Oct. 2005, Hokkaido University, Nitobe Prize　　　　　　　　　　　　　　　
TSUKAMOTO Takashi

Contribution of Proteorhodopsin to Light-Dependent Biological Responses in Hymenobacter nivis P3T Isolated from Red Snow in Antarctica
Kaori Kondo, Ryouhei Ohtake, Shunsuke Nakano, Mia Terashima, Hisaya Kojima, Manabu Fukui, Makoto Demura, Takashi Kikukawa, Takashi Tsukamoto
Biochemistry, 17 Sep. 2024
Scientific journal

Direct detection of the chloride release and uptake reactions of Natronomonas pharaonis halorhodopsin.
Chihaya Hamada, Keisuke Murabe, Takashi Tsukamoto, Takashi Kikukawa
The Journal of biological chemistry, 300, 9, 107712, 107712, Sep. 2024, [International Magazine]
English, Scientific journal, Membrane transport proteins undergo multistep conformational changes to fulfill the transport of substrates across biological membranes. Substrate release and uptake are the most important events of these multistep reactions that accompany significant conformational changes. Thus, their relevant structural intermediates should be identified to better understand the molecular mechanism. However, their identifications have not been achieved for most transporters due to the difficulty of detecting the intermediates. Herein, we report the success of these identifications for a light-driven chloride transporter halorhodopsin (HR). We compared the time course of two flash-induced signals during a single transport cycle. One is a potential change of Cl--selective membrane, which enabled us to detect tiny Cl--concentration changes due to the Cl- release and the subsequent Cl--uptake reactions by HR. The other is the absorbance change of HR reflecting the sequential formations and decays of structural intermediates. Their comparison revealed not only the intermediates associated with the key reactions but also the presence of two additional Cl--binding sites on the Cl--transport pathways. The subsequent mutation studies identified one of the sites locating the protein surface on the releasing side. Thus, this determination also clarified the Cl--transport pathway from the initial binding site until the release to the medium.

Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin.
Yukino Sato, Tsubasa Hashimoto, Koji Kato, Akiko Okamura, Kaito Hasegawa, Tsukasa Shinone, Yoshikazu Tanaka, Yoshiki Tanaka, Tomoya Tsukazaki, Takashi Tsukamoto, Makoto Demura, Min Yao, Takashi Kikukawa
The Journal of biological chemistry, 105393, 105393, 25 Oct. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Membrane transport proteins require a gating mechanism that opens and closes the substrate transport pathway to carry out unidirectional transport. The "gating" involves large conformational changes and is achieved via multistep reactions. However, these elementary steps have not been clarified for most transporters due to the difficulty of detecting the individual steps. Here, we propose these steps for the gate opening of the bacterial Na+ pump rhodopsin (NaR), which outwardly pumps Na+ upon illumination. We herein solved an asymmetric dimer structure of NaR from the bacterium Indibacter alkaliphilus. In one protomer, the Arg108 sidechain is oriented toward the protein center and appears to block a Na+ release pathway to the extracellular (EC) medium. In the other protomer, however, this sidechain swings to the EC side and then opens the release pathway. Assuming that the latter protomer mimics the Na+-releasing intermediate, we examined the mechanism for the swing motion of the Arg108 sidechain. On the EC surface of the first protomer, there is a characteristic cluster consisting of Glu10, Glu159, and Arg242 residues connecting three helices. In contrast, this cluster is disrupted in the second protomer. Our experimental results suggested that this disruption is a key process. The cluster disruption induces the outward movement of the Glu159-Arg242 pair and simultaneously rotates the seventh transmembrane helix. This rotation resultantly opens a space for the swing motion of the Arg108 sidechain. Thus, cluster disruption might occur during the photoreaction and then trigger sequential conformation changes leading to the gate-open state.

The preferential transport of NO3- by full-length Guillardia theta anion channelrhodopsin 1 is enhanced by its extended cytoplasmic domain.
Yuya Ohki, Tsukasa Shinone, Sayo Inoko, Miu Sudo, Makoto Demura, Takashi Kikukawa, Takashi Tsukamoto
The Journal of biological chemistry, 105305, 105305, 29 Sep. 2023, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
English, Scientific journal, Previous research of anion channelrhodopsins (ACRs) has been performed using cytoplasmic domain (CPD)-deleted constructs, and therefore have overlooked the native functions of full-length ACRs and the potential functional role(s) of the CPD. In this study, we used the recombinant expression of full-length Guillardia theta ACR1 (GtACR1_full) for pH measurements in Pichia pastoris cell suspensions as an indirect method to assess its anion transport activity, and for absorption spectroscopy and flash photolysis characterization of the purified protein. The results show that the CPD, which was predicted to be intrinsically disordered and possibly phosphorylated, enhanced NO3- transport compared to Cl- transport, which resulted in the preferential transport of NO3-. This correlated with the extended lifetime and large accumulation of the photocycle intermediate that is involved in the gate-open state. Considering that the depletion of a nitrogen source enhances the expression of GtACR1 in native algal cells, we suggest that NO3- transport could be the natural function of GtACR1_full in algal cells.

Structure and Heterogeneity of Retinal Chromophore in Chloride Pump Rhodopsins Revealed by Raman Optical Activity.
Masaiku Ohya, Takashi Kikukawa, Junpei Matsuo, Takashi Tsukamoto, Ryota Nagaura, Tomotsumi Fujisawa, Masashi Unno
The journal of physical chemistry. B, 18 May 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Chloride transport by microbial rhodopsins is actively being researched to understand how light energy is converted to drive ion pumping across cell membranes. Chloride pumps have been identified in archaea and eubacteria, and there are similarities and differences in the active site structures between these groups. Thus, it has not been clarified whether a common mechanism underlies the ion pump processes for all chloride-pumping rhodopsins. Here, we applied Raman optical activity (ROA) spectroscopy to two chloride pumps, Nonlabens marinus rhodopsin-3 (NM-R3) and halorhodopsin from the cyanobacterium Mastigocladopsis repens (MrHR). ROA is a vibrational spectroscopy that provides chiral sensitivity, and the sign of ROA signals can reveal twisting of cofactor molecules within proteins. Our ROA analysis revealed that the retinal Schiff base NH group orients toward the C helix and forms a direct hydrogen bond with a nearby chloride ion in NM-R3. In contrast, MrHR is suggested to contain two retinal conformations twisted in opposite directions; one conformation has a hydrogen bond with a chloride ion like NM-R3, while the other forms a hydrogen bond with a water molecule anchored by a G helix residue. These results suggest a general pump mechanism in which the chloride ion is "dragged" by the flipping Schiff base NH group upon photoisomerization.

Concerted primary proton transfer reactions in a thermophilic rhodopsin studied by time-resolved infrared spectroscopy at high temperature.
Kunisato Kuroi, Takashi Tsukamoto, Naoya Honda, Yuki Sudo, Yuji Furutani
Biochimica et biophysica acta. Bioenergetics, 1864, 3, 148980, 148980, 18 Apr. 2023, [Peer-reviewed], [Lead author], [International Magazine]
English, Scientific journal, The primary proton transfer reactions of thermophilic rhodopsin, which was first discovered in an extreme thermophile, Thermus thermophilus JL-18, were investigated using time-resolved Fourier transform infrared spectroscopy at various temperatures ranging from 298 to 343 K (25 to 70 °C) and proton transport activity analysis. The analyses were performed using counterion (D95E, D95N, D229E, and D229N) and proton donor mutants (E106D and E106Q) as well. First, the initial proton transfer from the protonated retinal Schiff base (PRSB) to D95 was identified. The temperature dependency showed that the proton transfer reaction in the intermediate states dramatically changed above 318 K (45 °C). In addition, the proton transfer reaction correlated well with the structural change from turn to β-strand in the protein moiety, suggesting that this step may be regulated by the rigidity of the loop region. We also elucidated that the proton transfer reaction from proton donor E106 to the retinal Schiff base occurred synchronously with the primary proton transfer from the PRSB to D95. Surprisingly, we discovered that the direction of proton transfer was regulated by the secondary counterion, D229. Comparative analysis of Gloeobacter rhodopsin from the mesophile, Gloeobacter violaceus, highlighted that the primary proton transfer reactions in thermophilic rhodopsin were optimized at high temperatures partly due to the specific turn to β-strand structural change. This was not observed in Gloeobacter rhodopsin and other related proteins such as bacteriorhodopsin.

