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Urui T, Shionoya T, Mizuno M, Inoue K, Kandori H, Mizutani Y. Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins. J Phys Chem B 2024; 128:2389-2397. [PMID: 38433395 DOI: 10.1021/acs.jpcb.3c08465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomomi Shionoya
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Urui T, Hayashi K, Mizuno M, Inoue K, Kandori H, Mizutani Y. Cis- Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping. J Phys Chem B 2024; 128:744-754. [PMID: 38204413 DOI: 10.1021/acs.jpcb.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kouhei Hayashi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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3
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Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
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Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
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4
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Meng X, Ganapathy S, van Roemburg L, Post M, Brinks D. Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway. ACS PHYSICAL CHEMISTRY AU 2023; 3:320-333. [PMID: 37520318 PMCID: PMC10375888 DOI: 10.1021/acsphyschemau.3c00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 08/01/2023]
Abstract
Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.
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Affiliation(s)
- Xin Meng
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Srividya Ganapathy
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, United States
| | - Lars van Roemburg
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Marco Post
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Daan Brinks
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Molecular Genetics, Erasmus University
Medical Center, 3015 GD Rotterdam, The Netherlands
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5
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Ganapathy S, Meng X, Mossel D, Jagt M, Brinks D. Expanding the family of genetically encoded voltage indicators with a candidate Heliorhodopsin exhibiting near-infrared fluorescence. J Biol Chem 2023; 299:104771. [PMID: 37127067 DOI: 10.1016/j.jbc.2023.104771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs), particularly those based on microbial rhodopsins, are gaining traction in neuroscience as fluorescent sensors for imaging voltage dynamics with high-spatiotemporal precision. Here we establish a novel GEVI candidate based on the recently discovered subfamily of the microbial rhodopsin clade, termed heliorhodopsins. We discovered that upon excitation at 530-560nm, wild type heliorhodopsin exhibits near infra-red fluorescence which is sensitive to membrane voltage. We characterized the fluorescence brightness, photostability, voltage sensitivity and kinetics of wild type heliorhodopsin in HEK293T cells and further examined the impact of mutating key residues near the retinal chromophore. The S237A mutation significantly improved the fluorescence response of heliorhodopsin by 76% providing a highly promising starting point for further protein evolution.
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Affiliation(s)
- Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands; Department of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, San Diego, USA
| | - Xin Meng
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Delizzia Mossel
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Mels Jagt
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Daan Brinks
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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6
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Barneschi L, Marsili E, Pedraza-González L, Padula D, De Vico L, Kaliakin D, Blanco-González A, Ferré N, Huix-Rotllant M, Filatov M, Olivucci M. On the fluorescence enhancement of arch neuronal optogenetic reporters. Nat Commun 2022; 13:6432. [PMID: 36307417 PMCID: PMC9616920 DOI: 10.1038/s41467-022-33993-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.
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Affiliation(s)
- Leonardo Barneschi
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Emanuele Marsili
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.8250.f0000 0000 8700 0572University of Durham, Department of Chemistry, South Road, Durham, DH1 3LE United Kingdom ,grid.5337.20000 0004 1936 7603Present Address: Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Laura Pedraza-González
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.5395.a0000 0004 1757 3729Present Address: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Daniele Padula
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Danil Kaliakin
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Alejandro Blanco-González
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Nicolas Ferré
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Miquel Huix-Rotllant
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Michael Filatov
- grid.258803.40000 0001 0661 1556Department of Chemistry, Kyungpook National University, Daegu, 702-701 South Korea
| | - Massimo Olivucci
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA ,grid.11843.3f0000 0001 2157 9291University of Strasbourg Institute for Advanced Studies, 5, alleé duGeń eŕ al Rouvillois, F-67083 Strasbourg, France
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7
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QuasAr Odyssey: the origin of fluorescence and its voltage sensitivity in microbial rhodopsins. Nat Commun 2022; 13:5501. [PMID: 36127376 PMCID: PMC9489792 DOI: 10.1038/s41467-022-33084-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/26/2022] [Indexed: 11/29/2022] Open
Abstract
Rhodopsins had long been considered non-fluorescent until a peculiar voltage-sensitive fluorescence was reported for archaerhodopsin-3 (Arch3) derivatives. These proteins named QuasArs have been used for imaging membrane voltage changes in cell cultures and small animals. However due to the low fluorescence intensity, these constructs require use of much higher light intensity than other optogenetic tools. To develop the next generation of sensors, it is indispensable to first understand the molecular basis of the fluorescence and its modulation by the membrane voltage. Based on spectroscopic studies of fluorescent Arch3 derivatives, we propose a unique photo-reaction scheme with extended excited-state lifetimes and inefficient photoisomerization. Molecular dynamics simulations of Arch3, of the Arch3 fluorescent derivative Archon1, and of several its mutants have revealed different voltage-dependent changes of the hydrogen-bonding networks including the protonated retinal Schiff-base and adjacent residues. Experimental observations suggest that under negative voltage, these changes modulate retinal Schiff base deprotonation and promote a decrease in the populations of fluorescent species. Finally, we identified molecular constraints that further improve fluorescence quantum yield and voltage sensitivity. The authors present an in-depth investigation of excited state dynamics and molecular mechanism of the voltage sensing in microbial rhodopsins. Using a combination of spectroscopic investigations and molecular dynamics simulations, the study proposes the voltage-modulated deprotonation of the chromophore as the key event in the voltage sensing. Thus, molecular constraints that may further improve the fluorescence quantum yield and the voltage sensitivity are presented.
