Magnus, C. J. et al. Ultrapotent chemogenetics for research and potential clinical applications. Science 364, eaav5282 (2019).
Jing, M. et al. A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies. Nat. Biotechnol. 36, 726–737 (2018).
Gouaux, E. & MacKinnon, R. Principles of selective ion transport in channels and pumps. Science 310, 1461–1465 (2005).
Yue, L., Navarro, B., Ren, D., Ramos, A. & Clapham, D. E. The cation selectivity filter of the bacterial sodium channel, NaChBac. J. Gen. Physiol. 120, 845–853 (2002).
Tang, L. et al. Structural basis for Ca2+ selectivity of a voltage-gated calcium channel. Nature 505, 56–61 (2014).
Nilius, B. et al. The single pore residue Asp542 determines Ca2+ permeation and Mg2+ block of the epithelial Ca2+ channel. J. Biol. Chem. 276, 1020–1025 (2001).
Ellinor, P. T., Yang, J., Sather, W. A., Zhang, J.-F. & Tsien, R. W. Ca2+ channel selectivity at a single locus for high-affinity Ca2+ interactions. Neuron 15, 1121–1132 (1995).
Yang, J., Elllnor, P. T., Sather, W. A., Zhang, J.-F. & Tsien, R. W. Molecular determinants of Ca2+ selectivity and ion permeation in L-type Ca2+ channels. Nature 366, 158–161 (1993).
Meyer, J. O. et al. Disruption of the key Ca2+ binding site in the selectivity filter of neuronal voltage-gated calcium channels inhibits channel trafficking. Cell Rep. 29, 22–33 (2019).
Long, S. B., Tao, X., Campbell, E. B. & MacKinnon, R. Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450, 376–382 (2007).
Derebe, M. G., Zeng, W., Li, Y., Alam, A. & Jiang, Y. Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore. Proc. Natl Acad. Sci. USA 108, 592–597 (2011).
Shen, P. S. et al. The structure of the polycystic kidney disease channel PKD2 in lipid nanodiscs. Cell 167, 763–773 (2016).
Magnus, C. J. et al. Chemical and genetic engineering of selective ion channel–ligand interactions. Science 333, 1292–1296 (2011).
Wu, Z. et al. A sensitive GRAB sensor for detecting extracellular ATP in vitro and in vivo. Neuron 110, 770–782 (2022).
Joh, N. H. et al. De novo design of a transmembrane Zn2+-transporting four-helix bundle. Science 346, 1520–1524 (2014).
Mravic, M. et al. Packing of apolar side chains enables accurate design of highly stable membrane proteins. Science 363, 1418–1423 (2019).
Mahendran, K. R. et al. A monodisperse transmembrane α-helical peptide barrel. Nat. Chem. 9, 411–419 (2017).
Krishnan R, S. et al. Assembly of transmembrane pores from mirror-image peptides. Nat. Commun. 13, 5377 (2022).
Lear, J. D., Wasserman, Z. R. & DeGrado, W. F. Synthetic amphiphilic peptide models for protein ion channels. Science 240, 1177–1181 (1988).
Xu, C. et al. Computational design of transmembrane pores. Nature 585, 129–134 (2020).
Scott, A. J. et al. Constructing ion channels from water-soluble α-helical barrels. Nat. Chem. 13, 643–650 (2021).
Berhanu, S. et al. Sculpting conducting nanopore size and shape through de novo protein design. Science 385, 282–288 (2024).
Vorobieva, A. A. et al. De novo design of transmembrane β barrels. Science 371, eabc8182 (2021).
Harding, M. M. The geometry of metal–ligand interactions relevant to proteins. Acta Crystallogr. D 55, 1432–1443 (1999).
Harding, M. M. The geometry of metal–ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal–donor interactions. Acta Crystallogr. D 56, 857–867 (2000).
Elinder, F. & Århem, P. Metal ion effects on ion channel gating. Q. Rev. Biophys. 36, 373–427 (2003).
Corry, B., Allen, T. W., Kuyucak, S. & Chung, S.-H. Mechanisms of permeation and selectivity in calcium channels. Biophys. J. 80, 195–214 (2001).
Hess, P. & Tsien, R. W. Mechanism of ion permeation through calcium channels. Nature 309, 453–456 (1984).
Sather, W. A. & McCleskey, E. W. Permeation and selectivity in calcium channels. Annu. Rev. Physiol. 65, 133–159 (2003).
Almers, W., McCleskey, E. W. & Palade, P. T. A non-selective cation conductance in frog muscle membrane blocked by micromolar external calcium ions. J. Physiol. 353, 565–583 (1984).
Cibulsky, S. M. & Sather, W. A. The EEEE locus is the sole high-affinity Ca2+ binding structure in the pore of a voltage-gated Ca2+ channel: block by Ca2+ entering from the intracellular pore entrance. J. Gen. Physiol. 116, 349–362 (2000).
Tang, L. et al. Structural basis for inhibition of a voltage-gated Ca2+ channel by Ca2+ antagonist drugs. Nature 537, 117–121 (2016).