Mutations conferring SO42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant.
Yuhei Doi, Jo Watanabe, Ryota Nii, Takashi Tsukamoto, Makoto Demura, Yuki Sudo, Takashi Kikukawa
Scientific reports, 12, 1, 16422, 16422, 30 Sep. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl- and Br-, but SyHR also transports SO42-, despite the close sequence similarity to MrHR. We sought a determinant that could confer SO42- pumping ability on MrHR and found that the removal of a negative charge at the anion entrance is a prerequisite for SO42- transport by MrHR. Consistently, the reverse mutation in SyHR significantly weakened SO42- pump activity. Notably, the MrHR and SyHR mutants did not show SO42- induced absorption spectral shifts or changes in the photoreactions, suggesting no bindings of SO42- in their initial states or the bindings to the sites far from the protein centers. In other words, unlike wild-type SyHR, these mutants take up SO42- into their centers after illumination and release it before the ends of the photoreactions.

Three-Dimensional Structure of the Antimicrobial Peptide Cecropin P1 in Dodecylphosphocholine Micelles and the Role of the C-Terminal Residues
Hao Gu, Takasumi Kato, Hiroyuki Kumeta, Yasuhiro Kumaki, Takashi Tsukamoto, Takashi Kikukawa, Makoto Demura, Hiroaki Ishida, Hans J. Vogel, Tomoyasu Aizawa
ACS Omega, American Chemical Society (ACS), 13 Sep. 2022, [Peer-reviewed]
Scientific journal

Real-Time Identification of Two Substrate-Binding Intermediates for the Light-Driven Sodium Pump Rhodopsin.
Tomoya Kato, Takashi Tsukamoto, Makoto Demura, Takashi Kikukawa
The Journal of biological chemistry, 100792, 100792, 18 May 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters due to the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na+ pump rhodopsin (NaR). We triggered the transport cycle of NaR using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions, and elucidated the sequential formation of the Na+-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na+ concentration, indicating that Na+ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na+ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na+ release on the extracellular side. Thus, there is an irreversible switch in "accessibility" during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na+ transport.

Preference of Proteomonas sulcata anion channelrhodopsin for NO3- revealed using a pH electrode method.
Chihiro Kikuchi, Hina Kurane, Takuma Watanabe, Makoto Demura, Takashi Kikukawa, Takashi Tsukamoto
Scientific reports, 11, 1, 7908, 7908, 12 Apr. 2021, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
English, Scientific journal, Ion channel proteins are physiologically important molecules in living organisms. Their molecular functions have been investigated using electrophysiological methods, which enable quantitative, precise and advanced measurements and thus require complex instruments and experienced operators. For simpler and easier measurements, we measured the anion transport activity of light-gated anion channelrhodopsins (ACRs) using a pH electrode method, which has already been established for ion pump rhodopsins. Using that method, we successfully measured the anion transport activity and its dependence on the wavelength of light, i.e. its action spectra, and on the anion species, i.e. its selectivity or preference, of several ACRs expressed in yeast cells. In addition, we identified the strong anion transport activity and the preference for NO3- of an ACR from a marine cryptophyte algae Proteomonas sulcata, named PsuACR_353. Such a preference was discovered for the first time in microbial pump- or channel-type rhodopsins. Nitrate is one of the most stable forms of nitrogen and is used as a nitrogen source by most organisms including plants. Therefore, PsuACR_353 may play a role in NO3- transport and might take part in NO3--related cellular functions in nature. Measurements of a mutant protein revealed that a Thr residue in the 3rd transmembrane helix, which corresponds to Cys102 in GtACR1, contributed to the preference for NO3-. These findings will be helpful to understand the mechanisms of anion transport, selectivity and preference of PsuACR_353.

Direct Detection of the Substrate Uptake and Release Reactions of the Light-Driven Sodium-Pump Rhodopsin.
Keisuke Murabe, Takashi Tsukamoto, Tomoyasu Aizawa, Makoto Demura, Takashi Kikukawa
Journal of the American Chemical Society, 142, 37, 16023, 16030, 06 Sep. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the requirements of the experimental methods, which are to detect the timing of the formation and decay of intermediates and to detect the timing of substrate uptake and release. We report successfully achieving this for the light-driven Na+ pump rhodopsin (NaR). Here, a Na+-selective membrane, which consists of polyvinyl chloride and a Na+ ionophore, was employed to detect Na+ uptake and release. When one side of the membrane was covered by the lipid-reconstituted NaR, continuous illumination induced an increase in membrane potential, which reflected Na+ uptake by the photolyzed NaR. Via use of nanosecond laser pulses, two kinds of data were obtained during a single transport cycle: one was the flash-induced absorbance change in NaR to detect the formation and decay of structural intermediates, and the other was the flash-induced change in membrane potential, which reflects the transient Na+ uptake and release reactions. Their comparison clearly indicated that Na+ is captured and released during the formation and decay of the O intermediate, the red-shifted intermediate that appears in the latter half of the transport cycle.

Spectroscopic Characterization of Halorhodopsin Reconstituted into Nanodisks Using Native Lipids.
Ayumi Yamamoto, Takashi Tsukamoto, Kenshiro Suzuki, Eri Hashimoto, Yoshihiro Kobashigawa, Kousuke Shibasaki, Takeshi Uchida, Fuyuhiko Inagaki, Makoto Demura, Koichiro Ishimori
Biophysical journal, 118, 11, 2853, 2865, 29 Apr. 2020, [Peer-reviewed], [Lead author], [International Magazine]
English, Scientific journal, We successfully reconstituted single Natronomonas pharaonis halorhodopsin (NpHR) trimers into a nanodisk (ND) using the native archaeal lipid (NL) and an artificial lipid having a zwitterionic headgroup, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Incorporation of single trimeric NpHR into NDs was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, size-exclusion chromatography, and visible circular dichroism spectroscopy. The Cl- binding affinity of NpHR in NDs using NL (NL-ND NpHR) or POPC (POPC-ND NpHR) was examined by absorption spectroscopy, showing that the Cl--releasing affinities (Kd,N↔O) of these ND-reconstituted NpHRs are more than 10 times higher than that obtained from native NpHR membrane fragments (MFs) harvested from a NpHR-overexpressing archaeal strain (MF NpHR). The photoreaction kinetics of these ND-reconstituted NpHRs revealed that the Cl- uptake was faster than that of MF NpHR. These differences in the Cl--releasing and uptake properties of ND-reconstituted NpHRs and MF NpHR may arise from suppression of protein conformational changes associated with Cl- release from the trimeric NpHR caused by ND reconstitution, conformational perturbation in the trimeric state, and loss of the trimer-trimer interactions. On the other hand, POPC-ND NpHR demonstrated accelerated Cl- uptake compared to NL-ND NpHR, suggesting that the negative charge on the archaeal membrane surface regulates the photocycle of NpHR. Although NL-ND NpHR and MF NpHR are embedded in the same lipid, the lower Cl--binding affinity at the initial state (Kd,initial) and faster recovering from the NpHR' state to the original state of the photoreaction cycle were observed for NL-ND NpHR, probably because of insufficient interactions with a chromophore in the native membrane, bacterioruberin in reconstituted NDs. Our results indicate that specific interactions of NpHR with surrounding lipids and bacterioruberin, structural flexibility of the membrane, and interactions between trimeric NpHRs may be necessary for efficient Cl- pumping.

Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained.
Satoshi Yasuda, Tomoki Akiyama, Sayaka Nemoto, Tomohiko Hayashi, Tetsuya Ueta, Keiichi Kojima, Takashi Tsukamoto, Satoru Nagatoishi, Kouhei Tsumoto, Yuki Sudo, Masahiro Kinoshita, Takeshi Murata
Journal of chemical information and modeling, 60, 3, 1709, 1716, 23 Mar. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal denaturation Tm is measured to be ∼91.8 °C, is chosen as a paradigmatic target. In the methodology, we first regard the residues whose side chains are missing in the crystal structure of the wild type (WT) as the "residues with disordered side chains," which make no significant contributions to the stability, unlike the other essential residues. We then undertake mutating each of the residues with disordered side chains to another residue except Ala and Pro, and the resultant mutant structure is constructed by modifying only the local structure around the mutated residue. This construction is based on the postulation that the structure formed by the other essential residues, which is nearly optimized in such a highly stable protein, should not be modified. The stability changes arising from the mutations are then evaluated using our physics-based free-energy function (FEF). We choose the mutations for which the FEF is much lower than for the WT and test them by experiments. We successfully find three mutants that are significantly more stable than the WT. A double mutant whose Tm reaches ∼100 °C is also discovered.

