[{"year":"2017","day":"15","publication":"Synthetic Protein Switches","page":"71 - 87","doi":"10.1007/978-1-4939-6940-1_5","date_published":"2017-03-15T00:00:00Z","date_created":"2018-12-11T11:49:24Z","publisher":"Springer","quality_controlled":"1","citation":{"ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Clifton","full_name":"Clifton, Ben","first_name":"Ben"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"publist_id":"6451","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["10643745"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":1596,"abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"oa_version":"None","scopus_import":1,"alternative_title":["Methods in Molecular Biology"],"month":"03","intvolume":" 1596","date_updated":"2021-01-12T08:22:13Z","department":[{"_id":"HaJa"}],"series_title":"Synthetic Protein Switches","_id":"957","type":"book_chapter","status":"public"},{"citation":{"mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6450","author":[{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"first_name":"William","full_name":"Zhang, William","last_name":"Zhang"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"first_name":"Megan","full_name":"O'Mara, Megan","last_name":"O'Mara"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"}],"title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"quality_controlled":"1","publisher":"Springer","year":"2017","day":"15","publication":"Synthetic Protein Switches","page":"89 - 99","date_published":"2017-05-15T00:00:00Z","doi":"10.1007/978-1-4939-6940-1_6","date_created":"2018-12-11T11:49:24Z","series_title":"Synthetic Protein Switches","_id":"958","type":"book_chapter","status":"public","date_updated":"2021-01-12T08:22:13Z","department":[{"_id":"HaJa"}],"abstract":[{"lang":"eng","text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors."}],"oa_version":"None","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"month":"05","intvolume":" 1596","publication_identifier":{"issn":["10643745"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":1596},{"acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","quality_controlled":"1","publisher":"Elsevier","year":"2017","isi":1,"publication":"Current Opinion in Biotechnology","day":"01","page":"8 - 14","date_created":"2018-12-11T11:49:45Z","doi":"10.1016/j.copbio.2017.02.006","date_published":"2017-12-01T00:00:00Z","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.006.","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier, pp. 8–14, 2017.","short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","apa":"Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.006","ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006","mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology, vol. 48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000418313200003"]},"publist_id":"6365","author":[{"first_name":"Viviana","last_name":"Agus","full_name":"Agus, Viviana"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"title":"Optogenetic methods in drug screening: Technologies and applications","abstract":[{"lang":"eng","text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function."}],"oa_version":"None","scopus_import":"1","intvolume":" 48","month":"12","publication_status":"published","publication_identifier":{"issn":["09581669"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":48,"_id":"1026","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-22T09:26:06Z","department":[{"_id":"HaJa"}]},{"_id":"1028","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-03-27T23:30:13Z","ddc":["540"],"department":[{"_id":"CaGu"},{"_id":"HaJa"}],"file_date_updated":"2019-01-18T09:39:55Z","abstract":[{"text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 56","publication_identifier":{"issn":["14337851"]},"publication_status":"published","file":[{"file_id":"5845","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-18T09:39:55Z","file_name":"2017_communications_Kainrath.pdf","creator":"dernst","date_updated":"2019-01-18T09:39:55Z","file_size":2614942}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"},{"relation":"part_of_dissertation","status":"public","id":"7680"}]},"volume":56,"issue":"16","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets [do not use to be deleted]","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6362","author":[{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart"},{"full_name":"Distel, Martin","last_name":"Distel","first_name":"Martin"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"external_id":{"isi":["000398154000038"]},"article_processing_charge":"No","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","isi":1,"year":"2017","day":"20","publication":"Angewandte Chemie - International Edition","page":"4608-4611","doi":"10.1002/anie.201611998","date_published":"2017-03-20T00:00:00Z","date_created":"2018-12-11T11:49:46Z"},{"author":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"publist_id":"5756","department":[{"_id":"HaJa"}],"title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","citation":{"ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure. Cell Press, 2016. https://doi.org/10.1016/j.str.2016.01.002.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. Cell Press. https://doi.org/10.1016/j.str.2016.01.002","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 2016;24(2):213-215. doi:10.1016/j.str.2016.01.002","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” Structure, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:10.1016/j.str.2016.01.002."},"date_updated":"2021-01-12T06:50:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","_id":"1440","page":"213 - 215","date_published":"2016-02-02T00:00:00Z","issue":"2","volume":24,"doi":"10.1016/j.str.2016.01.002","ec_funded":1,"date_created":"2018-12-11T11:52:02Z","publication_status":"published","year":"2016","day":"02","language":[{"iso":"eng"}],"publication":"Structure","publisher":"Cell Press","scopus_import":1,"quality_controlled":"1","month":"02","intvolume":" 24","oa_version":"None","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232)."}]