Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

Article Chemistry, Multidisciplinary

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

Chun-Fu Chang et al.

Summary: The varied excited-state relaxation dynamics in different microbial rhodopsins mainly originate from the difference in ground-state heterogeneity, specifically the protonation/deprotonation of the PRSB counterion.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

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Review Biophysics

Phospholipid Scrambling by G Protein-Coupled Receptors

George Khelashvili et al.

Summary: The rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. G protein-coupled receptors (GPCRs), such as opsins, exhibit constitutive scramblase activity in vitro, with opsins scrambling lipids at a unitary rate of >100,000 per second. This review discusses the physiological significance of GPCR scramblase activity and its regulation in cells.

ANNUAL REVIEW OF BIOPHYSICS (2022)

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Article Biochemistry & Molecular Biology

Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

Koichiro E. Kishi et al.

Summary: ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, has opened new possibilities in optogenetics with its unique properties. The cryo-EM structure of ChRmine, revealed at 2.0A resolution, uncovers architectural features distinct from other channelrhodopsins and lays the foundation for the creation of new channelrhodopsins for various biological applications.

CELL (2022)

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Article Biochemistry & Molecular Biology

Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins

Samagya Banskota et al.

Summary: We have developed and applied engineered DNA-free virus-like particles (eVLPs) for efficient delivery of gene editing tools, achieving high levels of base editing. By overcoming the limitations of cargo packaging, release, and localization, the fourth-generation eVLPs demonstrated efficient base editing in mouse and human cells. In addition, the off-target effects of eVLPs were significantly reduced compared to other delivery methods such as AAV or plasmid.

CELL (2022)

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Article Microbiology

Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea

Ariel Chazan et al.

Summary: The recently discovered rhodopsin family of heliorhodopsins (HeRs) are found in diverse microbial environments and their functional and biological roles remain unknown. Through experimental and computational screens, 10 readily expressed HeR genes were identified, and they were found to have diverse kinetic characteristics in terms of light absorption and photocycles. Analysis of genes neighboring HeRs suggests a potential involvement in light-induced membrane lipid modifications.

ENVIRONMENTAL MICROBIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Mutational analyses identify a single amino acid critical for colour tuning in proteorhodopsins

Jin-gon Shim et al.

Summary: This study reports a new site in microbial rhodopsins that controls spectral tuning. Amino acid substitutions at positions 189 and 105 in ISR34 were found to result in the maximum absorption red-shift, indicating their equal importance in spectral tuning. Structural changes resulting from amino acid substitutions are related to pK(a) values, pumping activity, and spectral tuning.

FEBS LETTERS (2022)

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Article Biochemistry & Molecular Biology

Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography

Kano Suzuki et al.

Summary: DTG/DTS rhodopsin is a light-driven proton-pumping microbial rhodopsin that utilizes a three residue motif (DTG or DTS) important for its function. It lacks a cytoplasmic proton donor residue, but can directly bind protons from the cytoplasmic solvent, enabling energy production and avoiding intracellular alkalization.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

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Article Chemistry, Physical

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations

Satoshi Yasuda et al.

Summary: A methodology was developed to identify thermostabilizing mutations in a membrane protein, resulting in the construction of quadruple mutants with a new thermal stability record in a class of outward proton pumping rhodopsins.

JOURNAL OF PHYSICAL CHEMISTRY B (2022)

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Article Chemistry, Multidisciplinary

Phototriggered Apoptotic Cell Death (PTA) Using the Light-Driven Outward Proton Pump Rhodopsin Archaerhodopsin-3

Shin Nakao et al.

Summary: Apoptosis is a crucial programmed cell death mechanism in multicellular organisms, and its dysregulation can lead to various diseases. Research has shown that controlling intracellular pH can regulate apoptotic cell death, with potential applications in selectively eliminating target cells with high spatiotemporal resolution.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Article Chemistry, Multidisciplinary

Light Driven Ultrafast Bioinspired Molecular Motors: Steering and Accelerating Photoisomerization Dynamics of Retinal

Elisabeth Gruber et al.

Summary: The study reveals that by locking the configuration of retinal chromophores, it is possible to achieve ultrafast excited-state decay, opening up a new pathway for designing red-light-driven ultrafast molecular rotary motors.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Article Biochemistry & Molecular Biology

Rethinking Opsins

Roberto Feuda et al.

Summary: Opsins, the protein components of animal visual photo-pigments, have been identified as moonlighting proteins with diverse physiological functions both dependent and independent of light. This highlights the need for revising basic assumptions regarding opsin expression, structure, classification, and evolution.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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Article Biotechnology & Applied Microbiology

Wireless closed-loop optogenetics across the entire dorsoventral spinal cord in mice

Claudia Kathe et al.

Summary: Optoelectronic system allows precise control over targeted neurons and pathways in the brain of untethered animals, but such technology for the spinal cord is not well established. In this study, a new system was developed for ultrafast, wireless, closed-loop manipulation of targeted neurons and pathways across the entire spinal cord in untethered mice.

NATURE BIOTECHNOLOGY (2022)

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Article Neurosciences

High-performance microbial opsins for spatially and temporally precise perturbations of large neuronal networks

Savitha Sridharan et al.

Summary: Structure-guided mutagenesis has been used to engineer new optogenetic tools with high potency and fast kinetics, enabling precise control of population neural activity at a large scale, and temporally and spatially. These new tools have been extensively benchmarked and characterized, providing a resource for patterned optogenetics experiments. Furthermore, when combined with optimized procedures for holographic photostimulation, these new tools allow for the coactivation of hundreds of spatially defined neurons simultaneously with a single hologram.

NEURON (2022)

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Review Physiology

OPTOPHYSIOLOGY: ILLUMINATING CELL PHYSIOLOGY WITH OPTOGENETICS

Peng Tan et al.

Summary: Optogenetics combines light and genetics to precisely control living cells, tissues, and organisms. It has advantages such as noninvasiveness, rapid responsiveness, tunability, and high spatiotemporal resolution. This review summarizes the fundamental photochemical properties of optogenetic tools and highlights applications in cellular physiology. It also discusses the progress and future trends in wireless optogenetics.

PHYSIOLOGICAL REVIEWS (2022)

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Article Multidisciplinary Sciences

Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers

Toshiaki Hosaka et al.

Summary: Time-resolved serial femtosecond crystallography was used to study the structural changes and ion transfer mechanisms in anion-pumping rhodopsins. The study revealed the conformational alterations during ion transfer and ion release, as well as the halide binding site for ion transfer.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Review Neurosciences

Red Light Optogenetics in Neuroscience

Kimmo Lehtinen et al.

