[{"oa":1,"pmid":1,"publication":"Nature","date_created":"2025-10-05T22:01:36Z","month":"11","scopus_import":"1","abstract":[{"text":"Protein design has focused on the design of ground states, ensuring that they are sufficiently low energy to be highly populated1. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another2,3. This is a challenging task because such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have focused on generating near-ideal structures4,5,6,7. Here we describe a general approach for designing systems that use an induced-fit power stroke8 to generate a structurally frustrated9 and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron–electron resonance spectroscopy and kinetic binding measurements show that incorporating excited states enables the design of effector-induced increases in dissociation rates as high as 5,700-fold. We highlight the power of this approach by designing rapid biosensors, kinetically controlled circuits and cytokine mimics that can be dissociated from their receptors within seconds, enabling dissection of the temporal dynamics of interleukin-2 signalling.","lang":"eng"}],"OA_place":"publisher","language":[{"iso":"eng"}],"page":"528-535","oa_version":"Published Version","doi":"10.1038/s41586-025-09549-z","citation":{"apa":"Broerman, A. J., Pollmann, C., Zhao, Y., Lichtenstein, M. A., Jackson, M. D., Tessmer, M. H., … Baker, D. (2025). Design of facilitated dissociation enables timing of cytokine signalling. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09549-z\">https://doi.org/10.1038/s41586-025-09549-z</a>","ieee":"A. J. Broerman <i>et al.</i>, “Design of facilitated dissociation enables timing of cytokine signalling,” <i>Nature</i>, vol. 647. Springer Nature, pp. 528–535, 2025.","chicago":"Broerman, Adam J., Christoph Pollmann, Yang Zhao, Mauriz A. Lichtenstein, Mark D. Jackson, Maxx H. Tessmer, Won Hee Ryu, et al. “Design of Facilitated Dissociation Enables Timing of Cytokine Signalling.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09549-z\">https://doi.org/10.1038/s41586-025-09549-z</a>.","ama":"Broerman AJ, Pollmann C, Zhao Y, et al. Design of facilitated dissociation enables timing of cytokine signalling. <i>Nature</i>. 2025;647:528-535. doi:<a href=\"https://doi.org/10.1038/s41586-025-09549-z\">10.1038/s41586-025-09549-z</a>","short":"A.J. Broerman, C. Pollmann, Y. Zhao, M.A. Lichtenstein, M.D. Jackson, M.H. Tessmer, W.H. Ryu, M. Ogishi, M.H. Abedi, D.D. Sahtoe, A. Allen, A. Kang, J. De La Cruz, E. Brackenbrough, B. Sankaran, A.K. Bera, D.M. Zuckerman, S. Stoll, K.C. Garcia, F.M. Praetorius, J. Piehler, D. Baker, Nature 647 (2025) 528–535.","ista":"Broerman AJ, Pollmann C, Zhao Y, Lichtenstein MA, Jackson MD, Tessmer MH, Ryu WH, Ogishi M, Abedi MH, Sahtoe DD, Allen A, Kang A, De La Cruz J, Brackenbrough E, Sankaran B, Bera AK, Zuckerman DM, Stoll S, Garcia KC, Praetorius FM, Piehler J, Baker D. 2025. Design of facilitated dissociation enables timing of cytokine signalling. Nature. 647, 528–535.","mla":"Broerman, Adam J., et al. “Design of Facilitated Dissociation Enables Timing of Cytokine Signalling.” <i>Nature</i>, vol. 647, Springer Nature, 2025, pp. 528–35, doi:<a href=\"https://doi.org/10.1038/s41586-025-09549-z\">10.1038/s41586-025-09549-z</a>."