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Szundi I, Kliger DS. Parallel photocycle kinetic model of anion channelrhodopsin GtACR1 function. Biophys J 2024; 123:1735-1750. [PMID: 38762755 PMCID: PMC11214052 DOI: 10.1016/j.bpj.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/14/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
The light-gated anion channelrhodopsin GtACR1 is an important optogenetic tool for neuronal silencing. Its photochemistry, including its photointermediates, is poorly understood. The current mechanistic view presumes BR-like kinetics and assigns the open channel to a blue-absorbing L intermediate. Based on time-resolved absorption and electrophysiological data, we recently proposed a red-absorbing spectral form for the open channel state. Here, we report the results of a comprehensive kinetic analysis of the spectroscopic data combined with channel current information. The time evolutions of the spectral forms derived from the spectroscopic data are inconsistent with the single chain mechanism and are analyzed within the concept of parallel photocycles. The spectral forms partitioned into conductive and nonconductive parallel cycles are assigned to intermediate states. Rejecting reversible connections between conductive and nonconductive channel states leads to kinetic schemes with two independent conductive states corresponding to the fast- and slow-decaying current components. The conductive cycle is discussed in terms of a single cycle and two parallel cycles. The reaction mechanisms and reaction rates for the wild-type protein, the A75E, and the low-conductance D234N and S97E protein variants are derived. The parallel cycles of channelrhodopsin kinetics, its relation to BR photocycle, and the role of the M intermediate in channel closure are discussed.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry & Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David S Kliger
- Department of Chemistry & Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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Szundi I, Kliger DS. The open channel state in anion channelrhodopsin GtACR1 is a red-absorbing intermediate. Biophys J 2024; 123:940-946. [PMID: 38462839 PMCID: PMC11052691 DOI: 10.1016/j.bpj.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/13/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024] Open
Abstract
Anion channelrhodopsin GtACR1 is a powerful optogenetic tool to inhibit nerve activity. Its kinetic mechanism was interpreted in terms of the bacteriorhodopsin photocycle, and the L intermediate was assigned to the open channel state. Here, we report the results of the comparison between the time dependence of the channel currents and the time evolutions of the K-like and L-like spectral forms. Based on the results, we question the current view on GtACR1 kinetics and the assignment of the L intermediate to the open channel state. We report evidence for a red-absorbing intermediate being responsible for channel opening.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California.
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Schleissner P, Szundi I, Chen E, Li H, Spudich JL, Kliger DS. Isospectral intermediates in the photochemical reaction cycle of anion channelrhodopsin GtACR1. Biophys J 2023; 122:4091-4103. [PMID: 37749886 PMCID: PMC10598346 DOI: 10.1016/j.bpj.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/15/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023] Open
Abstract
The most effective tested optogenetic tools available for neuronal silencing are the light-gated anion channel proteins found in the cryptophyte alga Guillardia theta (GtACRs). Molecular mechanisms of GtACRs, including the photointermediates responsible for the open channel state, are of great interest for understanding their exceptional conductance. In this study, the photoreactions of GtACR1 and its D234N, A75E, and S97E mutants were investigated using multichannel time-resolved absorption spectroscopy. For each of the proteins, the analysis showed two early microsecond transitions between K-like and L-like forms and two late millisecond recovery steps. Spectral forms associated with potential molecular intermediates of the proteins were derived and their evolutions in time were analyzed. The results indicate the presence of isospectral intermediates in the photocycles and expand the range of potential intermediates responsible for the open channel state.
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Affiliation(s)
- Pamela Schleissner
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - Istvan Szundi
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - Eefei Chen
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas
| | - David S Kliger
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, California.
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Govorunova EG, Sineshchekov OA, Spudich JL. Potassium-selective channelrhodopsins. Biophys Physicobiol 2023; 20:e201011. [PMID: 38362336 PMCID: PMC10865875 DOI: 10.2142/biophysico.bppb-v20.s011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/03/2023] [Indexed: 02/05/2023] Open
Abstract
Since their discovery 21 years ago, channelrhodopsins have come of age and have become indispensable tools for optogenetic control of excitable cells such as neurons and myocytes. Potential therapeutic utility of channelrhodopsins has been proven by partial vision restoration in a human patient. Previously known channelrhodopsins are either proton channels, non-selective cation channels almost equally permeable to Na+ and K+ besides protons, or anion channels. Two years ago, we discovered a group of channelrhodopsins that exhibit over an order of magnitude higher selectivity for K+ than for Na+. These proteins, known as "kalium channelrhodopsins" or KCRs, lack the canonical tetrameric selectivity filter found in voltage- and ligand-gated K+ channels, and use a unique selectivity mechanism intrinsic to their individual protomers. Mutant analysis has revealed that the key residues responsible for K+ selectivity in KCRs are located at both ends of the putative cation conduction pathway, and their role has been confirmed by high-resolution KCR structures. Expression of KCRs in mouse neurons and human cardiomyocytes enabled optical inhibition of these cells' electrical activity. In this minireview we briefly discuss major results of KCR research obtained during the last two years and suggest some directions of future research.