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8
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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9
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Axford D, Judge PJ, Bada Juarez JF, Kwan TOC, Birch J, Vinals J, Watts A, Moraes I. Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts. Acta Crystallogr D Struct Biol 2022; 78:52-58. [PMID: 34981761 PMCID: PMC8725165 DOI: 10.1107/s2059798321011220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022] Open
Abstract
Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 Å resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.
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Affiliation(s)
- Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Tristan O. C. Kwan
- National Physical Laboratory, Hampton Road, Teddington, London, United Kingdom
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Javier Vinals
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anthony Watts
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, London, United Kingdom
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10
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Shionoya T, Singh M, Mizuno M, Kandori H, Mizutani Y. Strongly Hydrogen-Bonded Schiff Base and Adjoining Polyene Twisting in the Retinal Chromophore of Schizorhodopsins. Biochemistry 2021; 60:3050-3057. [PMID: 34601881 DOI: 10.1021/acs.biochem.1c00529] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A transmembrane proton gradient is generated and maintained by proton pumps in a cell. Metagenomics studies have recently identified a new category of rhodopsin intermediates between type-1 rhodopsins and heliorhodopsins, named schizorhodopsins (SzRs). SzRs are light-driven inward proton pumps. Comprehensive resonance Raman measurements were conducted to characterize the structure of the retinal chromophore in the unphotolyzed state of four SzRs. The spectra of all four SzRs show that the retinal chromophore is in the all-trans and 15-anti configuration and that the Schiff base is protonated. The polyene chain is planar in the center of the retinal chromophore and is twisted in the vicinity of the protonated Schiff base. The protonated Schiff base in the SzRs forms a stronger hydrogen bond than that in outward proton-pumping rhodopsins. We determined that the hydrogen-bonding partner of the protonated Schiff base is not a water molecule but an amino acid residue, presumably an Asp residue in helix G. The present observations provide valuable insights into the inward proton-pumping mechanism of SzRs.
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Affiliation(s)
- Tomomi Shionoya
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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11
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Mei G, Cavini CM, Mamaeva N, Wang P, DeGrip WJ, Rothschild KJ. Optical Switching Between Long-lived States of Opsin Transmembrane Voltage Sensors. Photochem Photobiol 2021; 97:1001-1015. [PMID: 33817800 PMCID: PMC8596844 DOI: 10.1111/php.13428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/27/2022]
Abstract
Opsin-based transmembrane voltage sensors (OTVSs) are membrane proteins increasingly used in optogenetic applications to measure voltage changes across cellular membranes. In order to better understand the photophysical properties of OTVSs, we used a combination of UV-Vis absorption, fluorescence and FT-Raman spectroscopy to characterize QuasAr2 and NovArch, two closely related mutants derived from the proton pump archaerhodopsin-3 (AR3). We find both QuasAr2 and NovArch can be optically cycled repeatedly between O-like and M-like states using 5-min exposure to red (660 nm) and near-UV (405 nm) light. Longer red-light exposure resulted in the formation of a long-lived photoproduct similar to pink membrane, previously found to be a photoproduct of the BR O intermediate with a 9-cis retinylidene chromophore configuration. However, unlike QuasAr2 whose O-like state is stable in the dark, NovArch exhibits an O-like state which slowly partially decays in the dark to a stable M-like form with a deprotonated Schiff base and a 13-cis,15-anti retinylidene chromophore configuration. These results reveal a previously unknown complexity in the photochemistry of OTVSs including the ability to optically switch between different long-lived states. The possible molecular basis of these newly discovered properties along with potential optogenetic and biotechnological applications are discussed.
