Article
Chemistry, Physical
Rodrigo A. Vargas-Hernandez, Chern Chuang, Paul Brumer
Summary: This passage discusses the use of multi-objective optimization to find the best model for multiple target observables, as well as the approximation of predicted errors using Gaussian process models to reduce computational costs.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Sahoko Tomida, Shinya Kitagawa, Hideki Kandori, Yuji Furutani
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)
Article
Chemistry, Multidisciplinary
Jin Feng, Baofeng Li, Xinlu Wang, Xinlong Mao, Tengfei Ma, Dapeng Zhang, Siwei Bi
Summary: We studied the relationship between visual function and structural characteristics, focusing on the C=O terminal group, N = 6 conjugation length, and CH3 saturated group. The presence of C=O in the conjugated chain is determined by N = 6, which prevents its occurrence in shorter carotenoids. N = 6 ensures the high stability of retinal and sensitivity to the growth of conjugation length. The electron-withdrawing ability of the saturated group determines its oxidation-reduction ability. Among them, the CH3-saturated retinal has electronic properties closest to H-saturated derivatives. We provide a new perspective on the specificity of retinal structure, contributing to the understanding of the visual mechanism and serving as a foundation for structural improvement and functional expansion of retinal.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tomomi Shionoya, Manish Singh, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani
Summary: A new category of rhodopsins, named schizorhodopsins (SzRs), have been identified as light-driven inward proton pumps. Comprehensive resonance Raman measurements were conducted to characterize the structure of the retinal chromophore in the unphotolyzed state of four SzRs. The protonated Schiff base in SzRs forms a stronger hydrogen bond than that in outward proton-pumping rhodopsins, with the hydrogen-bonding partner being an amino acid residue, presumably an Asp residue in helix G.
Article
Chemistry, Physical
Leonardo Barneschi, Danil Kaliakin, Miquel Huix-Rotllant, Nicolas Ferre, Michael Filatov(Gulak), Massimo Olivucci
Summary: This study compares the performance of different electronic structure methods and implementation of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The results show that REKS method behaves differently in some systems compared to other methods, which can be attributed to the effect of the employed density functional approximation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Victor A. Lorenz-Fonfria, Kiyoshi Yagi, Shota Ito, Hideki Kandori
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)
Article
Chemistry, Physical
In Seong Lee, Seung Kyu Min
Summary: We propose a generalized combination of the DFTB and SSR methods by considering OC and LC functions, providing more accurate energy and gradient descriptions for microstates and correct descriptions for conical intersections with the multireference nature of SSR. Benchmark tests against other calculation methods demonstrate the accuracy of LC-OC-DFTB/SSR in excitation energies and conical intersection structures.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
P. A. Kusochek, V. V. Logvinov, A. Bochenkova
Summary: This study investigates the role of protein environment in the photoisomerization reactions of the retinal protonated Schiff base using simulations and modeling. The protein environment was found to change vibrational modes by pre-twisting the chromophore, facilitating specific photoisomerization reactions.
MOSCOW UNIVERSITY CHEMISTRY BULLETIN
(2021)
Article
Chemistry, Physical
Jesse Saari, Harri Ali-Loytty, Kimmo Lahtonen, Markku Hannula, Lauri Palmolahti, Antti Tukiainen, Mika Valden
Summary: The physicochemical properties of titanium dioxide depend strongly on the crystal structure, with rutile TiO2 having desirable properties for photonic applications. This study demonstrates the ALD-based fabrication of anatase and rutile TiO2 thin films controlled by precursor traces and oxide defects at different growth temperatures. The mixed phase TiO2 thin film with rutile as the primary phase can be utilized in a broad range of applications at low post deposition annealing temperatures.