Functional importance of the oligomer formation of the cyanobacterial H+ pump Gloeobacter rhodopsin
Azusa Iizuka, Kousuke Kajimoto, Tomotsumi Fujisawa, Takashi Tsukamoto, Tomoyasu Aizawa, Naoki Kamo, Kwang-Hwan Jung, Masashi Unno, Makoto Demura, Takashi Kikukawa
Scientific Reports, 9, 1, Springer Science and Business Media {LLC}, Dec. 2019, [Peer-reviewed]
English, Scientific journal, Many microbial rhodopsins self-oligomerize, but the functional consequences of oligomerization have not been well clarified. We examined the effects of oligomerization of a H+ pump, Gloeobacter rhodopsin (GR), by using nanodisc containing trimeric and monomeric GR. The monomerization did not appear to affect the unphotolyzed GR. However, we found a significant impact on the photoreaction: The monomeric GR showed faint M intermediate formation and negligible H+ transfer reactions. These changes reflected the elevated pKa of the Asp121 residue, whose deprotonation is a prerequisite for the functional photoreaction. Here, we focused on His87, which is a neighboring residue of Asp121 and conserved among eubacterial H+ pumps but replaced by Met in an archaeal H+ pump. We found that the H87M mutation removes the "monomerization effects": Even in the monomeric state, H87M contained the deprotonated Asp121 and showed both M formation and distinct H+ transfer reactions. Thus, for wild-type GR, monomerization probably strengthens the Asp121-His87 interaction and thereby elevates the pKa of Asp121 residue. This strong interaction might occur due to the loosened protein structure and/or the disruption of the interprotomer interaction of His87. Thus, the trimeric assembly of GR enables light-induced H+ transfer reactions through adjusting the positions of key residues.

Quantitation of the neural silencing activity of anion channelrhodopsins in Caenorhabditis elegans and their applicability for long-term illumination
Taro Yamanashi, Misayo Maki, Keiichi Kojima, Atsushi Shibukawa, Takashi Tsukamoto, Srikanta Chowdhury, Akihiro Yamanaka, Shin Takagi, Yuki Sudo
Scientific Reports, 9, 1, Springer Science and Business Media LLC, Mar. 2019, [Peer-reviewed]
Scientific journal

Implications for the impairment of the rapid channel closing of Proteomonas sulcata anion channelrhodopsin 1 at high Cl− concentrations
Takashi Tsukamoto, Chihiro Kikuchi, Hiromu Suzuki, Tomoyasu Aizawa, Takashi Kikukawa, Makoto Demura
Scientific Reports, 8, 1, 13445, 13445, Springer Science and Business Media LLC, Dec. 2018, [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, Natural anion channelrhodopsins (ACRs) have recently received increased attention because of their effectiveness in optogenetic manipulation for neuronal silencing. In this study, we focused on Proteomonas sulcata ACR1 (PsuACR1), which has rapid channel closing kinetics and a rapid recovery to the initial state of its anion channel function that is useful for rapid optogenetic control. To reveal the anion concentration dependency of the channel function, we investigated the photochemical properties of PsuACR1 using spectroscopic techniques. Recombinant PsuACR1 exhibited a Cl- dependent spectral red-shift from 531 nm at 0.1 mM to 535 nm at 1000 mM, suggesting that it binds Cl- in the initial state with a Kd of 5.5 mM. Flash-photolysis experiments revealed that the photocycle was significantly changed at high Cl- concentrations, which led not only to suppression of the accumulation of the M-intermediate involved in the Cl- non-conducting state but also to a drastic change in the equilibrium state of the other photo-intermediates. Because of this, the Cl- conducting state is protracted by one order of magnitude, which implies an impairment of the rapid channel closing of PsuACR1 in the presence of high concentrations of Cl-.

Correction to “High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment”
Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, Yasuhisa Mizutani
The Journal of Physical Chemistry B, 122, 42, 9826, 9826, American Chemical Society ({ACS}), 25 Oct. 2018, [Peer-reviewed]
Scientific journal

High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment
Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, Yasuhisa Mizutani
The Journal of Physical Chemistry B, 122, 27, 6945, 6953, American Chemical Society ({ACS}), Jul. 2018, [Peer-reviewed]
Scientific journal

Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative
Riho Takayama, Akimasa Kaneko, Takashi Okitsu, Satoshi P. Tsunoda, Kazumi Shimono, Misao Mizuno, Keiichi Kojima, Takashi Tsukamoto, Hideki Kandori, Yasuhisa Mizutani, Akimori Wada, Yuki Sudo
Journal of Physical Chemistry Letters, 9, 11, 2857, 2862, American Chemical Society, 07 Jun. 2018, [Peer-reviewed]
English, Scientific journal, Rhodopsin is widely distributed in organisms as a membrane-embedded photoreceptor protein, consisting of the apoprotein opsin and vitamin-A aldehyde retinal, A1-retinal and A2-retinal being the natural chromophores. Modifications of opsin (e.g., by mutations) have provided insight into the molecular mechanism of the light-induced functions of rhodopsins as well as providing tools in chemical biology to control cellular activity by light. Instead of the apoprotein opsin, in this study, we focused on the retinal chromophore and synthesized three vinylene derivatives of A2-retinal. One of them, C(14)-vinylene A2-retinal (14V-A2), was successfully incorporated into the opsin of a light-driven proton pump archaerhodopsin-3 (AR3). Electrophysiological experiments revealed that the opsin of AR3 (archaeopsin3, AO3) with 14V-A2 functions as a light-gated proton channel. The engineered proton channel showed characteristic photochemical properties, which are significantly different from those of AR3. Thus, we successfully produced a proton channel by replacing the chromophore of AR3.

Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria.
Yu Nakajima, Takashi Tsukamoto, Yohei Kumagai, Yoshitoshi Ogura, Tetsuya Hayashi, Jaeho Song, Takashi Kikukawa, Makoto Demura, Kazuhiro Kogure, Yuki Sudo, Susumu Yoshizawa
Microbes and environments, 33, 1, 89, 97, 29 Mar. 2018, [Peer-reviewed], [Domestic magazines]
English, Scientific journal, Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl--pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl- pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl--transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl--pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.

Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H+ transport mechanism.
Saki Inoue, Susumu Yoshizawa, Yu Nakajima, Keiichi Kojima, Takashi Tsukamoto, Takashi Kikukawa, Yuki Sudo
Physical chemistry chemical physics : PCCP, 20, 5, 3172, 3183, Royal Society of Chemistry ({RSC}), 31 Jan. 2018, [Peer-reviewed], [International Magazine]
English, Scientific journal, A new group of microbial rhodopsins named xenorhodopsins (XeR), which are closely related to the cyanobacterial Anabaena sensory rhodopsin, show a light-driven "inward" proton transport activity, as reported for one representative of this group from Parvularcula oceani (PoXeR). In this study, we functionally and spectroscopically characterized a new member of the XeR clade from a marine bacterium Rubricoccus marinus SG-29T (RmXeR). Escherichia coli cells expressing recombinant RmXeR showed a light-induced alkalization of the cell suspension, which was strongly impaired by a protonophore, suggesting that RmXeR is a light-driven "inward" proton pump as is PoXeR. The spectroscopic properties of purified RmXeR were investigated and compared with those of PoXeR and a light-driven "outward" proton pump, bacteriorhodopsin (BR) from the archaeon Halobacterium salinarum. Action spectroscopy revealed that RmXeR with all-trans retinal is responsible for the light-driven inward proton transport activity, but not with 13-cis retinal. From pH titration experiments and mutational analysis, we estimated the pKa values for the protonated Schiff base of the retinal chromophore and its counterion as 11.1 ± 0.07 and 2.1 ± 0.07, respectively. Of note, the direction of both the retinal composition change upon light-dark adaptation and the acid-induced spectral shift was opposite that of BR, which is presumably related to the opposite directions of ion transport (from outside to inside for RmXeR and from inside to outside for BR). Flash photolysis experiments revealed the appearances of three intermediates (L, M and O) during the photocycle. The proton uptake and release were coincident with the formation and decay of the M intermediate, respectively. Together with associated findings from other microbial rhodopsins, we propose a putative model for the inward proton transport mechanism of RmXeR.

Comparative evaluation of the stability of seven-transmembrane microbial rhodopsins to various physicochemical stimuli
Naoya Honda, Takashi Tsukamoto, Yuki Sudo
CHEMICAL PHYSICS LETTERS, 682, 6, 14, ELSEVIER SCIENCE BV, Aug. 2017, [Peer-reviewed]
English, Scientific journal, Rhodopsins are seven-transmembrane proteins that function as photoreceptors for a variety of biological processes. Their characteristic visible colors make rhodopsins a good model for membrane-embedded proteins. In this study, by utilizing their color changes, we performed comparative studies on the stability of five microbial rhodopsins using the same instruments, procedures and media. As denaturants, we employed four physicochemical stimuli: (i) thermal perturbation, (ii) the water-soluble reagent hydroxylamine, (iii) the detergent sodium dodecyl sulfate, and (iv) the organic solvent ethanol. On the basis of the results, models for stabilization mechanisms in rhodopsins against each stimulus is proposed. (C) 2017 Elsevier B.V. All rights reserved.

