@article{20430,
  abstract     = {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.},
  author       = {Broerman, Adam J. and Pollmann, Christoph and Zhao, Yang and Lichtenstein, Mauriz A. and Jackson, Mark D. and Tessmer, Maxx H. and Ryu, Won Hee and Ogishi, Masato and Abedi, Mohamad H. and Sahtoe, Danny D. and Allen, Aza and Kang, Alex and De La Cruz, Joshmyn and Brackenbrough, Evans and Sankaran, Banumathi and Bera, Asim K. and Zuckerman, Daniel M. and Stoll, Stefan and Garcia, K. Christopher and Praetorius, Florian M and Piehler, Jacob and Baker, David},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {528--535},
  publisher    = {Springer Nature},
  title        = {{Design of facilitated dissociation enables timing of cytokine signalling}},
  doi          = {10.1038/s41586-025-09549-z},
  volume       = {647},
  year         = {2025},
}

@article{18757,
  abstract     = {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.},
  author       = {Last, Mart G.F. and Abendstein, Leoni and Voortman, Lenard M. and Sharp, Thomas H.},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Streamlining segmentation of cryo-electron tomography datasets with Ais}},
  doi          = {10.7554/eLife.98552},
  volume       = {13},
  year         = {2024},
}

@article{17463,
  abstract     = {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.},
  author       = {Pillai, Arvind and Idris, Abbas and Philomin, Annika and Weidle, Connor and Skotheim, Rebecca and Leung, Philip J.Y. and Broerman, Adam and Demakis, Cullen and Borst, Andrew J. and Praetorius, Florian M and Baker, David},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {911–920 },
  publisher    = {Springer Nature},
  title        = {{De novo design of allosterically switchable protein assemblies}},
  doi          = {10.1038/s41586-024-07813-2},
  volume       = {632},
  year         = {2024},
}