},"_id":"20430","corr_author":"1","intvolume":"       647","OA_type":"hybrid","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2025-11-13T00:00:00Z","ddc":["570"],"publisher":"Springer Nature","PlanS_conform":"1","author":[{"full_name":"Broerman, Adam J.","first_name":"Adam J.","last_name":"Broerman"},{"full_name":"Pollmann, Christoph","first_name":"Christoph","last_name":"Pollmann"},{"first_name":"Yang","full_name":"Zhao, Yang","last_name":"Zhao"},{"first_name":"Mauriz A.","full_name":"Lichtenstein, Mauriz A.","last_name":"Lichtenstein"},{"full_name":"Jackson, Mark D.","first_name":"Mark D.","last_name":"Jackson"},{"first_name":"Maxx H.","full_name":"Tessmer, Maxx H.","last_name":"Tessmer"},{"full_name":"Ryu, Won Hee","first_name":"Won Hee","last_name":"Ryu"},{"first_name":"Masato","full_name":"Ogishi, Masato","last_name":"Ogishi"},{"full_name":"Abedi, Mohamad H.","first_name":"Mohamad H.","last_name":"Abedi"},{"first_name":"Danny D.","full_name":"Sahtoe, Danny D.","last_name":"Sahtoe"},{"last_name":"Allen","full_name":"Allen, Aza","first_name":"Aza"},{"first_name":"Alex","full_name":"Kang, Alex","last_name":"Kang"},{"first_name":"Joshmyn","full_name":"De La Cruz, Joshmyn","last_name":"De La Cruz"},{"last_name":"Brackenbrough","first_name":"Evans","full_name":"Brackenbrough, Evans"},{"first_name":"Banumathi","full_name":"Sankaran, Banumathi","last_name":"Sankaran"},{"full_name":"Bera, Asim K.","first_name":"Asim K.","last_name":"Bera"},{"full_name":"Zuckerman, Daniel M.","first_name":"Daniel M.","last_name":"Zuckerman"},{"first_name":"Stefan","full_name":"Stoll, Stefan","last_name":"Stoll"},{"first_name":"K. Christopher","full_name":"Garcia, K. Christopher","last_name":"Garcia"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","orcid":"0000-0002-0806-8101","full_name":"Praetorius, Florian M","first_name":"Florian M"},{"last_name":"Piehler","first_name":"Jacob","full_name":"Piehler, Jacob"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"quality_controlled":"1","date_updated":"2026-01-05T13:18:17Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"FlPr"}],"title":"Design of facilitated dissociation enables timing of cytokine signalling","file":[{"date_updated":"2026-01-05T13:17:47Z","access_level":"open_access","checksum":"b4ec44134e2eb320a724dc29158dfda2","file_size":22099921,"success":1,"file_id":"20951","date_created":"2026-01-05T13:17:47Z","relation":"main_file","file_name":"2025_Nature_Broerman.pdf","creator":"dernst","content_type":"application/pdf"}],"publication_status":"published","type":"journal_article","acknowledgement":"We thank P. J. Y. Leung, K. L. Shelley, A. Pillai, C. Demakis, M. Exposit, K. Thompson, C. Savvides, R. J. Ragotte, G. Ahn and M. Glögl for discussions and technical support; K. VanWormer and L. Goldschmidt for technical support; S. R. Gerben and A. Murray for protein production support; and X. Li, M. Lamb, Z. Taylor and V. Adebomi for LC–MS support. This work was supported by the Audacious Project at the Institute for Protein Design (A.J.B., A.K., J.D.L.C., E.B. and A.K.B.); by a gift from Microsoft (A.J.B.); by the Nordstrom Barrier Institute for Protein Design Directors Fund (M.H.A. and F.P.); by Bill and Melinda Gates Foundation OPP1156262 (A.K. and J.D.L.C.); by the Open Philanthropy Project Improving Protein Design Fund (E.B. and A.K.B.); by the National Institutes of Health (NIH) National Institute of Allergy and Infectious Disease grant R0AI160052 (A.K.B.); by CRI Irvington Postdoctoral Fellowship 315511 (Y.Z.); by National Cancer Institute K00 award 4K00CA274708 (M.O.); by National Science Foundation grant MCB 2119837 and NIH grant GM115805 (W.H.R. and D.M.Z.); by NIH grant GM151956 (S.S.); by NIH AI-51321 (K.C.G.); by the DFG grants PI 405/15 and SFB 1557 (C.P. and J.P.); and by the Howard Hughes Medical Institute (A.K.B., K.C.G. and D.B.). The EPR spectrometer used for the DEER experiments was in part supported by NIH grant S10OD021557. This research used resources (FMX/AMX) of the National Synchrotron Light Source II, a US Department of Energy (DoE) Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under contract DE-SC0012704. The Center for BioMolecular Structure (CBMS) is supported mainly by the NIH National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DoE Office of Biological and Environmental