Summary: Optogenetics is a promising field in neuroscience that utilizes light-activated proteins to control cellular functions. Red light-operated optogenetic tools offer advantages for in vivo studies, although they have limited penetration in biological tissues. This review focuses on the utilization of red light optogenetics in neuroscience and discusses the advantages, developments, and applications of this approach.

FRONTIERS IN CELLULAR NEUROSCIENCE (2022)

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Review Neurosciences

Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships

Elena G. Govorunova et al.

Summary: Cation and anion channelrhodopsins have been widely used as genetically encoded molecular tools to control cell membrane potential with light. The diversity of channelrhodopsins provides an exceptional platform for the study of structure-function evolution in membrane proteins.

FRONTIERS IN CELLULAR NEUROSCIENCE (2022)

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Article Multidisciplinary Sciences

Colocalized, bidirectional optogenetic modulations in freely behaving mice with a wireless dual-color optoelectronic probe

Lizhu Li et al.

Summary: In this study, a wireless, dual-color optogenetic probe with the co-expression of two spectrally distinct opsins was used to achieve bidirectional neuronal activity manipulation in a rodent model. The probe showed colocalized red and blue emissions and enabled chronic in vivo operations. It could interfere with dopaminergic neurons, resulting in different behaviors and social interactions among mice.

NATURE COMMUNICATIONS (2022)

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Article Chemistry, Multidisciplinary

Photonic Nanojet-Mediated Optogenetics

Jinghui Guo et al.

Summary: Optogenetics is a widely used technique in neuroscience research that can control neuronal activity. This study demonstrates the use of polystyrene microspheres as optical lenses to focus light on targeted neurons at low power, improving the efficacy of optogenetics.

ADVANCED SCIENCE (2022)

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Review Biochemistry & Molecular Biology

A Guide to time-resolved structural analysis of light-activated proteins

Harshwardhan Poddar et al.

Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.

FEBS JOURNAL (2022)

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Article Biochemistry & Molecular Biology

Characterization and Modification of Light-Sensitive Phosphodiesterases from Choanoflagellates

Yuehui Tian et al.

Summary: Researchers have discovered enzyme rhodopsins in fungi, algae and protists, which could be used for developing light-regulated phosphodiesterase tools in the future.

BIOMOLECULES (2022)

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Review Biochemistry & Molecular Biology

Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases

Matthias Broser

Summary: The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi exhibit unexpected properties, functioning exclusively as heterodimers with distinct retinal chromophores. The bimodal photoswitchable Neorhodopsin is particularly noteworthy for its near-infrared absorption and high fluorescence, which have not been observed in other retinal photoreceptors. This article discusses these properties in the context of retinal chromophore color-tuning approaches and provides a brief review of heterodimerization, shedding light on the development of optogenetic tools.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

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Article Biochemistry & Molecular Biology

Near-Infrared Activation of Sensory Rhodopsin II Mediated by NIR-to-Blue Upconversion Nanoparticles

Momo Yaguchi et al.

Summary: Direct optical activation of microbial rhodopsins in deep biological tissue is challenging due to ineffective light delivery. Lanthanide-doped upconversion nanoparticles (UCNPs) offer a solution by converting near-infrared (NIR) light to visible light. In this study, UCNP-assisted NIR activation of a blue light-sensitive microbial rhodopsin was investigated. The results show that the structural changes induced by UCNP-generated visible light are similar to those caused by direct blue light illumination.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

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Article Biology

Selective control of synaptically-connected circuit elements by all-optical synapses

Mansi Prakash et al.

Summary: Prakash et al. developed an approach to control synaptically connected elements using bioluminescent light, in which Luciferase-generated light, originating from a presynaptic axon terminal, modulates an opsin in its postsynaptic target to form an 'optical synapse'. They validated their optical synapses in cultured neurons and in mice in vivo and showed that they provide an approach to achieve synapse-specific and activity-dependent circuit control in vivo.

COMMUNICATIONS BIOLOGY (2022)

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Article Biology

Amino acid residue at position 188 determines the UV-sensitive bistable property of vertebrate non-visual opsin Opn5

Chihiro Fujiyabu et al.

Summary: Opsins are G protein-coupled receptors specialized in photoreception in animals. Opn5 is a separate opsin group responsible for non-visual photoreception. Among them, Opn5m and Opn5L2 can form a UV-sensitive resting state and switch to an active state. The residue at position 188 is found to determine the UV-sensitive bistable property of Opn5m.

COMMUNICATIONS BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Light-driven proton transfers and proton transport by microbial rhodopsins-A biophysical perspective

Leonid S. Brown

Summary: In the past twenty years, there have been significant breakthroughs in understanding the rules and mechanisms of proton transport in microbial rhodopsins, transitioning from atomic-level understanding to a confounding variety of new homologs. This review summarizes and discusses experimental data obtained on new microbial rhodopsin variants, with a focus on the vectoriality of proton transport and their structural determinants.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2022)

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Article Chemistry, Multidisciplinary

Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Jonathan R. Church et al.

Summary: Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. By substituting glutamine with leucine, the absorption wavelength of PR can be tuned, allowing it to adapt to different depths in the ocean. Our study reveals the tuning mechanism and provides guidance for rational design of spectral shifts.

CHEMISTRY-A EUROPEAN JOURNAL (2022)

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Article Chemistry, Multidisciplinary

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency

Xuchun Yang et al.

Summary: This study demonstrates the degeneracy between the reactive excited state and a neighboring state in rhodopsin, which causes the splitting of the rhodopsin population into subpopulations after 15 femtoseconds of light absorption. These subpopulations propagate with different velocities and contribute differently to the quantum efficiency. Furthermore, the study reveals that protein electrostatics modulate this splitting and link amino acid sequence variations to quantum efficiency modulation.

NATURE CHEMISTRY (2022)

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Article Multidisciplinary Sciences

Dynamics and mechanism of a light-driven chloride pump

Sandra Mous et al.

Summary: By combining time-resolved crystallography, spectroscopy, and multiscale simulations, we have elucidated the molecular mechanism and structural dynamics of a chloride-pumping rhodopsin throughout the transport cycle. We identified transient anion-binding sites, provided evidence for the use of light energy in the pumping mechanism, and discovered molecular gates that ensure unidirectional transport. These findings reveal key mechanistic features that enable finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.

SCIENCE (2022)

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Review Neurosciences

Review Ocular and extraocular roles of neuropsin in vertebrates

Hugo Calligaro et al.

