1
|
Huang S, Liu X, Lin S, Glynn C, Felix K, Sahasrabudhe A, Maley C, Xu J, Chen W, Hong E, Crosby AJ, Wang Q, Rao S. Control of polymers' amorphous-crystalline transition enables miniaturization and multifunctional integration for hydrogel bioelectronics. Nat Commun 2024; 15:3525. [PMID: 38664445 PMCID: PMC11045824 DOI: 10.1038/s41467-024-47988-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/26/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Soft bioelectronic devices exhibit motion-adaptive properties for neural interfaces to investigate complex neural circuits. Here, we develop a fabrication approach through the control of metamorphic polymers' amorphous-crystalline transition to miniaturize and integrate multiple components into hydrogel bioelectronics. We attain an about 80% diameter reduction in chemically cross-linked polyvinyl alcohol hydrogel fibers in a fully hydrated state. This strategy allows regulation of hydrogel properties, including refractive index (1.37-1.40 at 480 nm), light transmission (>96%), stretchability (139-169%), bending stiffness (4.6 ± 1.4 N/m), and elastic modulus (2.8-9.3 MPa). To exploit the applications, we apply step-index hydrogel optical probes in the mouse ventral tegmental area, coupled with fiber photometry recordings and social behavioral assays. Additionally, we fabricate carbon nanotubes-PVA hydrogel microelectrodes by incorporating conductive nanomaterials in hydrogel for spontaneous neural activities recording. We enable simultaneous optogenetic stimulation and electrophysiological recordings of light-triggered neural activities in Channelrhodopsin-2 transgenic mice.
Collapse
Affiliation(s)
- Sizhe Huang
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, USA
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Xinyue Liu
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Shaoting Lin
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, USA
| | - Christopher Glynn
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Kayla Felix
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Atharva Sahasrabudhe
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Collin Maley
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Jingyi Xu
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Weixuan Chen
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Eunji Hong
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, USA
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Alfred J Crosby
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA
| | - Qianbin Wang
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, USA.
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
| | - Siyuan Rao
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, USA.
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
| |
Collapse
|
2
|
Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. Channel Gating in Kalium Channelrhodopsin Slow Mutants. J Mol Biol 2024; 436:168298. [PMID: 37802216 DOI: 10.1016/j.jmb.2023.168298] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/24/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is the first discovered natural light-gated ion channel that shows higher selectivity to K+ than to Na+ and therefore is used to silence neurons with light (optogenetics). Replacement of the conserved cysteine residue in the transmembrane helix 3 (Cys110) with alanine or threonine results in a >1,000-fold decrease in the channel closing rate. The phenotype of the corresponding mutants in channelrhodopsin 2 is attributed to breaking of a specific interhelical hydrogen bond (the "DC gate"). Unlike CrChR2 and other ChRs with long distance "DC gates", the HcKCR1 structure does not reveal any hydrogen bonding partners to Cys110, indicating that the mutant phenotype is likely caused by disruption of direct interaction between this residue and the chromophore. In HcKCR1_C110A, fast photochemical conversions corresponding to channel gating were followed by dramatically slower absorption changes. Full recovery of the unphotolyzed state in HcKCR1_C110A was extremely slow with two time constants 5.2 and 70 min. Analysis of the light-minus-dark difference spectra during these slow processes revealed accumulation of at least four spectrally distinct blue light-absorbing photocycle intermediates, L, M1 and M2, and a UV light-absorbing form, typical of bacteriorhodopsin-like channelrhodopsins from cryptophytes. Our results contribute to better understanding of the mechanistic links between the chromophore photochemistry and channel conductance, and provide the basis for using HcKCR1_C110A as an optogenetic tool.
Collapse
Affiliation(s)
- Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Yumei Wang
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Fişek M, Jeanne JM. Two-Photon Optogenetic Stimulation of Drosophila Neurons. Methods Mol Biol 2021; 2191:97-108. [PMID: 32865741 DOI: 10.1007/978-1-0716-0830-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 06/11/2023]
Abstract
Optogenetics enables experimental control over neural activity using light. Channelrhodopsin and its variants are typically activated using visible light excitation but can also be activated using infrared two-photon excitation. Two-photon excitation can improve the spatial precision of stimulation in scattering tissue but has several practical limitations that need to be considered before use. Here we describe the methodology and best practices for using two-photon optogenetic stimulation of neurons within the brain of the fruit fly, Drosophila melanogaster, with an emphasis on projection neurons of the antennal lobe.