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Affiliation(s)
- Gaoxiang Mei
- Molecular Biophysics LaboratoryDepartment of PhysicsPhotonics CenterBoston UniversityBostonMA
| | - Cesar M. Cavini
- Molecular Biophysics LaboratoryDepartment of PhysicsPhotonics CenterBoston UniversityBostonMA
| | - Natalia Mamaeva
- Molecular Biophysics LaboratoryDepartment of PhysicsPhotonics CenterBoston UniversityBostonMA
| | | | - Willem J. DeGrip
- Department of Biophysical Organic ChemistryLeiden Institute of ChemistryLeiden UniversityLeidenThe Netherlands
- Department of BiochemistryRadboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Kenneth J. Rothschild
- Molecular Biophysics LaboratoryDepartment of PhysicsPhotonics CenterBoston UniversityBostonMA
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12
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Urui T, Mizuno M, Otomo A, Kandori H, Mizutani Y. Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates. J Phys Chem B 2021; 125:7155-7162. [PMID: 34167296 DOI: 10.1021/acs.jpcb.1c04010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Light is utilized as energy or information by rhodopsins (membrane proteins that contain a retinal chromophore). Heliorhodopsins (HeRs) are a new class of rhodopsins with low sequence identity (<15%) to microbial and animal rhodopsins. Their physiological roles remain unknown, although the involvement of a long-lived intermediate in the photocycle suggests a light-sensor function. Characterization of the molecular structures of the intermediates is essential to an understanding of the roles and mechanisms of HeRs. We determined the chromophore structures of the intermediates in HeR 48C12 by time-resolved resonance Raman spectroscopy and observed that the hydrogen bond of the protonated Schiff base strengthened prior to deprotonation. The chromophore is photoisomerized from the all-trans to the 13-cis form and is reisomerized in the transition from the O intermediate to the unphotolyzed state. Our results demonstrate that the chromophore structure evolves similarly to microbial rhodopsins, despite the dissimilarity in amino acid residues surrounding the chromophore.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akihiro Otomo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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13
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Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun 2021; 12:629. [PMID: 33504778 PMCID: PMC7840839 DOI: 10.1038/s41467-020-20596-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.
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Affiliation(s)
- Juan F Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Tristan O C Kwan
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK
| | - Kin Kuan Hoi
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hsin-Yung Yen
- OMass Therapeutics, The Schrodinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Anthony Vial
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Carol V Robinson
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK.
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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14
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Mei G, Mamaeva N, Ganapathy S, Wang P, DeGrip WJ, Rothschild KJ. Analog Retinal Redshifts Visible Absorption of QuasAr Transmembrane Voltage Sensors into Near-infrared. Photochem Photobiol 2019; 96:55-66. [PMID: 31556123 PMCID: PMC7004139 DOI: 10.1111/php.13169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/01/2022]
Abstract
Opsin‐based transmembrane voltage sensors (OTVSs) are increasingly important tools for neuroscience enabling neural function in complex brain circuits to be explored in live, behaving animals. However, the visible wavelengths required for fluorescence excitation of the current generation of OTVSs limit optogenetic imaging in the brain to depths of only a few mm due to the strong absorption and scattering of visible light by biological tissues. We report that substitution of the native A1 retinal chromophore of the widely used QuasAr1/2 OTVSs with the retinal analog MMAR containing a methylamino‐modified dimethylphenyl ring results in over a 100‐nm redshift of the maxima of the absorption and fluorescence emission bands to near 700 and 840 nm, respectively. FT‐Raman spectroscopy reveals that at pH 7 QuasAr1 with both the A1 and MMAR chromophores possess predominantly an all‐trans protonated Schiff base configuration with the MMAR chromophore exhibiting increased torsion of the polyene single‐/double‐bond system similar to the O‐intermediate of the BR photocycle. In contrast, the A1 and the MMAR chromophores of QuasAr2 exist partially in a 13‐cis PSB configuration. These results demonstrate that QuasArs containing the MMAR chromophore are attractive candidates for use as NIR‐OTVSs, especially for applications such as deep brain imaging.
