The Experts below are selected from a list of 6450 Experts worldwide ranked by ideXlab platform
Keiichi Inoue - One of the best experts on this subject based on the ideXlab platform.
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diversity mechanism and optogenetic applicatIon of light driven Ion pump rhodopsins
Advances in Experimental Medicine and Biology, 2021Co-Authors: Keiichi InoueAbstract:Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated Ion channels and light-driven Ion Pumps. While the former passively transport various types of catIons and anIons in a light-dependent manner, light-driven Ion Pumps actively transport specific Ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the Ion transport by these Pumps induces hyperpolarizatIon of membrane potential and inhibit neural firing, light-driven Ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of Ion-pumping rhodopsins from a wide variety of microbes, and functIonal characterizatIon studies has been revealing many new types of light-driven Ion Pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functIonal characterizatIon, molecular mechanism study, and optogenetic applicatIon of Ion-pumping rhodopsins were reviewed.
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the light driven sodium Ion pump a new player in rhodopsin research
BioEssays, 2016Co-Authors: Hideaki E. Kato, Hideki Kandori, Keiichi Inoue, Osamu NurekiAbstract:Rhodopsins are one of the most studied photoreceptor protein families, and Ion-translocating rhodopsins, both Pumps and channels, have recently attracted broad attentIon because of the development of optogenetics. Recently, a new functIonal class of Ion-pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functIonal studies enable us to compare three functIonally different Ion-pumping rhodopsins: outward proton pump, inward Cl− pump, and outward Na+ pump. Here, we review the current knowledge on structure-functIon relatIonships in these three light-driven Pumps, mainly focusing on Na+ Pumps. A structural and functIonal comparison reveals both unique and conserved features of these Ion Pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functIons. We also discuss some unresolved questIons and future perspectives in research of Ion-pumping rhodopsins, including optogenetics applicatIon and engineering of novel rhodopsins.
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converting a light driven proton pump into a light gated proton channel
Journal of the American Chemical Society, 2015Co-Authors: Keiichi Inoue, Shigehiko Hayashi, Hideki Kandori, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Yuki SudoAbstract:There are two types of membrane-embedded Ion transport machineries in nature. The Ion Pumps generate electrochemical potential by energy-coupled active Ion transportatIon, while the Ion channels produce actIon potential by stimulus-dependent passive Ion transportatIon. About 80% of the amino acid residues of the light-driven proton pump archaerhodopsin-3 (AR3) and the light-gated catIon channel channelrhodopsin (ChR) differ although they share the close similarity in architecture. Therefore, the questIon arises: How can these proteins functIon differently? The absorptIon maxima of Ion Pumps are red-shifted about 30–100 nm compared with ChRs, implying a structural difference in the retinal binding cavity. To modify the cavity, a blue-shifted AR3 named AR3-T was produced by replacing three residues located around the retinal (i.e., M128A, G132V, and A225T). AR3-T showed an inward H+ flux across the membrane, raising the possibility that it works as an inward H+ pump or an H+ channel. Electrophysiological ex...
Hideki Kandori - One of the best experts on this subject based on the ideXlab platform.
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the light driven sodium Ion pump a new player in rhodopsin research
BioEssays, 2016Co-Authors: Hideaki E. Kato, Hideki Kandori, Keiichi Inoue, Osamu NurekiAbstract:Rhodopsins are one of the most studied photoreceptor protein families, and Ion-translocating rhodopsins, both Pumps and channels, have recently attracted broad attentIon because of the development of optogenetics. Recently, a new functIonal class of Ion-pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functIonal studies enable us to compare three functIonally different Ion-pumping rhodopsins: outward proton pump, inward Cl− pump, and outward Na+ pump. Here, we review the current knowledge on structure-functIon relatIonships in these three light-driven Pumps, mainly focusing on Na+ Pumps. A structural and functIonal comparison reveals both unique and conserved features of these Ion Pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functIons. We also discuss some unresolved questIons and future perspectives in research of Ion-pumping rhodopsins, including optogenetics applicatIon and engineering of novel rhodopsins.
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converting a light driven proton pump into a light gated proton channel
Journal of the American Chemical Society, 2015Co-Authors: Keiichi Inoue, Shigehiko Hayashi, Hideki Kandori, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Yuki SudoAbstract:There are two types of membrane-embedded Ion transport machineries in nature. The Ion Pumps generate electrochemical potential by energy-coupled active Ion transportatIon, while the Ion channels produce actIon potential by stimulus-dependent passive Ion transportatIon. About 80% of the amino acid residues of the light-driven proton pump archaerhodopsin-3 (AR3) and the light-gated catIon channel channelrhodopsin (ChR) differ although they share the close similarity in architecture. Therefore, the questIon arises: How can these proteins functIon differently? The absorptIon maxima of Ion Pumps are red-shifted about 30–100 nm compared with ChRs, implying a structural difference in the retinal binding cavity. To modify the cavity, a blue-shifted AR3 named AR3-T was produced by replacing three residues located around the retinal (i.e., M128A, G132V, and A225T). AR3-T showed an inward H+ flux across the membrane, raising the possibility that it works as an inward H+ pump or an H+ channel. Electrophysiological ex...
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Water-containing hydrogen-bonding network in the active center of channelrhodopsin.