Collapse
Affiliation(s)
- Mehmet Fişek
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology, and Pharmacology, University College London, London, UK
| | - James M Jeanne
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
6
|
Abstract
Molecular dynamics (MD) simulations have been successfully used for modeling dynamic behavior of biologically relevant systems, such as ion channels in representative environments to decode protein structure-function relationships. Protocol presented here describes steps for generating input files and modeling a monomer of transmembrane cation channel, channelrhodopsin chimera (C1C2), in representative environment of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) planar lipid bilayer, TIP3P water and ions (Na+ and Cl-) using molecular dynamics package NAMD, molecular graphics/analysis tool VMD, and other relevant tools. MD simulations of C1C2 were performed at 303.15 K and in constant particle number, isothermal-isobaric (NpT) ensemble. The results of modeling have helped understand how key interactions in the center of the C1C2 channel contribute to channel gating and subsequent solvent transport across the membrane.
Collapse
Affiliation(s)
- Monika R VanGordon
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA.
| |
Collapse
|
7
|
Abstract
Photoelectric recording from populations of phototactic flagellate algae provides a means to study channelrhodopsin functions in vivo. Technical simplicity, versatility, high sensitivity, and reproducibility are the advantages of this assay over recording from individual algal cells by the suction pipette technique. Here we describe the principles and procedures of this assay.
Collapse
Affiliation(s)
- Oleg A Sineshchekov
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Elena G Govorunova
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John L Spudich
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| |
Collapse
|
8
|
Abstract
For a successful characterization of channelrhodopsins with biophysical methods like FTIR, Raman, EPR and NMR spectroscopy and X-ray crystallography, large amounts of purified protein are requested. For proteins of eukaryotic origin, which are poorly expressing in bacterial systems or not at all, the yeast Pichia pastoris represents a promising alternative for overexpression. Here we describe the methods for cloning, overexpression and mutagenesis as well as the purification procedures for channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2), channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) and the scaffold protein MSP1D1 for reconstitution of the membrane proteins into nanodiscs. Finally, protocols are provided to study CaChR1 by FTIR difference spectroscopy and by time-resolved UV/Vis spectroscopy.
Collapse
Affiliation(s)
- Maria Walter
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
9
|
Priest C, VanGordon MR, Rempe C, Chaudhari MI, Stevens MJ, Rick S, Rempe SB. Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2. Methods Mol Biol 2021; 2191:17-28. [PMID: 32865736 DOI: 10.1007/978-1-0716-0830-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.
Collapse
Affiliation(s)
- Chad Priest
- Sandia National Laboratories, Albuquerque, NM, USA
| | - Monika R VanGordon
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA
| | | | | | | | - Steve Rick
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA
| | | |
Collapse
|
10
|
Love AC, Prescher JA. Seeing (and Using) the Light: Recent Developments in Bioluminescence Technology. Cell Chem Biol 2020; 27:904-920. [PMID: 32795417 PMCID: PMC7472846 DOI: 10.1016/j.chembiol.2020.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023]
Abstract
Bioluminescence has long been used to image biological processes in vivo. This technology features luciferase enzymes and luciferin small molecules that produce visible light. Bioluminescent photons can be detected in tissues and live organisms, enabling sensitive and noninvasive readouts on physiological function. Traditional applications have focused on tracking cells and gene expression patterns, but new probes are pushing the frontiers of what can be visualized. The past few years have also seen the merger of bioluminescence with optogenetic platforms. Luciferase-luciferin reactions can drive light-activatable proteins, ultimately triggering signal transduction and other downstream events. This review highlights these and other recent advances in bioluminescence technology, with an emphasis on tool development. We showcase how new luciferins and engineered luciferases are expanding the scope of optical imaging. We also highlight how bioluminescent systems are being leveraged not just for sensing-but also controlling-biological processes.