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Affiliation(s)
- Gaoxiang Mei
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
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15
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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16
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Penzkofer A, Silapetere A, Hegemann P. Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 20:E4086. [PMID: 31438573 PMCID: PMC6747118 DOI: 10.3390/ijms20174086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
QuasAr1 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense by directed evolution. Here we report absorption and emission spectroscopic studies of QuasAr1 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of QuasAr1 was studied by long-time attenuation coefficient measurements at room temperature (23 ± 2 °C) and at 2.5 ± 0.5 °C. The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 65 ± 3 °C). In the protein melting process the originally present protonated retinal Schiff base (PRSB) with absorption maximum at 580 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Long-time storage of QuasAr1 at temperatures around 2.5 °C and around 23 °C caused gradual protonated retinal Schiff base isomer changes to other isomer conformations, de-protonation to retinal Schiff base isomers, and apoprotein structure changes showing up in ultraviolet absorption increase. Reaction coordinate schemes are presented for the thermal protonated retinal Schiff base isomerizations and deprotonations in parallel with the dynamic apoprotein restructurings.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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17
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Lee HJ, Huang KC, Mei G, Zong C, Mamaeva N, DeGrip WJ, Rothschild KJ, Cheng JX. Electronic Preresonance Stimulated Raman Scattering Imaging of Red-Shifted Proteorhodopsins: Toward Quantitation of the Membrane Potential. J Phys Chem Lett 2019; 10:4374-4381. [PMID: 31313926 DOI: 10.1021/acs.jpclett.9b01337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Voltage imaging allows mapping of the membrane potential in living cells. Yet, current intensity-based imaging approaches are limited to relative membrane potential changes, missing important information conveyed by the absolute value of the membrane voltage. This challenge arises from various factors affecting the signal intensity, such as concentration, illumination intensity, and photobleaching. Here, we demonstrate electronic preresonance hyperspectral stimulated Raman scattering (EPR-hSRS) for spectroscopic detection of the membrane voltage using a near-infrared-absorbing microbial rhodopsin expressed in E. coli. This newly developed near-infrared active microbial rhodopsin enables electronic preresonance SRS imaging at high sensitivity. By spectral profiling, we identified voltage-sensitive SRS peaks in the fingerprint region in single E. coli cells. These spectral signatures offer a new approach for quantitation of the absolute membrane voltage in living cells.
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Affiliation(s)
- Hyeon Jeong Lee
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Kai-Chih Huang
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Gaoxiang Mei
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
- Department of Physics , Boston University , Boston , Massachusetts 02215 , United States
| | - Cheng Zong
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Natalia Mamaeva
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
- Department of Physics , Boston University , Boston , Massachusetts 02215 , United States
| | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry , Leiden University , 2300 RA Leiden , The Netherlands
- Department of Biochemistry , Radboud University Medical School , 6500 HB Nijmegen , The Netherlands
| | - Kenneth J Rothschild
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
- Department of Physics , Boston University , Boston , Massachusetts 02215 , United States
- Department of Physiology and Biophysics , Boston University School of Medicine , Boston , Massachusetts 02218 , United States
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
- Department of Physics , Boston University , Boston , Massachusetts 02215 , United States
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18
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Ganapathy S, Kratz S, Chen Q, Hellingwerf KJ, de Groot HJM, Rothschild KJ, de Grip WJ. Redshifted and Near-infrared Active Analog Pigments Based upon Archaerhodopsin-3. Photochem Photobiol 2019; 95:959-968. [PMID: 30860604 PMCID: PMC6849744 DOI: 10.1111/php.13093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 01/01/2023]
Abstract
Archaerhodopsin‐3 (AR3) is a member of the microbial rhodopsin family of hepta‐helical transmembrane proteins, containing a covalently bound molecule of all‐trans retinal as a chromophore. It displays an absorbance band in the visible region of the solar spectrum (λmax 556 nm) and functions as a light‐driven proton pump in the archaeon Halorubrum sodomense. AR3 and its mutants are widely used in neuroscience as optogenetic neural silencers and in particular as fluorescent indicators of transmembrane potential. In this study, we investigated the effect of analogs of the native ligand all‐trans retinal A1 on the spectral properties and proton‐pumping activity of AR3 and its single mutant AR3 (F229S). While, surprisingly, the 3‐methoxyretinal A2 analog did not redshift the absorbance maximum of AR3, the analogs retinal A2 and 3‐methylamino‐16‐nor‐1,2,3,4‐didehydroretinal (MMAR) did generate active redshifted AR3 pigments. The MMAR analog pigments could even be activated by near‐infrared light. Furthermore, the MMAR pigments showed strongly enhanced fluorescence with an emission band in the near‐infrared peaking around 815 nm. We anticipate that the AR3 pigments generated in this study have widespread potential for near‐infrared exploitation as fluorescent voltage‐gated sensors in optogenetics and artificial leafs and as proton pumps in bioenergy‐based applications.