Summary: The ability to detect and adapt to ambient light is crucial for animal survival. Recent studies have shown that the UV-sensitive opsin, neuropsin (OPN5), plays an important role in regulating eye development and non-image-forming functions in response to light.

TRENDS IN NEUROSCIENCES (2022)

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Review Chemistry, Multidisciplinary

Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

Laura Pedraza-Gonzalez et al.

Summary: Rhodopsins, such as photoactive proteins, have become a popular target in optogenetics research. Computational methods, like the Automatic Rhodopsin Modeling (ARM) protocol, provide the necessary tools for analyzing experimental results and driving the design of new systems.

TOPICS IN CURRENT CHEMISTRY (2022)

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Article Medicine, Research & Experimental

A systematic comparison of optogenetic approaches to visual restoration

Michael J. Gilhooley et al.

Summary: In this study, two optogenetic tools, mammalian melanopsin and microbial red-shifted channelrhodopsin, were compared for their expression effects in a degenerate retina. The results showed that targeting bipolar cells with optogenetic tools produced faster kinetics and flatter intensity-response relationships compared to non-targeted or retinal-ganglion-cell-targeted tools.

MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT (2022)

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Article Cell Biology

Isolation and Crystallization of the D156C Form of Optogenetic ChR2

Liying Zhang et al.

Summary: In this study, the production and purification procedure of the D156C form of ChR2, which exhibits prolonged channel opening, was reported. Furthermore, conditions for growing ChR2 crystals that scatter X-rays to 6 angstrom were developed. The results provide a foundation for future structural studies of ChR2 in different states.

CELLS (2022)

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Article Biochemistry & Molecular Biology

The Impact of Retinal Configuration on the Protein-Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

Jonathan R. Church et al.

Summary: This study analyzes the absorption spectra and structural changes of jumping spider rhodopsin-1 (JSR1) through hybrid QM/MM simulations, revealing that the distance of a nearby tyrosine residue plays a significant role in predicting the absorption maximum.

MOLECULES (2022)

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Article Surgery

A Perspective on the Potential of Opsins as an Integral Mechanism of Photobiomodulation: It's Not Just the Eyes

Ann Liebert et al.

Summary: This study investigates the relationship between opsins and photobiomodulation, discussing the effects of different opsins on ion channel function, central and peripheral nervous systems, as well as the potential clinical implications of photobiomodulation in health maintenance and treatment of chronic diseases.

PHOTOBIOMODULATION PHOTOMEDICINE AND LASER SURGERY (2022)

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Article Chemistry, Multidisciplinary

Activation of the G-Protein-Coupled Receptor Rhodopsin by Water

Udeep Chawla et al.

Summary: Visual rhodopsin absorbs light and takes in approximately 80 water molecules to form a solvent-swollen active state, which is essential for activating the photoreceptor and is supported by molecular dynamics simulations. Force-based measurements show that the expansion of rhodopsin occurs through changes in cavity volumes and increased hydration in the active Meta II state. Furthermore, the binding and release of the C-terminal helix of transducin is coupled to hydration changes, potentially influencing visual signal amplification through a dynamic allosteric mechanism involving lipid and water interactions in the catalytic G-protein cycle.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Biochemistry & Molecular Biology

The functional characteristics of optogenetic gene therapy for vision restoration

Moritz Lindner et al.

Summary: The study explores optogenetic strategies to restore vision in patients blind from end-stage retinal degenerations and finds that optogenetic gene therapy can partially restore retinal responses to complex light stimuli. However, limitations exist which could be mitigated using bipolar-cell targeted gene-delivery approaches.

CELLULAR AND MOLECULAR LIFE SCIENCES (2021)

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Article Biology

Structure-based insights into evolution of rhodopsins

Dmitrii Zabelskii et al.

Summary: The study analyzed the structure and function of the fungal rhodopsin LR (Mac), showing that it has an ancient archaeal ancestry and may share a common ancestor with archaeal proton pumps. The findings suggest that eukaryotic and archaeal proton pumps likely have a common evolutionary history.

COMMUNICATIONS BIOLOGY (2021)

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Article Chemistry, Multidisciplinary

The Voltage Dependent Sidedness of the Reprotonation of the Retinal Schiff Base Determines the Unique Inward Pumping of Xenorhodopsin

Juliane Weissbecker et al.

Summary: The new class of microbial rhodopsins, xenorhodopsins (XeRs), extends the versatility of this family by serving as inward H+ pumps, offering an alternative optogenetic tool that can activate electrically excitable cells independently of surrounding physiological conditions. Functional and spectroscopic characterization of NsXeR reveals insights into the photodynamic behavior, pH-dependent kinetics, and potential-dependent vectoriality of photocurrent transients. Mutational studies on the putative intracellular H+ acceptor D220 provide further understanding of the kinetically independent switching mechanism.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Review Pharmacology & Pharmacy

Microbial Rhodopsins as Multi-functional Photoreactive Membrane Proteins for Optogenetics

Shin Nakao et al.

Summary: Utilizing photoactive membrane protein rhodopsins for optogenetics is an effective method to control biological activities, including ion pumps, ion channels, transcription regulators, and enzymes. These tools have high potential for basic and clinical research in pharmaceutical sciences.

BIOLOGICAL & PHARMACEUTICAL BULLETIN (2021)

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Editorial Material Biochemistry & Molecular Biology

How the discovery of microbial opsins led to the development of optogenetics

Jeffrey M. Friedman

Summary: This year's Lasker Award is awarded to Dieter Oesterhelt, Peter Hegemann, and Karl Deisseroth for their discovery of microbial opsins as light-activated ion conductors and the development of optogenetics using these proteins to regulate neural activity in awake, behaving animals. Optogenetics has revolutionized neuroscience and transformed our understanding of brain function.

CELL (2021)

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Article Chemistry, Multidisciplinary

Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores

Baptiste Demoulin et al.

Summary: The study shows that modifying the electrostatic environment of the chromophore through protein point mutations can affect its excited state properties, allowing control of its photophysics with the same power as chemical modifications of the chromophore. This fine control is essential for the design of bio-mimetic opto-electronic and photonic devices.

CHEMISTRY-A EUROPEAN JOURNAL (2021)

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Article Chemistry, Physical

Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin

Olga A. Smitienko et al.

Summary: The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated using femtosecond absorption laser spectroscopy. The dynamics of the ESR photoreaction were compared with bacteriorhodopsin (bR) reactions, showing similar primary intermediates. The study found a similar photoreaction pattern for all studied retinal proteins, with different timescales for excited state decays and retinal photoisomerization.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Review Biochemistry & Molecular Biology

Frontiers in Multiscale Modeling of Photoreceptor Proteins

Maria-Andrea Mroginski et al.

