Computational design of a genetically encoded iron biosensor

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2022-10

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Berksöz, Melike
Atılgan, Canan

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Genetically encoded fluorescent biosensors (GEFB) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are determined only in hindsight when the crystal structures of both ligand-bound and ligand-free forms are available. This makes the development of new biosensors for desired analytes a long trial-and-error process. In this work, we propose a novel design strategy that combines Alphafold2 (AF2) and all-atom molecular dynamics (MD) simulations as predictors of GEFB structure and dynamics. H. influenza ferric binding protein (FBP) is selected as a model sensor protein. Hydrogen bond occupancies around the chromophore are analyzed in apo and holo states of fused FBP. Hydrogen bond profile of intact GFP alone with neutral and anionic chromophore was used as a reference for dark and bright states respectively.

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https://hibit2022.ims.metu.edu.tr/
https://hdl.handle.net/11511/101300

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The International Symposium on Health Informatics and Bioinformatics

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Graduate School of Informatics, Conference / Seminar

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Citation Formats

M. Berksöz and C. Atılgan, “Computational design of a genetically encoded iron biosensor,” Erdemli, Mersin, TÜRKİYE, 2022, p. 1030, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr/.