TUBITAK project #121Z329.]

[1] M. Berksoz, A.R. Atilgan, B. Kocuk, C. Atilgan, Journal of Molecular Biology, accepted.

[2] M. Berksoz and C. Atilgan, Proteins, 92, 923 - 932 (2024).

[3] M. Berksoz and C. Atilgan, J. Chem. Theory Comput., 21, 4910–4920 (2025).

Bio: Canan Atılgan received her BS degree from the Department of Chemical Engineering of 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 an elected member of Bilim Akademisi - Science Academy, Türkiye and served as its President for the 2021-2024 term. She is an elected member of EMBO and Academia Europaea.

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 behavior 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 and nanobiosensor design are areas of current interest for her. She is also interested in science policy issues and new ways for disseminating scientific findings. http://people.sabanciuniv.edu/canan/