Summary: This article discusses the challenges in the theoretical description of photoreceptor proteins, as well as the development of new tools to address these challenges, based on discussions at the CECAM workshop in Tel Aviv, Israel. It also presents recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin, along with methodological developments.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2021)

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Article Pathology

Optogenetic control of cancer cell survival in ChR2-transfected HeLa cells

Claudio Cordova et al.

Summary: Optogenetics is a molecular biological technique involving transfection of cells with photosensitive proteins to study their biological effects. This study evaluated the impact of blue light on the survival of HeLa cells transfected with channelrhodopsin-2 (ChR2), revealing a significant correlation between the frequency and time of light stimulation and cell survival.

INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY (2021)

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Article Multidisciplinary Sciences

Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

Juan F. Bada Juarez et al.

Summary: The study reveals significant differences between the ground and dark-adapted states of Archaerhodopsin-3 (AR3), with dynamics of water molecules and internal water networks playing key roles in this desensitization process.

NATURE COMMUNICATIONS (2021)

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Article Biochemistry & Molecular Biology

Phototransduction in Anuran Green Rods: Origins of Extra-Sensitivity

Luba A. Astakhova et al.

Summary: The study examined the unique photoreceptors known as green rods (GRs) in anuran amphibians, confirming that they are highly specialized nocturnal vision receptors and more efficient single photon detectors than classic red rods (RRs). The slower phototransduction quenching rate of GRs compared to RRs was also highlighted.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Viral Transduction of Human Rod Opsin or Channelrhodopsin Variants to Mouse ON Bipolar Cells Does Not Impact Retinal Anatomy or Cause Measurable Death in the Targeted Cells

Phillip Wright et al.

Summary: The study evaluated the safety of viral gene delivery of human rod opsin and two channelrhodopsins in ON bipolar cells of the mouse retina. The results showed that delivery of these opsins did not cause significant changes in retinal health or impact the survival of targeted cells. Additionally, there was no increase in retinal inflammation in treated mice compared to controls.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Systematic profiling of temperature- and retinal-sensitive rhodopsin variants by deep mutational scanning

Andrew G. McKee et al.

Summary: Membrane protein variants with reduced conformational stability show enhanced cellular expression at lower temperatures and sensitivity to corrector molecules like 9-cis-retinal. Variants affecting a hydrophobic transmembrane domain exhibit stronger responses to changes in growth temperature and retinal compared to those affecting a polar transmembrane domain, suggesting multiple factors influence their sensitivity.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Cell Biology

Rhodopsins at a glance

Takashi Nagata et al.

Summary: Rhodopsins are a class of photoreceptive membrane proteins with a diverse range of functions, including microbial and animal rhodopsins. They exhibit distinctive characteristics in terms of function, structure, color discrimination mechanisms, and optogenetic applications, with a third rhodopsin family known as heliorhodopsin.

JOURNAL OF CELL SCIENCE (2021)

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Review Biology

Melanopsin phototransduction: beyond canonical cascades

Ely Contreras et al.

Summary: Melanopsin is a visual pigment expressed in a small subset of intrinsically photosensitive retinal ganglion cells, regulating both non-image forming and image-forming visual functions. Recent research has identified multiple subtypes of ipRGCs with unique properties, challenging the traditional view of melanopsin phototransduction as a single pathway.

JOURNAL OF EXPERIMENTAL BIOLOGY (2021)

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Article Quantum Science & Technology

A state-averaged orbital-optimized hybrid quantum-classical algorithm for a democratic description of ground and excited states

Saad Yalouz et al.

Summary: In the NISQ era, solving the electronic structure problem in chemistry through a combination of different algorithms is crucial. Research on active spaces and conical intersections is essential for improving the accuracy of quantum computers.

QUANTUM SCIENCE AND TECHNOLOGY (2021)

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Article Engineering, Biomedical

Multifunctional optrode for opsin delivery, optical stimulation, and electrophysiological recordings in freely moving rats

Kirti Sharma et al.

Summary: This study presents a multifunctional optrode combining a silicon-based neural probe, integrated microfluidic channel, and optical glass fiber for in vivo experiments. The optrode, weighing 0.97 g, allows for simultaneous drug delivery, optical stimulation, and neural recording, demonstrating utility in optogenetics and pharmacology with reduced tissue damage. This triple-modality device enables a single-step optogenetic surgery, achieving higher spatial specificity compared to conventional multi-step surgeries.

JOURNAL OF NEURAL ENGINEERING (2021)

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Article Engineering, Biomedical

In vivo blue light illumination for optogenetic inhibition: effect on local temperature and excitability of the rat hippocampus

Anirudh R. Acharya et al.

Summary: The study evaluated the heating effects of blue light on the brain and found that increasing light power densities and pulse durations logarithmically increased temperature peak, decreased population spike amplitude, and altered evoked potentials latencies. In rats expressing stGtACR2, illumination resulted in greater inhibition of evoked potentials compared to opsin-negative rats.

JOURNAL OF NEURAL ENGINEERING (2021)

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Article Biochemistry & Molecular Biology

Photocycle dynamics of the Archaerhodopsin 3 based fluorescent voltage sensor Archon2

Alfons Penzkofer et al.

Summary: The study focused on the retinal photocycle dynamics of the fluorescent voltage sensor Archon2 in pH 8 Tris buffer. It revealed the photoisomerization process of Ret_586 to Ret_535 in light-adapted state, which then gradually reverts back to Ret_586 in dark-adapted state. The results provide insights into the light-induced structural changes and absorption spectra characteristics of Archon2.

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants

Masaki Tsujimura et al.

Summary: The study demonstrates how the protein environment in Guillardia theta anion channelrhodopsin-1 (GtACR1) can shift the absorption wavelength, with mutations at certain residues increasing the absorption wavelength. Specifically, the T101A mutant of GtACR1 showed a higher absorption wavelength compared to the wild type, consistent with calculations.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2021)

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Article Biochemistry & Molecular Biology

Using a bistable animal opsin for switchable and scalable optogenetic inhibition of neurons

Jessica Rodgers et al.

Summary: There is no consensus on the best inhibitory optogenetic tool. Gi/o signalling is a native mechanism of neuronal inhibition, and Lamprey Parapinopsin (Lamplight) can be used for optogenetic silencing by switching between stable signalling active and inactive states with different wavelengths. The properties of Lamplight can be applied to achieve switchable neuronal hyperpolarisation and suppression of spontaneous spike firing in specific brain regions. Expressing Lamplight in ON bipolar cells can photosensitise retinas following advanced photoreceptor degeneration, showing potential for scalable, sustained, and reversible optogenetic inhibition.