Implications for the Light-Driven Chloride Ion Transport Mechanism of Nonlabens marinus Rhodopsin 3 by Its Photochemical Characteristics
Takashi Tsukamoto, Susumu Yoshizawa, Takashi Kikukawa, Makoto Demura, Yuki Sudo
JOURNAL OF PHYSICAL CHEMISTRY B, 121, 9, 2027, 2038, AMER CHEMICAL SOC, Mar. 2017, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal, 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 S1-08(T) 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, K-d) 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 predominantly possessed an all-trans-retinal, which is responsible for the light-driven Cl-pump function. Flash-photolysis experiments suggest that NM-R3 passes through five or six photochemically distinct intermediates (K, L(N), O-1, O-2, and NM-R3'). From these results, we assume that the Cl-is released and taken up during the L(N)-O-1 transition from a transiently formed cytoplasmic (CP) binding site and the O-2-NM R3' or the NM-R3'-original NM-R3 transitions from the extracellular (EC) side, respectively. We propose a mechanism for the Cl-transport by NM-R3 based on our results and its recently reported crystal structure.

Demonstration of a Light-Driven SO42- Transporter and Its Spectroscopic Characteristics
Akiko Niho, Susumu Yoshizawa, Takashi Tsukamoto, Marie Kurihara, Shinya Tahara, Yu Nakajima, Misao Mizuno, Hikaru Kuramochi, Tahei Tahara, Yasuhisa Mizutani, Yuki Sudo
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 139, 12, 4376, 4389, AMER CHEMICAL SOC, Mar. 2017, [Peer-reviewed], [Lead author]
English, Scientific journal, In organisms, ion transporters play essential roles in the generation and dissipation of ion gradients across cell membranes. Microbial rhodopsins selectively transport cognate ions using solar energy, in which the substrate ions identified to date have been confined to monovalent ions such as H+, Na+ and Cl-. Here we report a novel rhodopsin from the cyanobacterium Synechocystis sp. PCC 7509, which inwardly transports a polyatomic divalent sulfate ion, SO42-, with changes of its spectroscopic properties in both unphotolyzed and photolyzed states. Upon illumination, cells expressing the novel rhodopsin, named Synechocystis halorhodopsin (SyHR), showed alkalization of the medium only in the presence of Cl- or SO42-. That alkalization signal was enhanced by addition of a protonophore, indicating an inward transport of and SO42- with a subsequent secondary inward H+ movement across the membrane. The anion binding to SyHR was suggested by absorption spectral shifts from 542 to 536 nm for Cl- and from 542 to 556 nm for SO42-, and the affinities of Cl- and SO42- were estimated as 0.112 and 5.81 rriM, respectively. We then performed time-resolved spectroscopic measurements ranging from femtosecond to millisecond time domains to elucidate the structure and structural changes of SyHR during the photoreaction. Based on the results, we propose a photocycle model for SyHR in the absence or presence of substrate ions with the timing of their uptake and release. Thus, we demonstrate SyHR as the first light-driven polyatomic divalent anion (SO42-) transporter and report its spectroscopic characteristics.

A phylogenetically distinctive and extremely heat stable light-driven proton pump from the eubacterium Rubrobacter xylanophilus DSM 9941(T)
Kanae Kanehara, Susumu Yoshizawa, Takashi Tsukamoto, Yuki Sudo
SCIENTIFIC REPORTS, 7, 44427, NATURE PUBLISHING GROUP, Mar. 2017, [Peer-reviewed]
English, Scientific journal, Rhodopsins are proteins that contain seven transmembrane domains with a chromophore retinal and that function as photoreceptors for light-energy conversion and light-signal transduction in a wide variety of organisms. Here we characterized a phylogenetically distinctive new rhodopsin from the thermophilic eubacterium Rubrobacter xylanophilus DSM 9941(T) that was isolated from thermally polluted water. Although R. xylanophilus rhodopsin (RxR) is from Actinobacteria, it is located between eukaryotic and archaeal rhodopsins in the phylogenetic tree. Escherichia coli cells expressing RxR showed a light-induced decrease in environmental pH and inhibition by a protonophore, indicating that it works as a light-driven outward proton pump. We characterized purified RxR spectroscopically, and showed that it has an absorption maximum at 541 nm and binds nearly 100% all-trans retinal. The pK(a) values for the protonated retinal Schiff base and its counterion were estimated to be 10.7 and 1.3, respectively. Time-resolved flash-photolysis experiments revealed the formation of a red-shifted intermediate. Of note, RxR showed an extremely high thermal stability in comparison with other proton pumping rhodopsins such as thermophilic rhodopsin TR (by 16-times) and bacteriorhodopsin from Halobacterium salinarum (HsBR, by 4-times).

An inhibitory role of Arg-84 in anion channelrhodopsin-2 expressed in Escherichia coli
Satoko Doi, Takashi Tsukamoto, Susumu Yoshizawa, Yuki Sudo
SCIENTIFIC REPORTS, 7, 41879, NATURE PUBLISHING GROUP, Feb. 2017, [Peer-reviewed]
English, Scientific journal, Anion channelrhodopsin-2 (ACR2) was recently identified from the cryptophyte algae Guillardia theta and has become a focus of interest in part because of its novel light-gated anion channel activity and its extremely high neural silencing activity. In this study, we tried to express ACR2 in Escherichia coli cells as a recombinant protein. The E. coli cells expressing ACR2 showed an increase in pH upon blue-light illumination in the presence of monovalent anions and the protonophore carbonyl cyanide mchlorophenylhydrazone (CCCP), indicating an inward anion channel activity. Then, taking advantage of the E. coli expression system, we performed alanine-scanning mutagenesis on conserved basic amino acid residues. One of them, R84A, showed strong signals compared with the wild-type, indicating an inhibitory role of R84 on Cl-transportation. The signal was strongly enhanced in R84E, whereas R84K was less effective than the wild-type (i.e., R84). These results suggest that the positive charge at position 84 is critical for the inhibition. Thus we succeeded in functional expression of ACR2 in E. coli and found the inhibitory role of R84 during the anion transportation.

Live-cell single-molecule imaging of the cytokine receptor MPL for analysis of dynamic dimerization
Akihiko Sakamoto, Takashi Tsukamoto, Yuji Furutani, Yuki Sudo, Kazuyuki Shimada, Akihiro Tomita, Hitoshi Kiyoi, Takashi Kato, Takashi Funatsu
Journal of Molecular Cell Biology, 8, 6, 553, 555, OXFORD UNIV PRESS, Dec. 2016, [Peer-reviewed]
English

X-ray Crystallographic Structure of Thermophilic Rhodopsin IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION
Takashi Tsukamoto, Kenji Mizutani, Taisuke Hasegawa, Megumi Takahashi, Naoya Honda, Naoki Hashimoto, Kazumi Shimono, Keitaro Yamashita, Masaki Yamamoto, Seiji Miyauchi, Shin Takagi, Shigehiko Hayashi, Takeshi Murata, Yuki Sudo
JOURNAL OF BIOLOGICAL CHEMISTRY, 291, 23, 12223, 12232, AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, Jun. 2016, [Peer-reviewed], [Lead author]
English, Scientific journal, Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance.

Probing the Cl − -pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle
Takashi Kikukawa, Chikara Kusakabe, Asami Kokubo, Takashi Tsukamoto, Masakatsu Kamiya, Tomoyasu Aizawa, Kunio Ihara, Naoki Kamo, Makoto Demura
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1847, 8, 748, 758, Elsevier {BV}, Aug. 2015, [Peer-reviewed]
Scientific journal

Converting a Light-Driven Proton Pump into a Light-Gated Proton Channel
Keiichi Inoue, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Shigehiko Hayashi, Hideki Kandori, Yuki Sudo
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137, 9, 3291, 3299, AMER CHEMICAL SOC, Mar. 2015, [Peer-reviewed]
English, Scientific journal, 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 30100 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 experiments showed that the reverse membrane potential was nearly zero, indicating light-gated ion channeling activity of AR3-T. Spectroscopic characterization of AR3-T revealed similar photochemical properties to some of ChRs, including an all-trans retinal configuration, a strong hydrogen bond between the protonated retinal Schiff base and its counterion, and a slow photocycle. From these results, we concluded that the functional determinant in the H+ transporters is localized at the center of the membrane-spanning domain, but not in the cytoplasmic and extracellular domains.

Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1
Satoko Doi, Arisa Mori, Takashi Tsukamoto, Louisa Reissig, Kunio Ihara, Yuki Sudo
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 14, 9, 1628, 1636, ROYAL SOC CHEMISTRY, 2015, [Peer-reviewed]
English, Scientific journal, Channelrhodopsins have become a focus of interest because of their ability to control neural activity by light, used in a technology called optogenetics. The channelrhodopsin in the eukaryote Chlamydomonas reinhardtii (CrChR-1) is a light-gated cation channel responsible for motility changes upon photo-illumination and a member of the membrane-embedded retinal protein family. Recent crystal structure analysis revealed that CrChR-1 has unique extended modules both at its N- and C-termini compared to other microbial retinal proteins. This study reports the first successful expression of a ChR-1 variant in Escherichia coli as a holoprotein: the ChR-1 variant lacking both the N- and C-termini (CrChR-1_82-308). However, compared to ChR-1 having the extended modules (CrChR-1_1-357), truncation of the termini greatly altered the absorption maximum and photochemical properties, including the pK(a) values of its charged residues around the chromophore, the reaction rates in the photocycle and the photo-induced ion channeling activity. The results of some experiments regarding ion transport activity suggest that CrChR-1_82-308 has a proton channeling activity even in the dark. On the basis of these results, we discuss the structural and functional roles of the N- and C-terminal extended modules in CrChR-1.