JOURNAL OF PHYSICAL CHEMISTRY C
Article
Multidisciplinary Sciences
Wataru Shihoya, Keiichi Inoue, Manish Singh, Masae Konno, Shoko Hososhima, Keitaro Yamashita, Kento Ikeda, Akimitsu Higuchi, Tamaki Izume, Sae Okazaki, Masanori Hashimoto, Ritsu Mizutori, Sahoko Tomida, Yumeka Yamauchi, Rei Abe-Yoshizumi, Kota Katayama, Satoshi P. Tsunoda, Mikihiro Shibata, Yuji Furutani, Alina Pushkarev, Oded Beja, Takayuki Uchihashi, Hideki Kandori, Osamu Nureki
Article
Chemistry, Physical
Yasushi Imamoto, Hiroaki Sasayama, Mild Harigai, Yuji Furutani, Mikio Kataoka
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
Andrew Harris, Michalis Lazaratos, Malte Siemers, Ethan Watt, Anh Hoang, Sahoko Tomida, Luiz Schubert, Mattia Saita, Joachim Heberle, Yuji Furutani, Hideki Kandori, Ana-Nicoleta Bondar, Leonid S. Brown
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Biochemistry & Molecular Biology
Sahoko Tomida, Shota Ito, Tomoya Mato, Yuji Furutani, Keiichi Inoue, Hideki Kandori
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2020)
Article
Chemistry, Physical
Masanori Hashimoto, Kota Katayama, Yuji Furutani, Hideki Kandori
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Chemistry, Physical
Sahoko Tomida, Shinya Kitagawa, Hideki Kandori, Yuji Furutani
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)
Article
Biochemistry & Molecular Biology
Andrey Rozenberg, Igor Kaczmarczyk, Donna Matzov, Johannes Vierock, Takashi Nagata, Masahiro Sugiura, Kota Katayama, Yuma Kawasaki, Masae Konno, Yujiro Nagasaka, Mako Aoyama, Ishita Das, Efrat Pahima, Jonathan Church, Suliman Adam, Veniamin A. Borin, Ariel Chazan, Sandra Augustin, Jonas Wietek, Julien Dine, Yoav Peleg, Akira Kawanabe, Yuichiro Fujiwara, Ofer Yizhar, Mordechai Sheves, Igor Schapiro, Yuji Furutani, Hideki Kandori, Keiichi Inoue, Peter Hegemann, Oded Beja, Moran Shalev-Benami
Summary: This study reports a new subfamily of microbial rhodopsins called bestrhodopsins, which are fused with bestrophin channels. Cryo-EM analysis reveals that bestrhodopsins form pentameric megacomplexes and undergo photoconversion. Bestrhodopsins behave as light-modulated anion channels.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Masahiro Sugiura, Kazuki Ishikawa, Kota Katayama, Yuji Sumii, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Yuji Furutani, Norio Shibata, Leonid S. Brown, Hideki Kandori
Summary: This study reports a novel photochemical reaction mediated by a microbial rhodopsin, leading to the selective transition from the all-trans to 7-cis form.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Masanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki Kandori
Summary: Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to other rhodopsins. ATR-FTIR spectroscopy studies have demonstrated the binding of Zn2+ to HeR, specifically affecting the structure and function. The specific binding site of Zn2+ was found to be located at the cytoplasmic side of TaHeR.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Shoha Ochiai, Yuki Ichikawa, Sahoko Tomida, Yuji Furutani
Summary: Microbial rhodopsins are light-receptive proteins with various functions triggered by the photoisomerization of the retinal chromophore. The covalent bond linking the lysine residue and the protein backbone is not necessary for microbial rhodopsin function. However, a covalent bond at Lys-255 is important for the stable binding of the retinal chromophore and formation of an O intermediate to achieve light-driven Na+ pump function in KR2.
Article
Biochemistry & Molecular Biology
Kunisato Kuroi, Takashi Tsukamoto, Naoya Honda, Yuki Sudo, Yuji Furutani
Summary: This study investigated the primary proton transfer reactions of thermophilic rhodopsin and found that it is closely related to the structural change of the protein and optimized at high temperatures, which is not observed in other related proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2023)
Article
Biochemistry & Molecular Biology
Sahoko Tomida, Akimori Wada, Yuji Furutani
Summary: Water is essential for protein function, particularly in ion transportation and color regulation. The dehydration of a sodium-pumping rhodopsin caused a color change, suggesting the importance of water molecules. Specifically, the hydrogen-bonding network and deprotonation state of certain amino acid residues were found to be maintained by water molecules in the protein KR2.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Yue Zhao, Shota Kusama, Yuji Furutani, Wei-Hong Huang, Chih-Wei Luo, Takao Fuji
Summary: The authors present a fast mid-infrared hyperspectral imaging technique using chirped pulse upconversion of sub-cycle pulses. The imaging technique offers adjustable field of view, large spectral range, and a lateral resolution of 15 μm. They demonstrated effective identification and mapping of different components in various samples. This technique has great potential and can be applied in chemical analysis, biology, and medicine.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Masahiro Sugiura, Kazuki Ishikawa, Kota Katayama, Yuji Sumii, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Yuji Furutani, Norio Shibata, Leonid S. Brown, Hideki Kandori
Summary: This study reports on a novel photochemistry mediated by a microbial rhodopsin, which selectively transforms the all-trans form to the 7-cis form. The reaction occurs in the dark with the all-trans form, but isomerizes into the 7-cis form upon illumination, accompanied by changes in protein structure and protonation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Maho Yagi-Utsumi, Kazuhiro Aoki, Hiroki Watanabe, Chihong Song, Seiji Nishimura, Tadashi Satoh, Saeko Yanaka, Christian Ganser, Sae Tanaka, Vincent Schnapka, Ean Wai Goh, Yuji Furutani, Kazuyoshi Murata, Takayuki Uchihashi, Kazuharu Arakawa, Koichi Kato
Summary: The study found that the anhydrobiotic protein CAHS1 self-assembles to form a hydrogel and condensates under desiccation conditions, suggesting its crucial role in the desiccation tolerance of tardigrades.
SCIENTIFIC REPORTS
(2021)