EMBO REPORTS (2021)

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Article Multidisciplinary Sciences

Optogenetic stimulation of glutamatergic neurons in the cuneiform nucleus controls locomotion in a mouse model of Parkinson's disease

Maxime Fougere et al.

Summary: In a mouse model of PD, selective optogenetic stimulation of glutamatergic neurons in the cuneiform nucleus increased the number of locomotor initiations, extended the time spent in locomotion, and controlled locomotor speed. This suggests that glutamatergic neurons in the cuneiform nucleus may be a potential clinically relevant target to improve locomotor activity in parkinsonian conditions.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemistry & Molecular Biology

Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs

Meng Zhang et al.

Summary: Recent studies have uncovered the complex interactions between neurotensin receptor 1, neurotensin, and G proteins in a lipid bilayer environment, revealing a more intricate network of protein-protein interactions compared to structures obtained in detergent micelles. These findings provide new insights into the modulation of complex formation by lipid membranes and propose an allosteric mechanism for GDP release in G protein activation.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

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Article Multidisciplinary Sciences

Computed structures of core eukaryotic protein complexes

Ian R. Humphreys et al.

Summary: By utilizing proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling, we systematically identified and built accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. These models cover nearly 800 previously uncharacterized assemblies, providing comprehensive insights into key processes in eukaryotic cells.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Self-assembled multifunctional neural probes for precise integration of optogenetics and electrophysiology

Liang Zou et al.

Summary: The viral vector-delivery optrode system integrates optogenetics and electrophysiology to precisely manipulate and record neuronal populations, allowing long-term study of neural circuit functions.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Single molecule kinetics of bacteriorhodopsin by HS-AFM

Alma P. Perrino et al.

Summary: The study used high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bacteriorhodopsin under continuous light and short pulses. It found that the cytoplasmic gate opens 2.9 ms after photon absorption and stays open for proton capture for 13.2 ms, with a single molecule reaction cycle of approximately 20 s(-1).

NATURE COMMUNICATIONS (2021)

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Article Biology

The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy

Paul Fischer et al.

Summary: Enzymerhodopsins are a newly discovered class of rhodopsins, including several different types such as histidine kinase rhodopsin, rhodopsin phosphodiesterases, and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on enzyme activity remains partially understood, but is crucial for a deeper understanding of intra-molecular signaling pathways. By studying the light-induced dynamics of a RGC from the Catenaria anguillulae fungus, researchers gained insights into the catalytic process and structural rearrangements upon photo-activation of the protein.

ELIFE (2021)

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Review Physiology

Seeing the Light: The Use of Zebrafish for Optogenetic Studies of the Heart

Jonathan S. Baillie et al.

Summary: Optogenetics, as a powerful experimental technique for probing (patho-)physiological function, has been utilized in cardiac research for over a decade. The zebrafish, with its genetic and functional cardiac similarities to mammals, transparent embryo for in vivo visualization, and high-throughput capabilities, represents an experimental model with unrealized potential for cardiac optogenetic studies.

FRONTIERS IN PHYSIOLOGY (2021)

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Article Physiology

Optogenetic Stimulation of Gi Signaling Enables Instantaneous Modulation of Cardiomyocyte Pacemaking

Milan Cokic et al.

Summary: G-protein signaling pathways play a crucial role in regulating cardiac function, and optogenetic techniques utilizing opsin proteins allow precise activation in cardiomyocytes. The application of long wavelength-sensitive cone opsin (LWO) in this study demonstrated effective and specific activation of the G(i) signaling cascade in cardiomyocytes with high temporal precision.

FRONTIERS IN PHYSIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima

Andrey A. Shtyrov et al.

Summary: This study introduces simple models to estimate the direct effect of charged or polar residue substitutions in proteins from the rhodopsin family, without the need for extensive calculations. The models are based on absorption maximum values calculated at a theoretical level for the retinal chromophore in an external electrostatic field. The proposed approach was evaluated against various mutants and can be useful for interpreting experimental data and designing proteins with desired spectral properties.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Modified Rhodopsins From Aureobasidium pullulans Excel With Very High Proton-Transport Rates

Sabine Panzer et al.

Summary: Aureobasidium pullulans, a black fungus, possesses genes coding for putative opsins ApOps1, ApOps2, and ApOps3. Heterologous expression and site-directed mutagenesis enabled the creation of light-gated proton channels with potential for optogenetic applications.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Biochemistry & Molecular Biology

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Victor A. Lorenz-Fonfria et al.

Summary: The study revealed the fundamental vibrational characteristics of the chromophore in bacteriorhodopsin membrane protein and its role in the proton-pumping mechanism of the protein. By investigating vibrational spectra, researchers compared differences between all-trans and 13-cis retinal, and identified the overtone and combination transitions of the retinal's C-C stretching vibrations. The latest research suggests that the intensity of overtone C-C transitions in retinal may be overestimated.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Biology

Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2

Yuta Nakajima et al.

Summary: Mutations of amino acid at position 219 of the sodium pump rhodopsin, KR2, play a crucial role in color tuning of the retinal chromophore, with the exception of P219R. The red-shifting variations are mainly induced by electrostatic interactions of the G/P switch, while the blue-shifted P219R variant involves both electrostatic and steric changes accompanied by protonation state and hydrogen bond networks modifications. The complexity of the results highlights the difficulty in predicting the operation of the switch without considering atomistic details and environmental consequences of the side chain replacement.

COMMUNICATIONS BIOLOGY (2021)

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Article Chemistry, Multidisciplinary

Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins

Kin Kuan Hoi et al.

Summary: The study used native MS to investigate the spectra of membrane proteins in different membrane mimetics, revealing that SMA may favor selective solubilization of correctly folded proteins. The results provide insights into the correlation between PTMs, lipid interactions, and protein folding states.

NANO LETTERS (2021)

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Article Neurosciences

Efficient optogenetic silencing of neurotransmitter release with a mosquito rhodopsin

Mathias Mahn et al.

Summary: A mosquito homolog of vertebrate encephalopsin was found to effectively suppress synaptic transmission through a specific signaling pathway, triggering lasting synaptic output inhibition that recovers spontaneously in vitro and in vivo. This discovery opens up new avenues for functional exploration of long-range neuronal circuits in vivo.

NEURON (2021)

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Article Neurosciences

A photoswitchable GPCR-based opsin for presynaptic inhibition

Bryan A. Copits et al.