Irreversible Trimer to Monomer Transition of Thermophilic Rhodopsin upon Thermal Stimulation
Takashi Tsukamoto, Makoto Demura, Yuki Sudo
JOURNAL OF PHYSICAL CHEMISTRY B, 118, 43, 12383, 12394, AMER CHEMICAL SOC, Oct. 2014, [Peer-reviewed], [Lead author]
English, Scientific journal, Assembly is one of the keys to understand biological molecules, and it takes place in spatial and temporal domains upon stimulation. Microbial rhodopsin (also called retinal protein) is a membrane-embedded protein that has a retinal chromophore within seven-transmembrane alpha-helices and shows homo-, di-, tri-, penta-, and hexameric assemblies. Those assemblies are closely related to critical physiological properties such as stabilizing the protein structure and regulating their photoreaction dynamics. Here we investigated the assembly and disassembly of thermophilic rhodopsin (TR), which is a novel proton-pumping rhodopsin derived from a thermophile living at 75 degrees C. TR was characterized using size-exclusion chromatography and circular dichroism spectroscopy, and formed a trimer at 25 degrees C, but irreversibly dissociated into monomers upon thermal stimulation. The transition temperature was estimated to be 68 degrees C. The irreversible nature made it possible to investigate the photochemical properties of both the trimer and the monomer independently. Compared with the trimer, the absorption maximum of the monomer is blue-shifted by 6 nm without any changes in the retinal composition, pKa value for the counterion or the sequence of the proton movement. The photocycling rate of the monomeric TR was similar to that of the trimeric TR. A similar trimer-monomer transition upon thermal stimulation was observed for another eubacterial rhodopsin GR but not for the archaeal rhodopsins AR3 and HwBR, suggesting that the transition is conserved in bacterial rhodopsins. Thus, the thermal stimulation of TR induces the irreversible disassembly of the trimer.

Molecular and evolutionary aspects of microbial sensory rhodopsins.
Inoue K, Tsukamoto T, Sudo Y
Biochimica et biophysica acta, 1837, 5, 562, 577, May 2014, [Peer-reviewed]
Scientific journal

Sensory Rhodopsins
Jan. 2014, [Peer-reviewed]

Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells
Takashi Tsukamoto, Xianglan Li, Hiromi Morita, Takashi Minowa, Tomoyasu Aizawa, Nobutaka Hanagata, Makoto Demura
PLOS ONE, 8, 9, e75831, PUBLIC LIBRARY SCIENCE, Sep. 2013, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal, Recently, one of the interferon-induced transmembrane (IFITM) family proteins, IFITM3, has become an important target for the activity against influenza A (H1N1) virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane (TM1) domain and in the cytoplasmic (CP) loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 (FKBP11) to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid (17-ODYA), and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid (2BP), revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation.

Thermal and Spectroscopic Characterization of a Proton Pumping Rhodopsin from an Extreme Thermophile
Takashi Tsukamoto, Keiichi Inoue, Hideki Kandori, Yuki Sudo
JOURNAL OF BIOLOGICAL CHEMISTRY, 288, 30, 21581, 21592, AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, Jul. 2013, [Peer-reviewed], [Lead author]
English, Scientific journal, So far retinylidene proteins (approximate to rhodopsin) have not been discovered in thermophilic organisms. In this study we investigated and characterized a microbial rhodopsin derived from the extreme thermophilic bacterium Thermus thermophilus, which lives in a hot spring at around 75 degrees C. The gene for the retinylidene protein, named thermophilic rhodopsin (TR), was chemically synthesized with codon optimization. The codon optimized TR protein was functionally expressed in the cell membranes of Escherichia coli cells and showed active proton transport upon photoillumination. Spectroscopic measurements revealed that the purified TR bound only all-trans-retinal as a chromophore and showed an absorption maximum at 530 nm. In addition, TR exhibited both photocycle kinetics and pH-dependent absorption changes, which are characteristic of rhodopsins. Of note, time-dependent thermal denaturation experiments revealed that TR maintained its absorption even at 75 degrees C, and the denaturation rate constant of TR was much lower than those of other proton pumping rhodopsins such as archaerhodopsin-3 (200 x), Haloquadratum walsbyi bacteriorhodopsin (by 10-times), and Gloeobacter rhodopsin (100 x). Thus, these results suggest that microbial rhodopsins are also distributed among thermophilic organisms and have high stability. TR should allow the investigation of the molecular mechanisms of ion transport and protein folding.

Salt bridge in the conserved His-Asp cluster in Gloeobacter rhodopsin contributes to trimer formation
Takashi Tsukamoto, Takashi Kikukawa, Takuro Kurata, Kwang-Hwan Jung, Naoki Kamo, Makoto Demura
FEBS Letters, 587, 4, 322, 327, 14 Feb. 2013, [Peer-reviewed], [Lead author]
English, Scientific journal, Gloeobacter rhodopsin (GR) is a eubacterial proton pump having a highly conserved histidine near the retinal Schiff base counter-ion, aspartate. Various interactions between His and Asp of the eubacterial proton pump have been reported. Here, we showed the pH-dependent trimer/monomer transition of GR in the presence of dodecyl-β-d-maltoside by size-exclusion chromatography. The pH dependence was closely related to the protonation state of the counter-ion, Asp121. For the H87M mutant, pH dependence disappeared and a monomer became dominant. We concluded that the formation or breaking of the salt bridge between His87 and Asp121 inside the protein changes the quaternary structure. Structured summary of protein interactions: Rhodopsin and Rhodopsin bind by molecular sieving (View interaction) Rhodopsin and Rhodopsin bind by molecular sieving (View interaction: 1, 2) © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Homotrimer Formation and Dissociation of pharaonis Halorhodopsin in Detergent System
Takashi Tsukamoto, Takanori Sasaki, Kazuhiro J. Fujimoto, Takashi Kikukawa, Masakatsu Kamiya, Tomoyasu Aizawa, Keiichi Kawano, Naoki Kamo, Makoto Demura
BIOPHYSICAL JOURNAL, 102, 12, 2906, 2915, CELL PRESS, Jun. 2012, [Peer-reviewed], [Lead author]
English, Scientific journal, Halorhodopsin from NpHR is a light-driven Cl- pump that forms a trimeric NpHR-bacterioruberin complex in the native membrane. In the case of NpHR expressed in Escherichia coli cell, NpHR forms a robust homotrimer in a detergent DDM solution. To identify the important residue for the homotrimer formation, we carried out mutation experiments on the aromatic amino acids expected to be located at the molecular interface. The results revealed that Phe(150) was essential to form and stabilize the NpHR trimer in the DDM solution. Further analyses for examining the structural significance of Phe(150) showed the dissociation of the trimer in F150A (dimer) and F150W (monomer) mutants. Only the F150Y mutant exhibited dissociation into monomers in an ionic strength-dependent manner. These results indicated that spatial positions and interactions between F150-aromatic side chains were crucial to homotrimer stabilization. This finding was supported by QM calculations. In a functional respect, differences in the reaction property in the ground and photoexcited states were revealed. The analysis of photointermediates revealed a decrease in the accumulation of O, which is important for Cl- release, and the acceleration of the decay rate in L1 and L2, which are involved in Cl- transfer inside the molecule, in the trimer-dissociated mutants. Interestingly, the affinity of them to Cl- in the photoexcited state increased rather than the trimer, whereas that in the ground state was almost the same without relation to the oligomeric state. It was also observed that the efficient recovery of the photocycle to the ground state was inhibited in the mutants. In addition, a branched pathway that was not included in Cl- transportation was predicted. These results suggest that the trimer assembly may contribute to the regulation of the dynamics in the excited state of NpHR.