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Affiliation(s)
- Srividya Ganapathy
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Svenja Kratz
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Que Chen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Willem J de Grip
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Biochemistry, Radboud University Medical Center, Nijmegen, The Netherlands
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19
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Nishimura N, Mizuno M, Kandori H, Mizutani Y. Distortion and a Strong Hydrogen Bond in the Retinal Chromophore Enable Sodium-Ion Transport by the Sodium-Ion Pump KR2. J Phys Chem B 2019; 123:3430-3440. [DOI: 10.1021/acs.jpcb.9b00928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nao Nishimura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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20
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Mei G, Mamaeva N, Ganapathy S, Wang P, DeGrip WJ, Rothschild KJ. Raman spectroscopy of a near infrared absorbing proteorhodopsin: Similarities to the bacteriorhodopsin O photointermediate. PLoS One 2018; 13:e0209506. [PMID: 30586409 PMCID: PMC6306260 DOI: 10.1371/journal.pone.0209506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/06/2018] [Indexed: 02/07/2023] Open
Abstract
Microbial rhodopsins have become an important tool in the field of optogenetics. However, effective in vivo optogenetics is in many cases severely limited due to the strong absorption and scattering of visible light by biological tissues. Recently, a combination of opsin site-directed mutagenesis and analog retinal substitution has produced variants of proteorhodopsin which absorb maximally in the near-infrared (NIR). In this study, UV-Visible-NIR absorption and resonance Raman spectroscopy were used to study the double mutant, D212N/F234S, of green absorbing proteorhodopsin (GPR) regenerated with MMAR, a retinal analog containing a methylamino modified β-ionone ring. Four distinct subcomponent absorption bands with peak maxima near 560, 620, 710 and 780 nm are detected with the NIR bands dominant at pH <7.3, and the visible bands dominant at pH 9.5. FT-Raman using 1064-nm excitation reveal two strong ethylenic bands at 1482 and 1498 cm-1 corresponding to the NIR subcomponent absorption bands based on an extended linear correlation between λmax and γC = C. This spectrum exhibits two intense bands in the fingerprint and HOOP mode regions that are highly characteristic of the O640 photointermediate from the light-adapted bacteriorhodopsin photocycle. In contrast, 532-nm excitation enhances the 560-nm component, which exhibits bands very similar to light-adapted bacteriorhodopsin and/or the acid-purple form of bacteriorhodopsin. Native GPR and its mutant D97N when regenerated with MMAR also exhibit similar absorption and Raman bands but with weaker contributions from the NIR absorbing components. Based on these results it is proposed that the NIR absorption in GPR-D212N/F234S with MMAR arises from an O-like chromophore, where the Schiff base counterion D97 is protonated and the MMAR adopts an all-trans configuration with a non-planar geometry due to twists in the conjugated polyene segment. This configuration is characterized by extensive charge delocalization, most likely involving nitrogens atoms in the MMAR chromophore.
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Affiliation(s)
- Gaoxiang Mei
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts, United States of America
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts, United States of America
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden UniversityAR Leiden, The Netherlands
| | - Peng Wang
- Bruker Corporation, Billerica, MA, United States of America
| | - Willem J. DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden UniversityAR Leiden, The Netherlands
| | - Kenneth J. Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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21
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Quach B, Krogh-Madsen T, Entcheva E, Christini DJ. Light-Activated Dynamic Clamp Using iPSC-Derived Cardiomyocytes. Biophys J 2018; 115:2206-2217. [PMID: 30447994 PMCID: PMC6289097 DOI: 10.1016/j.bpj.2018.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/23/2018] [Accepted: 10/02/2018] [Indexed: 01/31/2023] Open
Abstract
iPSC-derived cardiomyocytes (iPSC-CMs) are a potentially advantageous platform for drug screening because they provide a renewable source of human cardiomyocytes. One obstacle to their implementation is their immature electrophysiology, which reduces relevance to adult arrhythmogenesis. To address this, dynamic clamp is used to inject current representing the insufficient potassium current, IK1, thereby producing more adult-like electrophysiology. However, dynamic clamp requires patch clamp and is therefore low throughput and ill-suited for large-scale drug screening. Here, we use optogenetics to generate such a dynamic-clamp current. The optical dynamic clamp (ODC) uses outward-current-generating opsin, ArchT, to mimic IK1, resulting in more adult-like action potential morphology, similar to IK1 injection via classic dynamic clamp. Furthermore, in the presence of an IKr blocker, ODC revealed expected action potential prolongation and reduced spontaneous excitation. The ODC presented here still requires an electrode to measure Vm but provides a first step toward contactless dynamic clamp, which will not only enable high-throughput screening but may also allow control within multicellular iPSC-CM formats to better recapitulate adult in vivo physiology.