Summary: This study introduces a GPCR-based opsin called parapinopsin (PPO), which can rapidly and reversibly inhibit the release of glutamate, GABA, and dopamine at presynaptic terminals by coupling with G(i/o) signaling cascades. PPO alters reward behaviors in a time-locked and reversible manner in vivo, filling a significant gap in the neuroscience toolkit for rapid and reversible synaptic inhibition.

NEURON (2021)

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Article Biochemistry & Molecular Biology

Optical Switching Between Long-lived States of Opsin Transmembrane Voltage Sensors

Gaoxiang Mei et al.

Summary: Opsin-based transmembrane voltage sensors (OTVSs) are widely used in optogenetic applications to measure voltage changes. In this study, QuasAr2 and NovArch were characterized using various spectroscopic techniques, revealing the ability to optically switch between different states, with NovArch showing a previously unknown complexity in its photophysical properties.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2021)

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Article Multidisciplinary Sciences

Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser

Ji-Hye Yun et al.

Summary: Utilizing time-resolved serial femtosecond crystallography, this study reveals the dynamic process of ion transport by chloride ion-pumping rhodopsin under light illumination, involving retinal isomerization, water molecule rearrangement, and residue conformational changes.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

Akimitsu Higuchi et al.

Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biology

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin

Kazumasa Oda et al.

Summary: Channelrhodopsins (ChRs) are microbial light-gated ion channels used in optogenetics for controlling neural activity with light. Time-resolved crystallographic analyses revealed conformational changes in ChR following photoactivation, suggesting early changes in the pore-forming helices trigger the opening of the ion conducting pore.

ELIFE (2021)

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Article Microbiology

Rapidly Improving High Light and High Temperature Tolerances of Cyanobacterial Cell Factories Through the Convenient Introduction of an AtpA-C252F Mutation

Shanshan Zhang et al.

Summary: Photosynthetic biomanufacturing is a promising method for green production of biofuels and biochemicals using carbon dioxide and solar energy. A convenient strategy has been proposed to rapidly improve the high light and high temperature tolerances of cyanobacterial chassis strains, enhancing cellular robustness and sucrose synthesizing capacities of the cell factories.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Microbiology

Assembly of Natively Synthesized Dual Chromophores Into Functional Actinorhodopsin

Kimleng Chuon et al.

Summary: Microbial rhodopsin, such as actinorhodopsin (ActR-13023), is a simple solar energy-capturing molecule that functions as a light-driven outward proton pump. The detection of the ActR-13023 gene and genes involved in chromophore synthesis pathway in the genome implies the functional expression of ActR-13023 for solar energy utilization through proton translocation.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter

Miao-Ping Chien et al.

Summary: Photoactivated genetically encoded voltage indicators, such as NovArch, allow for high fluorescence signals, optical sectioning, and high time resolution simultaneously. These tools have been successfully applied to optical mapping of membrane voltage in acute mouse brain slices and in spontaneously active neurons in vivo.

SCIENCE ADVANCES (2021)

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Article Biology

Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design

Keiichi Inoue et al.

Summary: Inoue, Takeuchi and colleagues propose a machine learning-based protocol to screen rhodopsins for their likelihood to be red-shifted. After experimental verification, their tool shows remarkable success at identifying rhodopsins that showed red-shift gains.

COMMUNICATIONS BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Extending the Anion Channelrhodopsin-Based Toolbox for Plant Optogenetics

Yang Zhou et al.

Summary: This study demonstrates the use of optogenetics to manipulate the growth of Nicotiana tabacum pollen tubes by expressing engineered ACRs. The performance of ACRs GtACR2 and ZipACR in Xenopus laevis oocytes, Nicotiana benthamiana leaves, and N. tabacum pollen tubes was enhanced by molecular engineering. The reduced light sensitivity in ZipACR1 offers potential for better temporal resolution in optogenetic control of anion fluxes in plants.

MEMBRANES (2021)

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Review Microbiology

Microbial Rhodopsins: The Last Two Decades

Andrey Rozenberg et al.

Summary: Microbial rhodopsins are a diverse group of photoreceptive proteins that are present in all domains of cellular life and even encoded in viral genomes. They are classified into two families: type 1 rhodopsins and heliorhodopsins, both having seven transmembrane helices with similar structures but opposite membrane orientation. These rhodopsins are involved in a variety of light-driven energy and sensory transduction processes.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021 (2021)

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Article Biochemistry & Molecular Biology

A neural circuit state change underlying skilled movements

Mark J. Wagner et al.

Summary: Our study explored the transition from autonomous to coherent spiking in cerebellar Purkinje neurons during skilled movement in mice. As mice learned the task, consistent neural synchronization emerged, and optogenetic manipulations demonstrated the bi-directional modulation of reaching direction. These findings suggest that olivo-cerebellar circuits enter a synchronized state promoting motor coordination during learned movements.

CELL (2021)

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Review Cell Biology

Opsins outside the eye and the skin: a more complex scenario than originally thought for a classical light sensor

Maria Nathalia Moraes et al.

Summary: Opsins have been found in organs and cells beyond light-exposed tissues, indicating functions beyond light-sensing including thermal detection. Recent studies, particularly in mammals, focus on understanding the role of opsins in peripheral tissues.

CELL AND TISSUE RESEARCH (2021)

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Article Chemistry, Physical

Thermostable light-driven inward proton pump rhodopsins

Yuma Kawasaki et al.

Summary: This study reports new Schizorhodopsins from methanogenic archaea, which show improved stability at high temperatures and exhibit light-driven inward proton transport. Additionally, it is the first time that thermally stable rhodopsins, besides outward proton pumps, have been discovered in high-temperature environments.

CHEMICAL PHYSICS LETTERS (2021)

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Article Chemistry, Physical

Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems

Dmitrii M. Nikolaev et al.

Summary: A novel technique for computing free energy differences between chromophore isomers is presented, using average electrostatic solvent configuration method and free energy perturbation theory. The method accurately estimates the relative stabilities and isomerization barriers between different systems, showing good agreement with experimental observations.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Protein Response Effects on Cofactor Excitation Energies from First Principles: Augmenting Subsystem Time-Dependent Density-Functional Theory with Many-Body Expansion Techniques

Linus Scholz et al.

Summary: The study demonstrates the use of a simple version of embedded sTDDFT-MBE method to predict protein response effects effectively, but a higher order MBE may be required to quantitatively reproduce reference effects.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Biology

Chimeric human opsins as optogenetic light sensitisers

Doron G. Hickey et al.