Expression of salinarum halorhodopsin in Escherichia coli cells: Solubilization in the presence of retinal yields the natural state
Yasutaka Yamashita, Takashi Kikukawa, Takashi Tsukamoto, Masakatsu Kamiya, Tomoyasu Aizawa, Keiichi Kawano, Seiji Miyauchi, Naoki Kamo, Makoto Demura
Biochimica et Biophysica Acta (BBA) - Biomembranes, 1808, 12, 2905, 2912, Elsevier {BV}, Dec. 2011, [Peer-reviewed]
Scientific journal

光で働く微生物のロドプシン-どのように?なんのために?を紐解いてきた50年
塚本卓, 出村誠, 化学, 76, 4, 2021, [Invited], [Lead author]

ヒト便試料の保存条件とメタボローム変動のNMR解析(Impact of sample storage conditions on NMR-based human fecal metabolomics)
宋 子豪, 包 克非, 北田 直也, 清水 由宇, 菊池 摩仁, 熊木 康裕, 大西 裕季, 塚本 卓, 菊川 峰志, 出村 誠, 中村 公則, 綾部 時芳, 山村 凌大, 中村 幸志, 玉腰 暁子, 相沢 智康, 腸内細菌学雑誌, 34, 2, 148, 148, Apr. 2020
(公財)腸内細菌学会, English

Overexpression of stable isotope-labeled cecropin P1 by using calmodulin-fusion protein system and NMR researches
GU Hao, 加藤貴純, 石田博昭, 熊木康裕, 塚本卓, 塚本卓, 菊川峰志, 菊川峰志, 出村誠, 出村誠, VOGEL HANS J., 相沢智康, 相沢智康, Abstracts. Annual Meeting of the NMR Society of Japan, 59th, 2020

微生物型ロドプシンTRのX線結晶構造解析
水谷健二, 橋本直記, 塚本卓, 須藤雄気, 村田武士, KEK Progress Report (Web), 2016-8, ROMBUNNO.242 (WEB ONLY), Jan. 2017
Japanese

Identification of thermostabilizing mutations for the Thermophilic Rhodopsin based on statistical thermodynamics　　　　　　　　　　　　　　　
Sayaka Nemoto, Satoshi Yasuda, Takashi Tsukamoto, Yuki Sudo, Masahiro Kinoshita, Takeshi Murata, 第54回 日本生物物理学会年会 つくば国際会議場、2016年11月25-27日, Nov. 2016

Retinal Proteins in Thermophilic Bacteria
Takashi TSUKAMOTO, Yuki SUDO, Seibutsu Butsuri, 55, 2, 092, 094, 2015
Biophysical Society of Japan, Japanese

時間分解赤外分光計測による好熱性ロドプシンTRの光反応解析
黒井邦巧, 塚本卓, 本田尚也, 須藤雄気, 古谷祐詞, 分子科学討論会講演プログラム&要旨(Web), 9th, ROMBUNNO.4P066 (WEB ONLY), 2015
Japanese

Molecular and evolutionary aspects of microbial sensory rhodopsins
Keiichi Inoue, Takashi Tsukamoto, Yuki Sudo, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837, 5, 562, 577, May 2014
Retinal proteins (similar to rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane alpha-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks. (C) 2013 Elsevier B.V. All rights reserved., ELSEVIER SCIENCE BV, English, Book review

牛α‐スペクトリンの遺伝子多型(E91K置換)による分子構造と赤血球膜物性の異常
木崎皓太, 富張瑞樹, 大津航, 新敷信人, 塚本卓, 宮園耕介, 菊川峰志, 出村誠, 大塚弥生, 佐藤耕太, 高桑雄一, 稲葉睦, 日本獣医学会学術集会講演要旨集, 154th, 338, 31 Aug. 2012
Japanese

ナノディスクを用いた膜タンパク質ハロロドプシンの機能解析
山本愛弓, 塚本卓, 小橋川敬博, 内田毅, 出村誠, 稲垣冬彦, 石森浩一郎, 日本蛋白質科学会年会プログラム・要旨集, 12th, 63, 31 May 2012
Japanese

ハロロドプシンの光反応サイクル中に起こるカロテノイドの吸光度変化
菊川峰志, 小久保麻実, 塚本卓, 井原邦夫, 加茂直樹, 出村誠, 日本蛋白質科学会年会プログラム・要旨集, 12th, 130, 31 May 2012
Japanese

牛α‐スペクトリン・アレルSpαBK91に起因するリピート1の構造異常と赤血球膜物性の変化
木崎皓太, 富張瑞樹, 大塚弥生, 塚本卓, 新敷信人, 菊川峰志, 出村誠, 大津航, 佐藤耕太, 高桑雄一, 稲葉睦, 日本膜学会年会講演要旨集, 34th, 63, 27 Apr. 2012
Japanese

膜タンパク質Ifitm5の立体構造研究;溶液NMR法による立体構造解析に向けた試料調製
塚本卓, LI Xiang Lan, 花方信孝, 出村誠, Abstr Annu Meet NMR Soc Jpn, 48th, 166, 167, 10 Nov. 2009
Japanese

1P091 Dissociation of Halorhodopsin Trimer in Detergent System(Membrane proteins,Oral Presentations)
Tsukamoto Takashi, Sasaki Takanori, Kubo Megumi, Kamiya Masakatsu, Aizawa Tomoyasu, Kawano Keiichi, Demura Makoto, Biophysics, 47, 1, S46, 20 Nov. 2007
The Biophysical Society of Japan General Incorporated Association, English

Anion Concentration Dependency on the Photocycle of PsuACR1: Implications for the Impairment of its Fast Channel Function.　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
18th International Conference on Retinal Proteins, 24 Sep. 2018, English, Poster presentation
[International presentation]

Substrate anion concentration significantly affects the fast channel function of Proteomonas sulcata anion channelrhodopsin-1　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第56回年会, 15 Sep. 2018, English, Oral presentation
[Domestic Conference]

Photochemical Properties of Microbial Rhodopsin Pumps and Channels　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
APSBMS 2018 Annual Meeting, 21 Jul. 2018, English, Invited oral presentation
[Invited], [International presentation]

塩濃度に依存したアニオンチャネルロドプシンの光化学的性質の変化　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会北海道支部例会, 17 Mar. 2018, Japanese, Oral presentation
[Domestic Conference]

Light-driven Cl- transport mechanism of Nonlabens marinus rhodopsin-3 studied by static and time-resolved spectroscopy　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会第55回年会, 19 Sep. 2017, English, Poster presentation
[Domestic Conference]

好熱性バクテリアのレチナールタンパク質：発見と物性解析のこれまでとこれから　　　　　　　　　　　　　　　
塚本 卓
第54回日本生化学会北海道支部例会, 07 Jul. 2017, Japanese, Invited oral presentation
[Invited], [Domestic Conference]

Structural basis for high thermal stability and efficient optogenetic function of thermophilic rhodopsin　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第54回年会, Nov. 2016, English, Poster presentation
[Domestic Conference]

Cl--pumping photoreaction of a bacterial halide-ion pumping rhodopsin with an archaeal-type TSA motif　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第54回年会, Nov. 2016, English, Poster presentation
[Domestic Conference]

微生物型ロドプシンの安定化機構の解明と光操作への展開　　　　　　　　　　　　　　　
塚本 卓
CREST「ファイバーレス光遺伝学による高次脳機能を支える本脳機能の解明」第１回ワークショップ, Nov. 2016, Japanese, Others
[Domestic Conference]

微生物型ロドプシンの光応答性と応用技術への展開　　　　　　　　　　　　　　　
塚本 卓
新学術領域研究「人工光合成」若手育成シンポジウム〜生物から学び、応用する光反応〜, Nov. 2016, Japanese, Public symposium
[Invited], [Domestic Conference]

高度好熱菌Thermus thermophilus 由来サーモフィリックロドプシンの物性研究　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会中四国支部講演会, May 2016, Japanese, Oral presentation
[Domestic Conference]

時間分解吸収分光法で膜タンパク質の反応中間体をとらえる　　　　　　　　　　　　　　　
塚本 卓
第２回創薬標的膜タンパク質の移ろいを“み（見・診・覧）る”研究会, Oct. 2015, Japanese, Others
[Domestic Conference]

X-ray Crystal Structure of TR: Implications for High Thermal Stability and High-Performance Optogenetic Availability　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第53回年会, Sep. 2015, English, Poster presentation
[Domestic Conference]

カロテノイドを光捕集系とするレチナールタンパク質の創成と展開　　　　　　　　　　　　　　　
塚本 卓
新学術研究「人工光合成」第4回合同班会議, Jun. 2015, Japanese, Public symposium
[Domestic Conference]

Structural and Functional Characterization of Thermophilic Rhodopsin　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
新学術研究「柔らかな分子系」第8回ワークショップ「やわらか光受容分子の理解と利用に迫るブレインストーミング研究会」, Jan. 2015, Japanese, Public symposium
[Domestic Conference]

高度高熱菌由来光受容膜タンパク質ロドプシンの機能・構造研究　　　　　　　　　　　　　　　
塚本 卓
第１回創薬標的膜タンパク質の移ろいを“み（見・診・覧）る”研究会, Nov. 2014, Japanese, Others
[Domestic Conference]