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Affiliation(s)
- Elena G. Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Oleg A. Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, 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 and Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
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The Mechanism of Channel Opening of Anion Channelrhodopsin GtACR1: A Molecular Dynamics Simulation. Processes (Basel) 2023. [DOI: 10.3390/pr11020510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Guillardia theta anion channelrhodopsin 1 (GtACR1) is a widely used inhibitor of optogenetics with unique conductance mechanisms and photochemistry. However, the molecular mechanism of light-gated anion conduction is poorly understood without a crystal structure for the intermediate state. In this study, we built the dark-state model based on the crystal structure of retinal and isomerized the model by twisting the C12-C13=C14-C15 dihedral step by step using molecular dynamics simulation. The conformational changes revealed the all-trans to 13-cis photoisomerization of the retinal chromophore cannot open the channel. There is no water influx, and a pre-opened K-like intermediate after photoisomerization of retinal is formed. During the opening of the ion channel, proton transfer occurs between E68 and D234. Steered molecular dynamics (SMD) and umbrella sampling indicated that the E68 and D234 were the key residues for chloride-ion conducting. We propose a revised channel opening pathway model of GtACR1 after analyzing (de)protonation of E68 and D234. Reprotonation of D234 will result in two different early L intermediates, named L1-like and L1‘-like, which correspond to the L1 and L1‘ intermediates reported in a recent study. Simulation results showed that L1-like may convert by parallel paths into L1‘-like and L2-like states. This model provides conformational details for the intermediate as well.
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Govorunova EG, Sineshchekov OA, Spudich JL. Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships. Front Cell Neurosci 2022; 15:800313. [PMID: 35140589 PMCID: PMC8818676 DOI: 10.3389/fncel.2021.800313] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) from phototactic algae have become widely used as genetically encoded molecular tools to control cell membrane potential with light. Recent advances in polynucleotide sequencing, especially in environmental samples, have led to identification of hundreds of channelrhodopsin homologs in many phylogenetic lineages, including non-photosynthetic protists. Only a few CCRs and ACRs have been characterized in detail, but there are indications that ion channel function has evolved within the rhodopsin superfamily by convergent routes. The diversity of channelrhodopsins provides an exceptional platform for the study of structure-function evolution in membrane proteins. Here we review the current state of channelrhodopsin research and outline perspectives for its further development.
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Li H, Huang CY, Govorunova EG, Sineshchekov OA, Yi A, Rothschild KJ, Wang M, Zheng L, Spudich JL. The crystal structure of bromide-bound GtACR1 reveals a pre-activated state in the transmembrane anion tunnel. eLife 2021; 10:65903. [PMID: 33998458 PMCID: PMC8172240 DOI: 10.7554/elife.65903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/16/2021] [Indexed: 12/16/2022] Open
Abstract
The crystal structure of the light-gated anion channel GtACR1 reported in our previous Research Article (Li et al., 2019) revealed a continuous tunnel traversing the protein from extracellular to intracellular pores. We proposed the tunnel as the conductance channel closed by three constrictions: C1 in the extracellular half, mid-membrane C2 containing the photoactive site, and C3 on the cytoplasmic side. Reported here, the crystal structure of bromide-bound GtACR1 reveals structural changes that relax the C1 and C3 constrictions, including a novel salt-bridge switch mechanism involving C1 and the photoactive site. These findings indicate that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark that facilitates channel opening by reducing free energy in the tunnel constrictions. The results provide direct evidence that the tunnel is the closed form of the channel of GtACR1 and shed light on the light-gated channel activation mechanism.
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Affiliation(s)
- Hai Li
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Elena G Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Oleg A Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, United States
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Lei Zheng
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
| | - John L Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center - McGovern Medical School, Houston, United States
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