Summary: Chimeric human opsins were created with different intracellular domains from melanopsin, which affected their activity in the Gi and G(q/11) pathways. The study highlighted the importance of Ga coupling efficiency in cellular responses and introduced human opsins with unique properties for potential applications in basic research and translational therapies.

JOURNAL OF EXPERIMENTAL BIOLOGY (2021)

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Article Chemistry, Physical

Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12

Sahoko Tomida et al.

Summary: Heliorhodopsin (HeR) is a new class of rhodopsin discovered in 2018, exhibiting unique structural features compared to typical microbial rhodopsins. Functional analysis using low-temperature light-induced FTIR spectroscopy revealed changes in hydrogen bonding and structural rearrangement during retinal photoisomerization in HeR 48C12. These findings provide insights into the molecular mechanisms underlying energy storage and propagation in HeR upon retinal photoisomerization.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Chemistry, Physical

Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration

Marvin Asido et al.

Summary: A transient near-UV absorption signature was identified in Krokinobacter eikastus rhodopsin 2 (KR2) which could serve as a marker for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations revealed that this signature corresponds to S-0 -> S-3 and/or S-0 -> S-5 transitions, and these transitions show negligible spectral shift with changes in the protein environment. The study also explored potential optogenetic applications through near-UV quenching experiments, demonstrating ultrafast regeneration of the parent state of KR2.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)

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Article Biochemistry & Molecular Biology

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

Chenfei Shen et al.

Summary: Many experiments have been conducted to investigate the color tuning of Proteorhodopsin (PR). In this study, the EE-GMFCC method was used to predict excitation energies of PRs, and results showed good correlation with experimental data. The electrostatic interactions from nearby residues, especially ASP97 and ASP227, were found to be responsible for the color tuning of PR. The study demonstrates the potential of EE-GMFCC method in accurately predicting absorption spectral shifts for biomacromolecules.

MOLECULES (2021)

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Article Multidisciplinary Sciences

Localization atomic force microscopy

George R. Heath et al.

Summary: This study introduces a new technique called localization AFM (LAFM) that overcomes traditional AFM resolution limits by applying localization image reconstruction algorithms, allowing for structural analysis of biomolecules at the single-molecule level.

NATURE (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Review Neurosciences

Probing neural codes with two-photon holographic optogenetics

Hillel Adesnik et al.

Summary: Multiphoton holographic optogenetics is a tailored technique that can bridge the gap between experimental and theoretical neuroscience, offering spatial precision and the ability to create highly specific neural activity patterns to reveal fundamental aspects of neural coding for sensation, cognition and behavior. This technology has the potential to accelerate neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.

NATURE NEUROSCIENCE (2021)

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Article Biochemistry & Molecular Biology

An optogenetic assay method for electrogenic transporters using Escherichia coli co-expressing light-driven proton pump

Masahiro Hayashi et al.

Summary: In this study, a novel measurement system for electrogenic transporters was developed, utilizing isotope-free and label-free methods to co-express specific proteins in Escherichia coli. The system successfully demonstrated light-induced inward proton transport coupled with negative electrogenic transport, with a pH increase dependent on oxalate concentration but not on the expression level of the light-driven proton pump. This optogenetic assay method showed validity by not observing pH increase in nonfunctional mutants of the electrogenic transporter.

PROTEIN SCIENCE (2021)

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Review Biochemistry & Molecular Biology

Deconstructing the transmembrane core of class A G protein-coupled receptors

Steven O. Smith

Summary: Class A G protein-coupled receptors, which have evolved to recognize a wide range of ligands, possess a highly conserved core within their seven-transmembrane helix framework. However, there is still no consensus on the mechanism of ligand binding coupling or the roles of specific residues within the core. Recent insights from crystallography and NMR spectroscopy provide a new perspective on decomposing the core into its essential structural and functional elements, shedding new light on this important region.

TRENDS IN BIOCHEMICAL SCIENCES (2021)

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Article Multidisciplinary Sciences

Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

Stephan Hirschi et al.

Summary: The cryo-EM structure of pentameric green-light absorbing proteorhodopsin together with molecular dynamics simulations and functional studies provides insights into the proton translocation pathway and oligomerization, and a protonation-dependent mechanism for intracellular half channel hydration.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

BiPOLES is an optogenetic tool developed for bidirectional dual-color control of neurons

Johannes Vierock et al.

Summary: The authors report a Bidirectional Pair of Opsins for Light-induced Excitation and Silencing, BiPOLES, which enables potent neuronal excitation and inhibition with light of two different wavelengths. This tool allows for sensitive, reliable dual-color neuronal spiking and silencing with single- or two-photon excitation, optical tuning of the membrane voltage, and independent optogenetic control of two neuronal populations. The utility of BiPOLES is demonstrated in worms, fruit flies, mice and ferrets.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Reverse optogenetics of G protein signaling by zebrafish non-visual opsin Opn7b for synchronization of neuronal networks

Raziye Karapinar et al.

Summary: Opn7b is a non-visual G protein-coupled receptor expressed in zebrafish that can be controlled by light to modulate neuronal activity and neural circuit properties.

NATURE COMMUNICATIONS (2021)

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Article Physics, Applied

Conformational changes of a membrane protein determined by infrared difference spectroscopy beyond the diffraction limit

Raffaella Polito et al.

Summary: Optogenetics is a revolutionary method for studying neural activity by exploiting the optical stimulation of neurons. This study investigates the effect of gold surfaces on the photocycle of the optogenetic protein ChR2, finding that ChR2 proteins maintain their function in a 14-nm-wide gap between two gold surfaces. These results are relevant for optogenetic applications requiring physical contact between nanoscale metallic probes and neuronal cell membranes, paving the way for spectroscopic studies of transmembrane proteins at the nanoscale.

PHYSICAL REVIEW APPLIED (2021)

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Review Biochemistry & Molecular Biology

Imaging Voltage with Microbial Rhodopsins

Xiao Min Zhang et al.

Summary: Membrane potential, a critical parameter reflecting neuron excitability, is traditionally measured invasively by electrodes, but new fluorescent probe technologies offer high spatiotemporal resolution for individual cell activity. Genetically encoded voltage indicators show superior performance in accurately targeting genetic populations and revealing neuronal dynamics. Microbial rhodopsins, commonly used in optogenetics to manipulate neuronal activities, can also serve as fluorescent voltage indicators, with recent advances in their design and application summarized in this review.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Review Biochemistry & Molecular Biology

Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins

Kazuhiro J. Fujimoto

Summary: The photo-functional chromophore retinal demonstrates diverse optical absorption properties depending on its interactions with proteins and other chromophores. Quantum chemical calculations have revealed molecular mechanisms underlying light absorption in rhodopsins, providing insights into unique optical properties and strategies for artificial design.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Multidisciplinary Sciences

Discovery of a microbial rhodopsin that is the most stable in extreme environments

Jin-gon Shim et al.