Wu, J. et al. Structure of the voltage-gated calcium channel Cav1.1 at 3.6 Å resolution. Nature 537, 191–196 (2016).
Saotome, K., Singh, A. K., Yelshanskaya, M. V. & Sobolevsky, A. I. Crystal structure of the epithelial calcium channel TRPV6. Nature 534, 506–511 (2016).
Hou, X., Outhwaite, I. R., Pedi, L. & Long, S. B. Cryo-EM structure of the calcium release-activated calcium channel Orai in an open conformation. eLife 9, e62772 (2020).
Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).
Dauparas, J. et al. Robust deep learning–based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Zhu, W., Shenoy, A., Kundrotas, P. & Elofsson, A. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes. Bioinformatics 39, btad424 (2023).
Feldman, D. et al. Optical pooled screens in human cells. Cell 179, 787–799 (2019).
Pravda, L. et al. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46, W368–W373 (2018).
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2024).
Kim, W. et al. Rapid and sensitive protein complex alignment with Foldseek-Multimer. Nat. Methods 22, 469–472 (2025).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665–W667 (2004).
Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128 (2018).
Vennekens, R. et al. Permeation and gating properties of the novel epithelial Ca2+ channel. J. Biol. Chem. 275, 3963–3969 (2000).
Hille, B. Ion Channels of Excitable Membranes (Sinauer, 2001).
Voets, T. et al. CaT1 and the calcium release-activated calcium channel manifest distinct pore properties. J. Biol. Chem. 276, 47767–47770 (2001).
Yue, L., Peng, J.-B., Hediger, M. A. & Clapham, D. E. CaT1 manifests the pore properties of the calcium-release-activated calcium channel. Nature 410, 705–709 (2001).
McNally, B. A., Somasundaram, A., Yamashita, M. & Prakriya, M. Gated regulation of CRAC channel ion selectivity by STIM1. Nature 482, 241–245 (2012).
Prakriya, M. The molecular physiology of CRAC channels. Immunol. Rev. 231, 88–98 (2009).
Hoth, M. & Penner, R. Depletion of intracellular calcium stores activates a calcium current in mast cells. Nature 355, 353–356 (1992).
Lansman, J. B., Hess, P. & Tsien, R. W. Blockade of current through single calcium channels by Cd2+, Mg2+, and Ca2+. Voltage and concentration dependence of calcium entry into the pore. J. Gen. Physiol. 88, 321–347 (1986).
Bers, D. M., Patton, C. W. & Nuccitelli, R. in Methods in Cell Biology Vol. 99 (ed. Whitaker, M.) 1–26 (Academic Press, 2010).
Hou, X., Burstein, S. R. & Long, S. B. Structures reveal opening of the store-operated calcium channel Orai. eLife 7, e36758 (2018).
Zhang, K., Wu, H., Hoppe, N., Manglik, A. & Cheng, Y. Fusion protein strategies for cryo-EM study of G protein-coupled receptors. Nat. Commun. 13, 4366 (2022).
Brunette, T. J. et al. Exploring the repeat protein universe through computational protein design. Nature 528, 580–584 (2015).
Drożdżyk, K. et al. Cryo-EM structures and functional properties of CALHM channels of the human placenta. eLife 9, e55853 (2020).
Demura, K. et al. Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies. Sci. Adv. 6, eaba8105 (2020).
Sharpe, H. J., Stevens, T. J. & Munro, S. A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142, 158–169 (2010).
Levental, I. & Lyman, E. Regulation of membrane protein structure and function by their lipid nano-environment. Nat. Rev. Mol. Cell Biol. 24, 107–122 (2023).
Dauparas, J. et al. Atomic context-conditioned protein sequence design using LigandMPNN. Nat. Methods 22, 717–723 (2025).
Hoover, D. & Lubkowski, J. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 30, e43 (2002).
Jiang, D., Gamal El-Din, T., Zheng, N. & Catterall, W. A. in Methods in Enzymology Vol. 653 (eds Minor, D. L. & Colecraft, H. M.) Ch. 5 (Academic Press, 2021).
Jiang, D. et al. Open-state structure and pore gating mechanism of the cardiac sodium channel. Cell 184, 5151–5162 (2021).
Jiang, D. et al. Structure of the cardiac sodium channel. Cell 180, 122–134 (2020).
Lenaeus, M., Gamal El-Din, T. M., Tonggu, L., Zheng, N. & Catterall, W. A. Structural basis for inhibition of the cardiac sodium channel by the atypical antiarrhythmic drug ranolazine. Nat. Cardiovasc. Res. 2, 587–594 (2023).
Tonggu, L. et al. Dual receptor-sites reveal the structural basis for hyperactivation of sodium channels by poison-dart toxin batrachotoxin. Nat. Commun. 15, 2306 (2024).
Mastronarde, D. N. SerialEM: a program for automated tilt series acquisition on Tecnai microscopes using prediction of specimen position. Microsc. Microanal. 9, 1182–1183 (2003).
Sun, M. et al. Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM. J. Struct. Biol. 213, 107745 (2021).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