Research (KP1607011). This work is based on research performed at the Northeastern Collaborative Access Team beamlines, which are funded by the NIGMS (P30 GM124165). The research used resources of the Advanced Photon Source, a US DoE Office of Science User Facility operated for the DoE Office of Science by Argonne National Laboratory under contract DE-AC02-06CH11357. The Berkeley Center for Structural Biology is supported by the NIH, NIGMS and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences and US DoE (DE-AC02-05CH11231).","isi":1,"day":"13","year":"2025","volume":647,"external_id":{"isi":["001577755600001"],"pmid":["40993395"]},"article_type":"original","file_date_updated":"2026-01-05T13:17:47Z"},{"citation":{"mla":"Last, Mart G. F., et al. “Streamlining Segmentation of Cryo-Electron Tomography Datasets with Ais.” <i>ELife</i>, vol. 13, 98552, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/eLife.98552\">10.7554/eLife.98552</a>.","ista":"Last MGF, Abendstein L, Voortman LM, Sharp TH. 2024. Streamlining segmentation of cryo-electron tomography datasets with Ais. eLife. 13, 98552.","short":"M.G.F. Last, L. Abendstein, L.M. Voortman, T.H. Sharp, ELife 13 (2024).","apa":"Last, M. G. F., Abendstein, L., Voortman, L. M., &#38; Sharp, T. H. (2024). Streamlining segmentation of cryo-electron tomography datasets with Ais. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.98552\">https://doi.org/10.7554/eLife.98552</a>","chicago":"Last, Mart G.F., Leoni Abendstein, Lenard M. Voortman, and Thomas H. Sharp. “Streamlining Segmentation of Cryo-Electron Tomography Datasets with Ais.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/eLife.98552\">https://doi.org/10.7554/eLife.98552</a>.","ieee":"M. G. F. Last, L. Abendstein, L. M. Voortman, and T. H. Sharp, “Streamlining segmentation of cryo-electron tomography datasets with Ais,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","ama":"Last MGF, Abendstein L, Voortman LM, Sharp TH. Streamlining segmentation of cryo-electron tomography datasets with Ais. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/eLife.98552\">10.7554/eLife.98552</a>"},"oa_version":"Published Version","doi":"10.7554/eLife.98552","intvolume":"        13","OA_type":"gold","_id":"18757","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible, and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available on GitHub. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based on in situ tomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET."}],"OA_place":"publisher","oa":1,"month":"12","publication":"eLife","date_created":"2025-01-05T23:01:57Z","pmid":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-12-20T00:00:00Z","article_number":"98552","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"DOAJ_listed":"1","file":[{"access_level":"open_access","checksum":"a4f0f906e4d5c1078208b317e78699d1","date_updated":"2025-01-08T08:51:45Z","relation":"main_file","file_name":"2024_eLife_Last.pdf","creator":"dernst","content_type":"application/pdf","success":1,"file_size":7445664,"file_id":"18774","date_created":"2025-01-08T08:51:45Z"}],"type":"journal_article","publication_status":"published","has_accepted_license":"1","date_updated":"2025-01-08T08:52:51Z","department":[{"_id":"FlPr"}],"title":"Streamlining segmentation of cryo-electron tomography datasets with Ais","article_processing_charge":"Yes","quality_controlled":"1","author":[{"full_name":"Last, Mart G.F.","first_name":"Mart G.F.","last_name":"Last"},{"first_name":"Leoni","full_name":"Abendstein, Leoni","orcid":"0000-0001-7634-5353","last_name":"Abendstein","id":"14f1f051-cd9d-11ef-9c94-8b942a882560"},{"first_name":"Lenard M.","full_name":"Voortman, Lenard M.","last_name":"Voortman"},{"last_name":"Sharp","first_name":"Thomas H.","full_name":"Sharp, Thomas H."