Journal of the American Chemical Society, 2014Co-Authors: Shota Ito, Hideaki E. Kato, Reiya Taniguchi, Tatsuya Iwata, Osamu Nureki, Hideki KandoriAbstract:Channelrhodopsin (ChR) functIons as a light-gated Ion channel in Chlamydomonas reinhardtii. Passive transport of catIons by ChR is fundamentally different from the active transport by light-driven Ion Pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the Ion Pumps are used for neural silencing. Ion-transport functIons by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibratIons) than those of other microbial (2-6 water vibratIons) and animal (6-8 water vibratIons) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterIon (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated Ion channel.
Anton Ivanov - One of the best experts on this subject based on the ideXlab platform.
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controlling epileptiform activity with organic electronic Ion Pumps
Advanced Materials, 2015Co-Authors: Ilke Uguz, Sahika Inal, Adam Williamson, Jonathan Rivnay, Loig Kergoat, Amanda Jonsson, Marc Ferro, Anton IvanovAbstract:In treating epilepsy, the ideal solutIon is to act at a seizure's onset, but only in the affected regIons of the brain. Here, an organic electronic Ion pump is demonstrated, which directly delivers ...
Yuki Sudo - One of the best experts on this subject based on the ideXlab platform.
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implicatIons for the light driven chloride Ion transport mechanism of nonlabens marinus rhodopsin 3 by its photochemical characteristics
Journal of Physical Chemistry B, 2017Co-Authors: Takashi Tsukamoto, Susumu Yoshizawa, Takashi Kikukawa, Makoto Demura, Yuki SudoAbstract:Several new retinal-based photoreceptor proteins that act as light-driven electrogenic halide Ion Pumps have recently been discovered. Some of them, called “NTQ” rhodopsins, contain a conserved Asn–Thr–Gln motif in the third or C-helix. In this study, we investigated the photochemical characteristics of an NTQ rhodopsin, Nonlabens marinus rhodopsin 3 (NM-R3), which was discovered in the N. marinus S1-08T strain, using static and time-resolved spectroscopic techniques. We demonstrate that NM-R3 binds a Cl– in the vicinity of the retinal chromophore accompanied by a spectral blueshift from 568 nm in the absence of Cl– to 534 nm in the presence of Cl–. From the Cl– concentratIon dependence, we estimated the affinity (dissociatIon constant, Kd) for Cl– in the original state as 24 mM, which is ca. 10 times weaker than that of archaeal halorhodopsins but ca. 3 times stronger than that of a marine bacterial Cl– pumping rhodopsin (C1R). NM-R3 showed no dark–light adaptatIon of the retinal chromophore and predomin...
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converting a light driven proton pump into a light gated proton channel
Journal of the American Chemical Society, 2015Co-Authors: Keiichi Inoue, Shigehiko Hayashi, Hideki Kandori, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Yuki SudoAbstract:There are two types of membrane-embedded Ion transport machineries in nature. The Ion Pumps generate electrochemical potential by energy-coupled active Ion transportatIon, while the Ion channels produce actIon potential by stimulus-dependent passive Ion transportatIon. About 80% of the amino acid residues of the light-driven proton pump archaerhodopsin-3 (AR3) and the light-gated catIon channel channelrhodopsin (ChR) differ although they share the close similarity in architecture. Therefore, the questIon arises: How can these proteins functIon differently? The absorptIon maxima of Ion Pumps are red-shifted about 30–100 nm compared with ChRs, implying a structural difference in the retinal binding cavity. To modify the cavity, a blue-shifted AR3 named AR3-T was produced by replacing three residues located around the retinal (i.e., M128A, G132V, and A225T). AR3-T showed an inward H+ flux across the membrane, raising the possibility that it works as an inward H+ pump or an H+ channel. Electrophysiological ex...
Ville R I Kaila - One of the best experts on this subject based on the ideXlab platform.
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energetics and dynamics of a light driven sodium pumping rhodopsin
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Dage Sundholm, Carlmikael Suomivuori, Ana P Gamizhernandez, Ville R I KailaAbstract:The conversIon of light energy into Ion gradients across biological membranes is one of the most fundamental reactIons in primary biological energy transductIon. Recently, the structure of the first light-activated Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolutIon [Kato HE, et al. (2015) Nature 521:48–53]. To elucidate its molecular mechanism for Na+ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulatIons of transient photocycle states. Our simulatIons show how the dynamics of key residues regulate water and Ion access between the bulk and the buried light-triggered retinal site. We identify putative Na+ binding sites and show how protonatIon and conformatIonal changes gate the Ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculatIons that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the Ion translocatIon and gating mechanisms in KR2 may provide a basis for the ratIonal design of novel light-driven Ion Pumps with optogenetic applicatIons.
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spectral tuning of rhodopsin and visual cone pigments
Journal of the American Chemical Society, 2014Co-Authors: Xiuwen Zhou, Dage Sundholm, Tomasz Adam Wesolowski, Ville R I KailaAbstract:Retinal is the light-absorbing biochromophore responsible for the activatIon of visIon pigments and light-driven Ion Pumps. Nature has evolved molecular tuning mechanisms that significantly shift the optical properties of the retinal pigments to enable their absorptIon of visible light. Using large-scale quantum chemical calculatIons at the density functIonal theory level combined with frozen density embedding theory, we show here how the protein environment of visIon pigments tunes the absorptIon of retinal by electrostatically dominated interactIons between the chromophore and the surrounding protein residues. The calculatIons accurately reproduce the experimental absorptIon maxima of rhodopsin and the red, green, and blue color pigments. We further identify key interactIons responsible for the color-shifting effects by mutating the rhodopsin structure in silico, and we find that deprotonatIon of the retinyl is likely to be responsible for the blue-shifted absorptIon in the blue cone visIon pigment.