Collapse
Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
11
|
Kojima K, Miyoshi N, Shibukawa A, Chowdhury S, Tsujimura M, Noji T, Ishikita H, Yamanaka A, Sudo Y. Green-Sensitive, Long-Lived, Step-Functional Anion Channelrhodopsin-2 Variant as a High-Potential Neural Silencing Tool. J Phys Chem Lett 2020; 11:6214-6218. [PMID: 32697087 DOI: 10.1021/acs.jpclett.0c01406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Anion channelrhodopsin-2 (GtACR2) was identified from the alga Guillardia theta as a light-gated anion channel, providing a powerful neural silencing tool for optogenetics. To expand its molecular properties, we produced here GtACR2 variants by strategic mutations on the four residues around the retinal chromophore (i.e., R129, G152, P204, and C233). After the screening with the Escherichia coli expression system, we estimated spectral sensitivities and the anion channeling function by using the HEK293 expression system. Among the mutants, triple (R129M/G152S/C233A) and quadruple (R129M/G152S/P204T/C233A) mutants showed the significantly red-shifted absorption maxima (λmax = 498 and 514 nm, respectively) and the long-lived channel-conducting states (the half-life times were 3.4 and 5.4 s, respectively). In addition, both mutants can be activated and inactivated by different wavelengths, representing their step-functional ability. We nicknamed the quadruple mutant "GLaS-ACR2" from its green-sensitive, long-lived, step-functional properties. The unique characteristics of GLaS-ACR2 suggest its high potential as a neural silencing tool.
Collapse
Affiliation(s)
- Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Natsuki Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Srikanta Chowdhury
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8654, Japan
| | - Tomoyasu Noji
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Akihiro Yamanaka
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| |
Collapse
|
12
|
Bang Y, Kim YY, Song YK. An efficient cell type specific conjugating method for incorporating various nanostructures to genetically encoded AviTag expressed optogenetic opsins. Biochem Biophys Res Commun 2020; 530:581-587. [PMID: 32753317 DOI: 10.1016/j.bbrc.2020.07.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/22/2020] [Indexed: 11/20/2022]
Abstract
Here, we report genetically encoded AviTag conjugating system for Channelrhodopsin-2(ChR2) in order to attach various nanostructures to the membrane protein in a cell type specific manner. First, AviTag peptide sequence is cloned to N-terminal site of ChR2 construct and expressed at the membrane of primary-cultured hippocampal neurons via lentiviral transduction. Second, with the help of BirA enzyme and ATP, biotin coated quantum dots (Qdots) and streptavidin (SAv) coated Qdots are successfully bound to AviTag sites at the membrane where ChR2 is located and confirmed by fluorescence imaging. Moreover, we synthesize biotinylated Traptavidin-DNA conjugate probes containing a desthio-biotin that has weaker affinity than a regular biotin, and successfully exchange them with pre-conjugated Biotin-AviTag-ChR2 site at the membrane of neuronal cells which can potentially solve the crosslinking issue of Avidin linked probes. Therefore, we expect the AviTag-ChR2 fusion platform to become a great tool for incorporating various nanostructures at the specific sites of a cellular membrane in order to overcome the limits of optogenetic opsins.
Collapse
Affiliation(s)
- Yongbin Bang
- Program in Nano Science and Technology, Seoul National University, Seoul, 08826, South Korea
| | - Young-Youb Kim
- Program in Nano Science and Technology, Seoul National University, Seoul, 08826, South Korea
| | - Yoon-Kyu Song
- Program in Nano Science and Technology, Seoul National University, Seoul, 08826, South Korea; Advanced Institutes of Convergence Technology, 864-1 Iui-dong, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16229, South Korea.
| |
Collapse
|
13
|
Abstract
Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn-Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the "aborted bicycle-pedal" mechanism. In addition, RPSB photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which could trigger subsequent channel opening and ion conduction.
Collapse
Affiliation(s)
- Ruibin Liang
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Fang Liu
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| |
Collapse
|
14
|
Kim YS, Kato HE, Yamashita K, Ito S, Inoue K, Ramakrishnan C, Fenno LE, Evans KE, Paggi JM, Dror RO, Kandori H, Kobilka BK, Deisseroth K. Crystal structure of the natural anion-conducting channelrhodopsin GtACR1. Nature 2018; 561:343-348. [PMID: 30158696 PMCID: PMC6340299 DOI: 10.1038/s41586-018-0511-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/13/2018] [Indexed: 01/08/2023]
Abstract
The naturally occurring channelrhodopsin variant anion channelrhodopsin-1 (ACR1), discovered in the cryptophyte algae Guillardia theta, exhibits large light-gated anion conductance and high anion selectivity when expressed in heterologous settings, properties that support its use as an optogenetic tool to inhibit neuronal firing with light. However, molecular insight into ACR1 is lacking owing to the absence of structural information underlying light-gated anion conductance. Here we present the crystal structure of G. theta ACR1 at 2.9 Å resolution. The structure reveals unusual architectural features that span the extracellular domain, retinal-binding pocket, Schiff-base region, and anion-conduction pathway. Together with electrophysiological and spectroscopic analyses, these findings reveal the fundamental molecular basis of naturally occurring light-gated anion conductance, and provide a framework for designing the next generation of optogenetic tools.