}],"ddc":["570"],"publisher":"eLife Sciences Publications","file_date_updated":"2025-01-08T08:51:45Z","external_id":{"pmid":["39704648"]},"article_type":"original","day":"20","volume":13,"year":"2024","acknowledgement":"We thank A Koster and M Barcena for helpful discussions and kindly sharing the coronaviral replication organelle datasets. We are also grateful to van den Hoek et al., 2022 and Wu et al., 2023, for uploading the data that we used for Figure 5 onto EMPIAR and EMDB, as well as to the authors of various other datasets uploaded to these databases that are not discussed in this manuscript but that were useful for testing the software. We also thank the reviewers, whose comments were very helpful in improving the manuscript and the software. Finally, we are grateful the early Ais users who provided us with feedback on the software and reported issues. This research was supported by the following grants to THS: European Research Council H202 Grant 759517; European Union’s Horizon Europe Program IMAGINE grant 101094250, and the Netherlands Organization for Scientific Research Grant VI.Vidi.193.014."},{"pmid":1,"publication":"Nature","date_created":"2024-08-25T22:01:08Z","month":"08","oa":1,"scopus_import":"1","abstract":[{"text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry.","lang":"eng"}],"page":"911–920 ","language":[{"iso":"eng"}],"corr_author":"1","_id":"17463","intvolume":"       632","oa_version":"Published Version","doi":"10.1038/s41586-024-07813-2","citation":{"short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920.","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>, vol. 632, Springer Nature, 2024, pp. 911–920, doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. <i>Nature</i>. 2024;632:911–920. doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>","chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>.","apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>","ieee":"A. Pillai <i>et al.</i>, “De novo design of allosterically switchable protein assemblies,” <i>Nature</i>, vol. 632. Springer Nature, pp. 911–920, 2024."},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2024-08-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","publisher":"Springer Nature","ddc":["570"],"author":[{"last_name":"Pillai","first_name":"Arvind","full_name":"Pillai, Arvind"},{"full_name":"Idris, Abbas","first_name":"Abbas","last_name":"Idris"},{"last_name":"Philomin","first_name":"Annika","full_name":"Philomin, Annika"},{"full_name":"Weidle, Connor","first_name":"Connor","last_name":"Weidle"},{"full_name":"Skotheim, Rebecca","first_name":"Rebecca","last_name":"Skotheim"},{"first_name":"Philip J.Y.","full_name":"Leung, Philip J.Y.","last_name":"Leung"},{"last_name":"Broerman","full_name":"Broerman, Adam","first_name":"Adam"},{"first_name":"Cullen","full_name":"Demakis, Cullen","last_name":"Demakis"},{"full_name":"Borst, Andrew J.","first_name":"Andrew J.","last_name":"Borst"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","title":"De novo design of allosterically switchable protein assemblies","department":[{"_id":"FlPr"}],"date_updated":"2025-09-08T09:00:16Z","has_accepted_license":"1","publication_status":"published","type":"journal_article","file":[{"date_created":"2024-09-09T12:01:14Z","file_id":"18005","file_size":16572040,"success":1,"content_type":"application/pdf","creator":"dernst","file_name":"2024_Nature_Pillai.pdf","relation":"main_file","date_updated":"2024-09-09T12:01:14Z","checksum":"39127601621a360ec0edc538627eb211","access_level":"open_access"}],"isi":1,"acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","year":"2024","volume":632,"day":"22","article_type":"original","external_id":{"pmid":["39143214"],"isi":["001300534300019"]},"file_date_updated":"2024-09-09T12:01:14Z"}]