Physicochemical Characterization of a Light-Driven Proton Pump from an Extreme Thermophile　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
16th International Conference on Retinal Proteins, Oct. 2014, English, Poster presentation
[International presentation]

Temperature-Dependent Irreversible Structural Transition of Thermophilic Rhodopsin　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第52回年会, Sep. 2014, English, Poster presentation
[Domestic Conference]

骨芽細胞膜タンパク質IFITM5の分子機構：翻訳後修飾，相互作用，および細胞機能　　　　　　　　　　　　　　　
塚本 卓
分子・物質合成プラットフォーム平成25年度シンポジウム, Mar. 2014, Japanese, Public symposium
[Domestic Conference]

2P233 Temperature-Dependent Irreversible Structural Transition of Thermophilic Rhodopsin(18A. Photobiology:Vision & Photoreception,Poster)
Tsukamoto Takashi, Demura Makoto, Sudo Yuki
Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association, English
2014 - 2014

3P101 Functional significance of homotrimer formation in the Nanodisc-embedded Halorhodopsin(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Suzuki Kenshiro, Yamamoto Ayumi, Tsukamoto Takashi, Kobashigawa Yoshihiro, Uchida Takeshi, Inagaki Fuyuhiko, Demura Makoto, Ishimori Koichiro
Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association, English
2014 - 2014

生理的温度条件下における高度好熱菌由来ロドプシン・TRの物性に関する研究　　　　　　　　　　　　　　　
塚本 卓
分子研研究会「ロドプシン研究の故きを温ねて新しきを知る」, Nov. 2013, Japanese, Public symposium
[Domestic Conference]

Thermophilic rhodopsin: The first light-driven proton pump from an extreme thermophile　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第51回年会, Oct. 2013, English, Poster presentation
[Domestic Conference]

高度好熱菌Thermus thermophilus由来微生物型ロドプシンの分光学的解析　　　　　　　　　　　　　　　
塚本 卓
2012年度生物物理学会中部支部講演会, Feb. 2013, Japanese, Oral presentation
[Domestic Conference]

3P105 Effects of homotrimer formation on chloride pump activity in membrane mimetics, Nanodisc, embedded Halorhodopsin(03. Membrane proteins,Poster)
Suzuki Kenshiro, Yamamoto Ayumi, Tsukamoto Takashi, Kobashigawa Toshihiro, Uchida Takeshi, Inagaki Fuyuhiko, Demura Makoto, Ishimori Koichiro
Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association, English
2013 - 2013

1P243 Expression of channelrhodopsin-1 in Esherichia coli(18A. Photobiology: Vision & Photoreception,Poster)
Mori Arisa, Tsukamoto Takashi, Yagasaki Zin, Homma Michio, Ihara Kunio, Sudo Yuki
Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association, English
2013 - 2013

1P247 Light-induced inward proton transport in a blue-shifted archaerhodopsin-3 mutant(18A. Photobiology: Vision & Photoreception,Poster)
Inoue Keiichi, Tsukamoto Takashi, Yagasaki Jin, Shimono Kazumi, Miyauchi Seiji, Hayashi Shigehiko, Kandori Hideki, Sudo Yuki
Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association, English
2013 - 2013

1P244 Thermophilic rhodopsin: The first light-driven proton pump from an extreme thermophile(18A. Photobiology: Vision & Photoreception,Poster)
Tsukamoto Takashi, Sudo Yuki
Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association, English
2013 - 2013

2P244 Analysis of Cl^- release and uptake steps of light-driven Cl^- pump Natronomonas pharaonis halorhodopsin(18A. Photobiology: Vision & Photoreception,Poster)
Kikukawa Takashi, Kusakabe Chikara, Kokubo Asami, Tsukamoto Takashi, Kamiya Masakatsu, Aizawa Tomoyasu, Ihara Kunio, Kamo Naoki, Demura Makoto
Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association, English
2013 - 2013

Homo-trimeric structure of Gloeobacter rhodopsin is regulated by the protonation state of Asp121, a counterion of the protonated Schiff base　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
15th International Conference on Retinal Proteins, Oct. 2012, English, Poster presentation
[International presentation]

Homotrimeric assembly of a cyanobacterial ion-pump Gloeobacter rhodopsin　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第50回年会, Sep. 2012, English, Poster presentation
[Domestic Conference]

DDM可溶化系におけるGloeobacter rhodopsinの多量体形成に関する研究　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会2011年度北海道支部例会, Mar. 2012, Japanese, Oral presentation
[Domestic Conference]

Study of the oligomeric assembly of Gloeobacter rhodopsin in DDM solution　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
9th Japan-Korea Bilateral Symposium on Biological NMR, Mar. 2012, English, Others
[International presentation]

2PT179 Homo-trimeric assembly of a cyanobacterial ion-pump Gloeobacter rhodopsin(The 50th Annual Meeting of the Biophysical Society of Japan)
Tsukamoto Takashi, Kikukawa Takashi, Kamiya Masakatsu, Aizawa Tomoyasu, Kawano Keiichi, Jung Kwang-Hwan, Kamo Naoki, Demura Makoto
Seibutsu Butsuri, 2012, The Biophysical Society of Japan General Incorporated Association, English
2012 - 2012

The role of cysteines in the first transmembrane domain of IFITM5 for the intermolecular interaction with FKBP11　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
第34回日本分子生物学会年会, Dec. 2011, Japanese, Oral presentation
[Domestic Conference]

Role of Ser171 for the stabilization of NpHR trimer　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会第49回年会, Sep. 2011, English, Oral presentation
[Domestic Conference]

Trimerization of halorhodopsin by the aromatic-interemolecular interaction and its functional modulation in detergent system　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第48回年会, Sep. 2010, English, Poster presentation
[Domestic Conference]

Trimer formation of N. pharaonis halorhodopsin is stabilized by the intermolecular interaction among Phe150 residues and leads to functional modulation in detergent solution　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
14th International Conference on Retinal Proteins, Aug. 2010, English, Poster presentation
[International presentation]

Expression, purification and characterization of osteoblast-specific membrane protein IFITM5 in detergent solubilized system　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
第10回日本蛋白質科学会年会, Jun. 2010, Japanese, Poster presentation
[Domestic Conference]

膜タンパク質IFITM5の立体構造研究；溶液NMR法による立体構造解析に向けた試料調製　　　　　　　　　　　　　　　
塚本 卓
第48回NMR討論会, Nov. 2009, Japanese, Poster presentation
[Domestic Conference]

ハロロドプシンNpHRの三量体構造はF150残基の対称性によって安定化される　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会第47回年会, Oct. 2009, English, Poster presentation
[Domestic Conference]

Structural study of IFITM5, a human double transmembrane protein; sample preparation for NMR analysis　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第47回年会, Oct. 2009, English, Poster presentation
[Domestic Conference]

Structural study of halorhodopsin: What makes its trimeric assembly stable in the DDM-solubilized system?　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
7th Japan-Korea Bilateral Symposium on Biological NMR, Jul. 2009, English, Others
[International presentation]

Molecular dynamics of photo-excited halorhodopsin in the monomer and trimer states　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
Hokkaido University – Mahidol University Joint Symposium, May 2009, English, Others
[International presentation]

Molecular interaction and functional modulation of light-driven anion pump - halorhodopsin　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
第9回日本蛋白質科学会年会, May 2009, Japanese, Poster presentation
[Domestic Conference]

Molecular dynamics of photo-excited halorhodopsin in the monomer and trimer states　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
揺らぎと生体機能第2回公開シンポジウム, Mar. 2009, Japanese, Public symposium
[Domestic Conference]

Is the photoactivity of halorhodopsin modulated by the assembly of homotrimer?” 3P-097　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
日本生物物理学会第46回年会, Dec. 2008, English, Poster presentation
[Domestic Conference]

Trimer assembly of Natronomonas pharaonis halorhodopsin, NpHR, in lipid bilayer and detergent　　　　　　　　　　　　　　　
TSUKAMOTO Takashi
13th International Conference on Retinal Proteins, Jun. 2008, English, Poster presentation
[International presentation]

ハロロドプシン三量体の界面活性剤中での解離　　　　　　　　　　　　　　　
塚本 卓
日本生物物理学会第45回年会, Dec. 2007, Japanese, Oral presentation
[Domestic Conference]