Collapse
Affiliation(s)
- Yoon Seok Kim
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Japan.
| | | | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Charu Ramakrishnan
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Lief E Fenno
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Kathryn E Evans
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
15
|
Adam S, Bondar AN. Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin. PLoS One 2018; 13:e0201298. [PMID: 30086158 PMCID: PMC6080761 DOI: 10.1371/journal.pone.0201298] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Channelrhodopsins are light-sensitive ion channels whose reaction cycles involve conformation-coupled transfer of protons. Understanding how channelrhodopsins work is important for applications in optogenetics, where light activation of these proteins triggers changes in the transmembrane potential across excitable membranes. A fundamental open question is how the protein environment ensures that unproductive proton transfer from the retinal Schiff base to the nearby carboxylate counterion is avoided in the resting state of the channel. To address this question, we performed combined quantum mechanical/molecular mechanical proton transfer calculations with explicit treatment of the surrounding lipid membrane. The free energy profiles computed for proton transfer to the counterion, either via a direct jump or mediated by a water molecule, demonstrate that, when retinal is all-trans, water and protein electrostatic interactions largely favour the protonated retinal Schiff base state. We identified a conserved lysine group as an essential structural element for the proton transfer energetics in channelrhodopsins.
Collapse
Affiliation(s)
- Suliman Adam
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| |
Collapse
|
16
|
Abstract
Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. In a 4-µs MM simulation of a dark-adapted ChR2 dimer, water entered the vestibules of the closed channel. Retinal all-trans to 13-cis isomerization, simulated with metadynamics, triggered a major restructuring of the charge cluster forming the channel gate. On a microsecond time scale, water penetrated the gate to form a membrane-spanning preopen pore between helices H1, H2, H3, and H7. This influx of water into an ion-impermeable preopen pore is consistent with time-resolved infrared spectroscopy and electrophysiology experiments. In the retinal 13-cis state, D253 emerged as the proton acceptor of the Schiff base. Upon proton transfer from the Schiff base to D253, modeled by QM/MM simulations, we obtained an early-M/P2390-like intermediate. Rapid rotation of the unprotonated Schiff base toward the cytosolic side effectively prevents its reprotonation from the extracellular side. From MM and QM simulations, we gained detailed insight into the mechanism of ChR2 photoactivation and early events in pore formation. By rearranging the network of charges and hydrogen bonds forming the gate, water emerges as a key player in light-driven ChR2 channel opening.
Collapse
Affiliation(s)
- Albert Ardevol
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
- Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| |
Collapse
|
17
|
Pomeroy JE, Nguyen HX, Hoffman BD, Bursac N. Genetically Encoded Photoactuators and Photosensors for Characterization and Manipulation of Pluripotent Stem Cells. Theranostics 2017; 7:3539-3558. [PMID: 28912894 PMCID: PMC5596442 DOI: 10.7150/thno.20593] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/14/2017] [Indexed: 12/28/2022] Open
Abstract
Our knowledge of pluripotent stem cell biology has advanced considerably in the past four decades, but it has yet to deliver on the great promise of regenerative medicine. The slow progress can be mainly attributed to our incomplete understanding of the complex biologic processes regulating the dynamic developmental pathways from pluripotency to fully-differentiated states of functional somatic cells. Much of the difficulty arises from our lack of specific tools to query, or manipulate, the molecular scale circuitry on both single-cell and organismal levels. Fortunately, the last two decades of progress in the field of optogenetics have produced a variety of genetically encoded, light-mediated tools that enable visualization and control of the spatiotemporal regulation of cellular function. The merging of optogenetics and pluripotent stem cell biology could thus be an important step toward realization of the clinical potential of pluripotent stem cells. In this review, we have surveyed available genetically encoded photoactuators and photosensors, a rapidly expanding toolbox, with particular attention to those with utility for studying pluripotent stem cells.
Collapse
Affiliation(s)
- Jordan E. Pomeroy
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
- Division of Cardiology, Department of Medicine, Duke University Health System, Durham, North Carolina, USA
| | - Hung X. Nguyen
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Brenton D. Hoffman
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 1427, Fitzpatrick CIEMAS, Durham, North Carolina 27708, USA
| |
Collapse
|