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Tajima S, Kim YS, Fukuda M, Jo Y, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell 2023; 186:4325-4344.e26. [PMID: 37652010 PMCID: PMC7615185 DOI: 10.1016/j.cell.2023.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.
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Affiliation(s)
- Seiya Tajima
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - YoungJu Jo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Seiwa Nakamura
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | | | - Shunki Takaramoto
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Suhyang Kim
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Hisako Ikeda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Jaeah Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell 2022; 185:672-689.e23. [PMID: 35114111 PMCID: PMC7612760 DOI: 10.1016/j.cell.2022.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
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Affiliation(s)
- Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Elina Thadhani
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Takashi Nagata
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masae Konno
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Sean Quirin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tyler Benster
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tomoko Uemura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma, Kanazawa, Japan; High-Speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan; RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Palo Alto, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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