Summary: Tara76 rhodopsin is a highly stable proton-pumping rhodopsin, exhibiting strong resistance to various stress factors. It is suitable for a wide range of applications in the fields of bioengineering and biotechnology.

ISCIENCE (2021)

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Review Biophysics

Unique Cl- pump rhodopsin with close similarity to H+ pump rhodopsin

Takashi Kikukawa

Summary: Microbial rhodopsin is a membrane protein found in unicellular microorganisms, similar to animal rhodopsin in structure but with diverse functions as a photosignal receptor, light-activated ion transporter, and enzyme. The third Cl- pump microbial rhodopsin has distinct phylogenetic characteristics from other microbial rhodopsins, representing a model for functional differentiation from H+ pumps like bacteriorhodopsin.

BIOPHYSICS AND PHYSICOBIOLOGY (2021)

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Article Astronomy & Astrophysics

Sub-picosecond C=C bond photo-isomerization: evidence for the role of excited state mixing

Damianos Agathangelou et al.

Summary: This review article revisits the question of how proteins tune the isomerization speed and quantum yield, focusing on the delicate mixing of reactive and non-reactive excited states due to steric properties and electrostatic interactions with the protein environment. It outlines further avenues and new approaches that promise to advance our understanding of these intimately coupled chromophore-protein systems.

COMPTES RENDUS PHYSIQUE (2021)

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Article Biochemical Research Methods

Pipeline for 2-photon all-optical physiology in mouse: From viral titration and optical window implantation to binarization of calcium transients

Roberta Guimaraes Backhaus et al.

Summary: 2-photon all-optical physiology combines in vivo 2-photon calcium imaging and optogenetics for reading and manipulating neuronal microcircuits at single-cell resolution. The protocol includes optimized co-expression, virus injection, 2-photon imaging, and an analysis algorithm for calcium transients related to action potentials.

STAR PROTOCOLS (2021)

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Article Ecology

The rhodopsin-retinochrome system for retinal re-isomerization predates the origin of cephalopod eyes

Oliver Voecking et al.

Summary: The study revealed the presence of orthologs of cephalopod retinochrome and RALBP in mollusks outside cephalopods. Additionally, orthologs of retinoid binding protein RLBP1 were found in polyplacophoran mollusks, cephalopods, and a phoronid. The expression of retinochrome, visual rhodopsin, RALBP, and RLBP1 were co-expressed in the larval chiton photoreceptor cells, along with multiple retinal dehydrogenases which may contribute to the rhodopsin-retinochrome system.

BMC ECOLOGY AND EVOLUTION (2021)

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Article Biology

Ion Transport Activity Assay for Microbial Rhodopsin Expressed in Escherichia coli Cells

Masae Konno et al.

Summary: Microbial rhodopsins have diverse functions and require rapid identification of their roles; the patch-clamp method is used for investigating ion transport mechanisms; the Escherichia coli expression system can evaluate ion transport capacity.

BIO-PROTOCOL (2021)

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Article Biophysics

Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy

Izuru Kawamura et al.

Summary: This study utilized solid-state NMR to analyze the structural information of Middle Rhodopsin (MR), revealing the presence of different retinal configurations and variations in hydrogen bond strength. The study also found differences in the orientation of certain amino acids in MR compared to other microbial rhodopsins, contributing to stable retinal conformations in dark-adapted MR.

BIOPHYSICS AND PHYSICOBIOLOGY (2021)

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Article Biophysics

Role of Thr82 for the unique photochemistry of TAT rhodopsin

Teppei Sugimoto et al.

Summary: The research revealed that mutating Thr82 to Asp in TAT rhodopsin significantly increased the pKa of the Schiff base, suggesting T82 as a key determinant of its unique photochemistry. The photocycle of T82D TAT rhodopsin exhibited distinct behaviors under different pH conditions, indicating a significant impact of pH on the photoreaction dynamics.

BIOPHYSICS AND PHYSICOBIOLOGY (2021)

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Article Biophysics

Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K

Shunpei Hanai et al.

Summary: Structural studies of primate color visual pigments have been conducted using difference FTIR spectroscopy at different temperatures, revealing changes in the properties and structures of the Batho and BL intermediates.

BIOPHYSICS AND PHYSICOBIOLOGY (2021)

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Article Neurosciences

Step-function luminopsins for bimodal prolonged neuromodulation

Ken Berglund et al.

JOURNAL OF NEUROSCIENCE RESEARCH (2020)

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Review Pharmacology & Pharmacy

Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development

Javier Garcia-Nafria et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 60 (2020)

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Article Dermatology

Opsin 3 is a key regulator of ultraviolet A-induced photoageing in human dermal fibroblast cells

Y. Lan et al.

BRITISH JOURNAL OF DERMATOLOGY (2020)

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Article Biochemistry & Molecular Biology

Lamprey Parapinopsin (UVLamP): a Bistable UV-Sensitive Optogenetic Switch for Ultrafast Control of GPCR Pathways

Dennis Eickelbeck et al.

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Ultrafast Photoreaction Dynamics of a Light-Driven Sodium-Ion-Pumping Retinal Protein from Krokinobacter eikastus Revealed by Femtosecond Time-Resolved Absorption Spectroscopy

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Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance

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Near-IR Resonance Raman Spectroscopy of Archaerhodopsin 3: Effects of Transmembrane Potential

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Ultrasensitive Measurements of Microbial Rhodopsin Photocycles Using Photochromic FRET

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Rhodopsin in Nanodiscs Has Native embrane-like Photointermediates

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Vertebrate Ancient-Long Opsin Has Molecular Properties Intermediate between Those of Vertebrate and Invertebrate Visual Pigments

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Spectrally Silent Intermediates during the Photochemical Reactions of Salinibacter Sensory Rhodopsin I

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The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects

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Vibrational analysis of excited and ground electronic states of all-trans retinal protonated Schiff-bases

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Light Activation of Rhodopsin: Insights from Molecular Dynamics Simulations Guided by Solid-State NMR Distance Restraints

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Structure and function in rhodopsin: A tetracycline-inducible system in stable mammalian cell lines for high-level expression of opsin mutants

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Structural determinants of spectral tuning in retinal proteins-bacteriorhodopsin vs sensory rhodopsin II

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Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

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