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Affiliation(s)
- Bonnie Quach
- Cardiovascular Research Institute, New York, New York; Weill Cornell Medicine, New York, New York
| | - Trine Krogh-Madsen
- Cardiovascular Research Institute, New York, New York; Weill Cornell Medicine, New York, New York
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, District of Columbia
| | - David J Christini
- Cardiovascular Research Institute, New York, New York; Weill Cornell Medicine, New York, New York.
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22
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Otomo A, Mizuno M, Singh M, Shihoya W, Inoue K, Nureki O, Béjà O, Kandori H, Mizutani Y. Resonance Raman Investigation of the Chromophore Structure of Heliorhodopsins. J Phys Chem Lett 2018; 9:6431-6436. [PMID: 30351947 DOI: 10.1021/acs.jpclett.8b02741] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heliorhodopsins (HeRs) are a new category of retinal-bound proteins recently discovered through functional metagenomics analysis that exhibit obvious differences from type-1 microbial rhodopsins. We conducted the first detailed structural characterization of the retinal chromophore in HeRs using resonance Raman spectroscopy. The observed spectra clearly show that the Schiff base of the chromophore is protonated and forms a strong hydrogen bond to a species other than a water molecule, highly likely a counterion residue. The vibrational mode of the Schiff base of HeRs exhibits similarities with that of photosensory microbial rhodopsins, that is consistent with the previous proposal that HeRs function as photosensors. We also revealed unusual spectral features of the in-plane chain vibrations of the chromophore, suggesting an unprecedented geometry of the Schiff base caused by a difference in the retinal pocket structure of HeRs. These data demonstrate structural characteristics of the photoreceptive site in this novel type of rhodopsin family.
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Affiliation(s)
- Akihiro Otomo
- Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Misao Mizuno
- Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
| | - Wataru Shihoya
- Department of Biological Sciences , Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi , Bunkyo-ku, Tokyo 113-0032 , Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
- OptoBioTechnology Research Center , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
- The Institute for Solid State Physics , The University of Tokyo , Kashiwa 277-8581 , Japan
| | - Osamu Nureki
- Department of Biological Sciences , Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi , Bunkyo-ku, Tokyo 113-0032 , Japan
| | - Oded Béjà
- Faculty of Biology , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
- OptoBioTechnology Research Center , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
| | - Yasuhisa Mizutani
- Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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23
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Shionoya T, Mizuno M, Tsukamoto T, Ikeda K, Seki H, Kojima K, Shibata M, Kawamura I, Sudo Y, Mizutani Y. High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment. J Phys Chem B 2018; 122:6945-6953. [PMID: 29893559 DOI: 10.1021/acs.jpcb.8b04894] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Thermophilic rhodopsin (TR) is a light-driven proton pump from the extreme thermophile Thermus thermophilus JL-18. Previous studies on TR solubilized with detergent showed that the protein exhibits high thermal stability and forms a trimer at room temperature but irreversibly dissociates into monomers when incubated at physiological temperature (75 °C). In the present study, we used resonance Raman (RR) spectroscopy, solid-state NMR spectroscopy, and high-speed atomic force microscopy to analyze the oligomeric structure of TR in a lipid environment. The obtained spectra and microscopic images demonstrate that TR adopts a pentameric form in a lipid environment and that this assembly is stable at the physiological temperature, in contrast to the behavior of the protein in the solubilized state. These results indicate that the thermal stability of the oligomeric assembly of TR is higher in a lipid environment than in detergent micelles. The observed RR spectra also showed that the retinal chromophore is strongly hydrogen bonded to an internal water molecule via a protonated Schiff base, which is characteristic of proton-pumping rhodopsins. The obtained data strongly suggest that TR functions in the pentameric form at physiological temperature in the extreme thermophile T. thermophilus JL-18. We utilized the high thermal stability of the monomeric form of solubilized TR and here report the first RR spectra of the monomeric form of a microbial rhodopsin. The observed RR spectra revealed that the monomerization of TR alters the chromophore structure: there are changes in the bond alternation of the polyene chain and in the hydrogen-bond strength of the protonated Schiff base. The present study revealed the high thermal stability of oligomeric assemblies of TR in the lipid environment and suggested the importance of using TR embedded in lipid membrane for elucidation of its functional mechanism.