Chemistry　　　　　　　　　　　　　　　
Hokkaido University
2022 - Present

SDGs and Life Science　　　　　　　　　　　　　　　
Hokkaido University
2020 - Present

生体高分子学実験　　　　　　　　　　　　　　　
北海道大学
2017 - Present

実験生物科学　　　　　　　　　　　　　　　
北海道大学
2018 - 2023

物理学　　　　　　　　　　　　　　　
北海道大学
2018 - 2021

細胞構造科学　　　　　　　　　　　　　　　
北海道大学
2017 - 2018

コミュニケーション入門　　　　　　　　　　　　　　　
岡山大学

薬学基本実習　　　　　　　　　　　　　　　
岡山大学

薬学基礎実習　　　　　　　　　　　　　　　
岡山大学

物理学　　　　　　　　　　　　　　　
岡山大学

2024 - Present
日本蛋白質科学会　　　　　　　　　　　　　　　

2007 - Present
THE BIOPHYSICAL SOCIETY OF JAPAN　　　　　　　　　　　　　　　

アニオンチャネルロドプシンの動的なイオン選択性メカニズムの解明
科学研究費助成事業 基盤研究(C)
01 Apr. 2023 - 31 Mar. 2026
塚本 卓
日本学術振興会, 基盤研究(C), 北海道大学, 23K05675

過渡現象解析で追求する膜輸送タンパク質の多段階構造変化と輸送素過程の連関
科学研究費助成事業 基盤研究(B)
01 Apr. 2022 - 31 Mar. 2025
菊川 峰志, 宮内 正二, 塚本 卓, 海野 雅司
日本学術振興会, 基盤研究(B), 北海道大学, 22H02579

全長型アニオンチャネルロドプシンのイオン輸送機能：C末端ドメインの役割について
科学研究費助成事業 基盤研究(C)
01 Apr. 2022 - 31 Mar. 2025
出村 誠, 塚本 卓
日本学術振興会, 基盤研究(C), 北海道大学, 22K06120

天然全長型アニオンチャネルロドプシンの見過ごされてきた分子機能　　　　　　　　　　　　　　　
2022年度秋山記念生命科学研究助成金
Sep. 2022 - Mar. 2023
公益財団法人秋山記念生命科学振興財団, 北海道大学大学院先端生命科学研究院, Principal investigator

トライアル研究支援制度　　　　　　　　　　　　　　　
トライアル研究支援制度
Oct. 2021 - Mar. 2022
北海道大学, 北海道大学, Principal investigator

生体分子中の窒素の特性を、中性子回折と計算化学により解明する　　　　　　　　　　　　　　　
科学研究費補助金
Feb. 2019 - Mar. 2021
尾瀬 農之
日本学術振興会, Competitive research funding

イオン輸送型ロドプシンのアミノ酸変異による輸送方式の変換とその分子機構の解明　　　　　　　　　　　　　　　
KAKENHI
Apr. 2018 - Mar. 2020
TSUKAMOTO Takashi
JSPS, Principal investigator, Competitive research funding

Investigation, modification and utilization of the retinal proteins
Grants-in-Aid for Scientific Research
01 Apr. 2015 - 31 Mar. 2018
Sudo Yuki, TSUKAMOTO Takashi
Retinal protein, also called "rhodopsin", has a vitamin-A aldehyde as a chromophore. It is widely distributed in the three biological domains (animals, bacteria, archaea), and is responsible for various light-dependent functions. In addition to such biological interests, recently, the new technology called "optogenetics" which is a method for controlling biological activities by light, has been established as a collaborative work with the retinal proteins. In this research, based on the background, we investigated the retinal proteins fundamentally by using various methods. Then we modified the molecular properties to develop the novel optogenetics tools that can be widely utilized for scientific research.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Okayama University, 15H04363

光駆動細胞内向きプロトン輸送タンパク質の分子機構の解明と応用技術　　　　　　　　　　　　　　　
若手研究人材・ネットワーク育成補助金（ノースタレント補助金）
Jun. 2017 - Mar. 2018
塚本 卓
ノーステック財団, Principal investigator, Competitive research funding

スタートアップ経費
Apr. 2017 - Mar. 2018
塚本 卓
北海道大学, Principal investigator, Competitive research funding

高度好熱菌ロドプシンにおける構造安定性の追求（研究課題番号：15K18519）　　　　　　　　　　　　　　　
Grants-in-Aid for Scientific Research (KAKEN)
Apr. 2015 - Mar. 2018
TSUKAMOTO Takashi
JSPS, Principal investigator, Competitive research funding

Time-resolved infrared spectroscopy of the thermophilic rhodopsin under various pressures and temperatures
Grants-in-Aid for Scientific Research
28 Aug. 2015 - 31 Mar. 2017
Kuroi Kunisato, Tsukamoto Takashi
We investigated the photoreaction of the thermophilic rhodopsin (TR) by time-resolved Fourier transform infrared spectroscopy (TR-FTIR) under various temperature and pressure conditions to thermodynamically characterize its photoreaction. First, from the TR-FTIR measurement of TR and its mutants at 50 degree, we revealed the intramolecular proton transfer mechanism of TR. Second, from the TR-FTIR measurement of TR at various temperatures from 30 to 70 degrees, we found that the photoreaction mechanism of TR seemed to switch at about 40 degree. Finally, we developed the measurement system of high-pressure TR-FTIR, and applied it to the photoreaction of the bacteriorhodopsin (BR). We succeeded in measuring the TR-FTIR spectra of BR under high-pressure for the first time. However, due to the bad signal to noise ratio of the system, unfortunately we couldn’t apply that system to TR by the end of this project.
Japan Society for the Promotion of Science, Grant-in-Aid for Research Activity Start-up, 15H06837

カロテノイド結合型ロドプシンの２光子吸収による活性化の可能性調査　　　　　　　　　　　　　　　
Research for Specific Issues, PRESTO
Oct. 2016 - Mar. 2017
TSUKAMOTO Takashi
JST, Principal investigator, Competitive research funding

時間分解赤外分光法によるレチナールタンパク質の構造ダイナミクスの解析　　　　　　　　　　　　　　　
平成28年度自然科学研究機構分子科学研究所共同利用研究（前期）
Apr. 2016 - Sep. 2016
塚本 卓
自然科学研究機構分子科学研究所, Principal investigator, Competitive research funding

若手研究者スタートアップ研究支援事業
Jul. 2014 - Jun. 2016
塚本 卓
岡山大学, Principal investigator, Competitive research funding

時間分解赤外分光法によるレチナールタンパク質の構造ダイナミクスの解析　　　　　　　　　　　　　　　
平成27年度自然科学研究機構分子科学研究所共同利用研究（後期）
Oct. 2015 - Mar. 2016
塚本 卓
自然科学研究機構分子科学研究所, Principal investigator, Competitive research funding

Knit a Network! ロールモデル座談会　　　　　　　　　　　　　　　
16 Sep. 2021 - 16 Sep. 2021
Appearance
Seminar
北海道ダイバーシティ研究環境推進ネットワーク事務局

Hirameki Tokimeki Science　　　　　　　　　　　　　　　
08 Aug. 2017 - 08 Aug. 2017
Lecturer
Seminar
JSPS
ひらめき☆ときめきサイエンス

高校生限定プログラム　　　　　　　　　　　　　　　
07 Aug. 2017 - 07 Aug. 2017
Lecturer
Seminar
北海道大学
オープンキャンパス

物理化学分野『色を感じる視覚のふしぎ』　　　　　　　　　　　　　　　
25 Oct. 2014
Lecturer
Open college
リケジョへの誘い 岡大方式サイエンス・トライアル

中高生理系選択支援事業『理系応援キャラバン隊』　　　　　　　　　　　　　　　
2007 - 2012
Lecturer
Visiting lecture
北海道大学女性研究者支援室
中高生理系選択支援事業『理系応援キャラバン隊』

MISSION: 遺伝子コードを解読せよ！〜PCRと電気泳動で米の品種を特定する〜　　　　　　　　　　　　　　　
2011
Lecturer
Open college
日本学術振興会
ひらめき☆ときめきサイエンス

タンパク質のイロいろ　　　　　　　　　　　　　　　
Apr. 2009
Lecturer
Science cafe
第7回北大大学院生によるサイエンスライブ

抗菌タンパク質リゾチームでバイ菌をやっつけろ！　　　　　　　　　　　　　　　
2009
Lecturer
Open college
北海道大学
北海道大学オープンキャンパス

生命のミステリー 〜生命分子のかたちと働き〜『アトムの磁力でタンパク質を調べつくす！〜生物だって実は分子からできている〜』　　　　　　　　　　　　　　　
2009
Lecturer
Open college
日本学術振興会
ひらめき☆ときめきサイエンス

タンパク質のはなし―いのちを支えるかたちとはたらき　　　　　　　　　　　　　　　
Jan. 2009
Lecturer
Lecture
北海道大学平成遠友夜学校

抗菌タンパク質リゾチームでバイ菌をやっつけろ！　　　　　　　　　　　　　　　
2008
Lecturer
Open college
北海道大学
北海道大学オープンキャンパス

生命のミステリー 〜生き物のかたちと働き〜『アトムの磁力でタンパク質を調べつくす！〜生物だって実は分子からできている〜』　　　　　　　　　　　　　　　
2008
Lecturer
Open college
日本学術振興会
ひらめき☆ときめきサイエンス