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Affiliation(s)
- Tomomi Shionoya
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , 1-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | | | - Hayato Seki
- Graduate School of Engineering , Yokohama National University , Hodogaya-ku, Yokohama 240-8501 , Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , 1-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | | | - Izuru Kawamura
- Graduate School of Engineering , Yokohama National University , Hodogaya-ku, Yokohama 240-8501 , Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , 1-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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Zhang XC, Zhou Y, Cao C. Proton transfer during class-A GPCR activation: do the CWxP motif and the membrane potential act in concert? BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0056-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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25
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Yi A, Li H, Mamaeva N, Fernandez De Cordoba RE, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Structural Changes in an Anion Channelrhodopsin: Formation of the K and L Intermediates at 80 K. Biochemistry 2017; 56:2197-2208. [PMID: 28350445 DOI: 10.1021/acs.biochem.7b00002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A recently discovered natural family of light-gated anion channelrhodopsins (ACRs) from cryptophyte algae provides an effective means of optogenetically silencing neurons. The most extensively studied ACR is from Guillardia theta (GtACR1). Earlier studies of GtACR1 have established a correlation between formation of a blue-shifted L-like intermediate and the anion channel "open" state. To study structural changes of GtACR1 in the K and L intermediates of the photocycle, a combination of low-temperature Fourier transform infrared (FTIR) and ultraviolet-visible absorption difference spectroscopy was used along with stable-isotope retinal labeling and site-directed mutagenesis. In contrast to bacteriorhodopsin (BR) and other microbial rhodopsins, which form only a stable red-shifted K intermediate at 80 K, GtACR1 forms both stable K and L-like intermediates. Evidence includes the appearance of positive ethylenic and fingerprint vibrational bands characteristic of the L intermediate as well as a positive visible absorption band near 485 nm. FTIR difference bands in the carboxylic acid C═O stretching region indicate that several Asp/Glu residues undergo hydrogen bonding changes at 80 K. The Glu68 → Gln and Ser97 → Glu substitutions, residues located close to the retinylidene Schiff base, altered the K:L ratio and several of the FTIR bands in the carboxylic acid region. In the case of the Ser97 → Glu substitution, a significant red-shift of the absorption wavelength of the K and L intermediates occurs. Sequence comparisons suggest that L formation in GtACR1 at 80 K is due in part to the substitution of the highly conserved Leu or Ile at position 93 in helix 3 (BR sequence) with the homologous Met105 in GtACR1.
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Affiliation(s)
- Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Roberto E Fernandez De Cordoba
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Johan Lugtenburg
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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26
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Yi A, Mamaeva N, Li H, Spudich JL, Rothschild KJ. Resonance Raman Study of an Anion Channelrhodopsin: Effects of Mutations near the Retinylidene Schiff Base. Biochemistry 2016; 55:2371-80. [PMID: 27039989 DOI: 10.1021/acs.biochem.6b00104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optogenetics relies on the expression of specific microbial rhodopsins in the neuronal plasma membrane. Most notably, this includes channelrhodopsins, which when heterologously expressed in neurons function as light-gated cation channels. Recently, a new class of microbial rhodopsins, termed anion channel rhodopsins (ACRs), has been discovered. These proteins function as efficient light-activated channels strictly selective for anions. They exclude the flow of protons and other cations and cause hyperpolarization of the membrane potential in neurons by allowing the inward flow of chloride ions. In this study, confocal near-infrared resonance Raman spectroscopy (RRS) along with hydrogen/deuterium exchange, retinal analogue substitution, and site-directed mutagenesis were used to study the retinal structure as well as its interactions with the protein in the unphotolyzed state of an ACR from Guillardia theta (GtACR1). These measurements reveal that (i) the retinal chromophore exists as an all-trans configuration with a protonated Schiff base (PSB) very similar to that of bacteriorhodopsin (BR), (ii) the chromophore RRS spectrum is insensitive to changes in pH from 3 to 11, whereas above this pH the Schiff base (SB) is deprotonated, (iii) when Ser97, the homologue to Asp85 in BR, is replaced with a Glu, it remains in a neutral form (i.e., as a carboxylic acid) but is deprotonated at higher pH to form a blue-shifted species, (iv) Asp234, the homologue of the protonated retinylidene SB counterion Asp212 in BR, does not serve as the primary counteranion for the protonated SB, and (v) substitution of Glu68 with an Gln increases the pH at which SB deprotonation is observed. These results suggest that Glu68 and Asp234 located near the SB exist in a neutral state in unphotolyzed GtACR1 and indicate that other unidentified negative charges stabilize the protonated state of the GtACR1 SB.
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Affiliation(s)
- Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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27
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Novel expression and characterization of a light driven proton pump archaerhodopsin 4 in a Halobacterium salinarum strain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:390-398. [DOI: 10.1016/j.bbabio.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/22/2014] [Accepted: 12/25/2014] [Indexed: 11/19/2022]
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28
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Ogren JI, Mamaev S, Russano D, Li H, Spudich JL, Rothschild KJ. Retinal chromophore structure and Schiff base interactions in red-shifted channelrhodopsin-1 from Chlamydomonas augustae. Biochemistry 2014; 53:3961-70. [PMID: 24869998 PMCID: PMC4072394 DOI: 10.1021/bi500445c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Channelrhodopsins (ChRs), which form
a distinct branch of the microbial
rhodopsin family, control phototaxis in green algae. Because ChRs
can be expressed and function in neuronal membranes as light-gated
cation channels, they have rapidly become an important optogenetic
tool in neurobiology. While channelrhodopsin-2 from the unicellular
alga Chlamydomonas reinhardtii (CrChR2) is the most commonly used and extensively studied optogenetic
ChR, little is known about the properties of the diverse group of
other ChRs. In this study, near-infrared confocal resonance Raman
spectroscopy along with hydrogen–deuterium exchange and site-directed
mutagenesis were used to study the structure of red-shifted ChR1 from Chlamydomonas augustae (CaChR1). These
measurements reveal that (i) CaChR1 has an all-trans-retinal structure similar to those of the light-driven
proton pump bacteriorhodopsin (BR) and sensory rhodopsin II but different
from that of the mixed retinal composition of CrChR2,
(ii) lowering the pH from 7 to 2 or substituting neutral residues
for Glu169 or Asp299 does not significantly shift the ethylenic stretch
frequency more than 1–2 cm–1 in contrast
to BR in which a downshift of 7–9 cm–1 occurs
reflecting neutralization of the Asp85 counterion, and (iii) the CaChR1 protonated Schiff base (SB) has stronger hydrogen
bonding than BR. A model is proposed to explain these results whereby
at pH 7 the predominant counterion to the SB is Asp299 (the homologue
to Asp212 in BR) while Glu169 (the homologue to Asp85 in BR) exists
in a neutral state. We observe an unusual constancy of the resonance
Raman spectra over the broad range from pH 9 to 2 and discuss its
implications. These results are in accord with recent visible absorption
and current measurements of CaChR1 [Sineshchekov,
O. A., et al. (2013) Intramolecular proton transfer in channelrhodopsins. Biophys. J. 104, 807–817; Li, H., et al. (2014) Role
of a helix B lysine residue in the photoactive site in channelrhodopsins. Biophys. J. 106, 1607–1617].
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Affiliation(s)
- John I Ogren
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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29
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Kundu A, Yamaguchi S, Tahara T. Evaluation of pH at Charged Lipid/Water Interfaces by Heterodyne-Detected Electronic Sum Frequency Generation. J Phys Chem Lett 2014; 5:762-766. [PMID: 26270850 DOI: 10.1021/jz500107e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although the interface pH at a biological membrane is important for biological processes at the membrane, there has been no systematic study to evaluate it. We apply novel interface-selective nonlinear spectroscopy to the evaluation of the pH at model biological membranes (lipid/water interfaces). It is clearly shown that the pH at the charged lipid/water interfaces is substantially deviated from the bulk pH. The pH at the lipid/water interface is higher than that in the bulk when the head group of the lipid is positively charged, whereas the pH at the lipid/water interface is lower when the lipid has a negatively charged head group.
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Affiliation(s)
- Achintya Kundu
- †Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Shoichi Yamaguchi
- †Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- †Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- ‡Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), Wako, Saitama 351-0198, Japan
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