Article
Biochemistry & Molecular Biology
Mengqi Wang, Yimeng Zhao, Yoshiki Hayashi, Koichi Ito, Motoyuki Hattori
Summary: MgtE is a Mg2+-selective channel regulated by intracellular Mg2+ concentration and plays an important role in cellular Mg2+ homeostasis. Multiple Mg2+ binding sites in MgtE family proteins have been identified, showing the conservation and diversity of the cytoplasmic Mg2+ binding site in these proteins.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2023)
Article
Multidisciplinary Sciences
Xinyu Teng, Danqi Sheng, Jin Wang, Ye Yu, Motoyuki Hattori
Summary: This study demonstrates the stronger binding of the metal-binding site of the MgtE TM domain to Mg2+ compared to Ca2+, and the higher resolution structure determination reveals hexahydrated Ca2+, providing mechanistic insights into the ion selectivity of MgtE for Mg2+ over Ca2+.
Article
Biochemistry & Molecular Biology
Fei Jin, Minxuan Sun, Takashi Fujii, Yurika Yamada, Jin Wang, Andres D. Maturana, Miki Wada, Shichen Su, Jinbiao Ma, Hironori Takeda, Tsukasa Kusakizako, Atsuhiro Tomita, Yoshiko Nakada-Nakura, Kehong Liu, Tomoko Uemura, Yayoi Nomura, Norimichi Nomura, Koichi Ito, Osamu Nureki, Keiichi Namba, So Iwata, Ye Yu, Motoyuki Hattori
Summary: Our study revealed the transmembrane structure of MgtE in the absence of Mg2+ ions through cryo-electron microscopy, showing the Mg2+-dependent pore opening mechanism and the kink motions of TM2 and TM5 helices at glycine residues crucial for channel activity. This provides structure-based mechanistic insights into the channel gating of MgtE.
Article
Cell Biology
Neha Gupta, Cristina Soriano-Ubeda, Paula Stein, Virginia Savy, Brian N. Papas, Goli Ardestani, Ingrid Carvacho, Dominique Alfandari, Carmen J. Williams, Rafael A. Fissore
Summary: TRPM7 is a crucial chanzyme for embryo development. It maintains magnesium (Mg2+) homeostasis, prevents oxidative stress, and promotes gene expression necessary for developmental progression and cell-lineage specification.
Article
Multidisciplinary Sciences
Weichao Peng, Shuaihu Yan, Ke Zhou, Hai-Chen Wu, Lei Liu, Yuliang Zhao
Summary: By using a modified density gradient ultracentrifugation method, ultrashort single-walled carbon nanotubes (SWCNTs) with a narrow conductance range can be separated and inserted into lipid bilayers to construct high-resolution nanopore sensors. These SWCNT nanopores exhibit 3-5 times higher ion mobility compared to bulk mobility, and are capable of discriminating homologous and isomeric proteinogenic amino acids, which is challenging for other types of nanopore sensors. These findings hold great importance for the development of protein sequencing technologies.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ravikumar Reddi, Kimberly Matulef, Erika A. Riederer, Matthew R. Whorton, Francis Valiyaveetil
Summary: This study presents the crystal structure of the K(v)1.2 channel in a C-type inactivated state, revealing changes in the selectivity filter that disrupt ion binding sites and propagate to the extracellular mouth and turret regions of the channel pore. The findings highlight the importance of the interplay between ion occupancy at the binding sites and the selectivity filter in regulating the conductive and inactivated conformations of the channel.
Article
Biochemistry & Molecular Biology
Kaihua Zhang, David Julius, Yifan Cheng
Summary: This study utilized cryo-EM to visualize conformational transitions of TRPV1, revealing the dynamic transitions of its selectivity filter in response to algogenic agents. The findings also demonstrate a general framework for understanding how TRP channels function as polymodal signal integrators.
Article
Multidisciplinary Sciences
Yichen Huang, Fei Jin, Yosuke Funato, Zhijian Xu, Weiliang Zhu, Jing Wang, Minxuan Sun, Yimeng Zhao, Ye Yu, Hiroaki Miki, Motoyuki Hattori
Summary: CNNM/CorC family proteins play a crucial role in Mg2+ transport in organisms. Structural and functional analyses provide important clues for the Mg2+ export activity of CorC.
Article
Chemistry, Physical
Francisco Lagunas, Grant Alexander, Adriana Lee Punaro, Christian Moscosa, Linhua Hu, Jordi Cabana, Robert F. Klie
Summary: Mg batteries hold potential for high energy density rechargeable energy storage devices, but the lack of cathode materials that can efficiently de/insert Mg(2+) hinders their development. Despite promising predictions, experimental systems have not been able to compete with available Li-ion technologies. This highlights the need for fundamental studies on Mg electrochemistry.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Biology
Kangcheng Song, Miao Wei, Wenjun Guo, Li Quan, Yunlu Kang, Jing-Xiang Wu, Lei Chen
Summary: TRPC5 channel is a nonselective cation channel involved in various physiological processes. Inhibitors of TRPC5, such as clemizole and HC-070, stabilize the ion channel in a nonconductive closed state, potentially offering new therapeutic strategies for anxiety disorders, depression, and kidney diseases. The cryo-EM structures of human TRPC5 with inhibitors provide insights into the binding sites and inhibitory mechanisms, facilitating the development of more effective inhibitors targeting TRPC5.
Editorial Material
Biochemistry & Molecular Biology
Elena O. Gracheva, Sviatoslav N. Bagriantsev
Summary: David Julius and Ardem Patapoutian were awarded this year's Nobel Prize in Physiology or Medicine for explaining the molecular basis for sensing heat, cold and mechanical force, marking the end of a scientific journey to identify the mechanisms in the somatosensory system mediating the detection of internal and external environments.
Article
Biochemistry & Molecular Biology
Satyaki Chatterjee, Rupasree Brahma, H. Raghuraman
Summary: This study monitored the structural dynamics, hydration dynamics, and conformational heterogeneity of MgtE in micelles and membranes, revealing substantial alterations in the organization and dynamics of MgtE in physiologically important phospholipid membranes compared to micelles, accompanied by significant changes in hydration dynamics and conformational heterogeneity. The results highlight the importance of lipid-protein interactions and provide insights into the gating mechanism of magnesium channels, particularly MgtE.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Neurosciences
I-Shan Chen, Jodene Eldstrom, David Fedida, Yoshihiro Kubo
Summary: G-protein-gated inwardly rectifying K+ (GIRK; Kir3.x) channels play important roles in controlling cell excitation in various organs. Disease-associated mutations in these channels can lead to loss of K+ selectivity, with the G156S mutation showing a unique ion permeation pathway compared to other mutants.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Biology
Suhaila Rajab, Leah Bismin, Simone Schwarze, Alexandra Pinggera, Ingo H. Greger, Hannes Neuweiler
Summary: This study reveals the dynamics of closure of ligand-binding domains (LBDs) of the three major ionotropic glutamate receptor subtypes, showing pronounced sub-millisecond fluctuations in the apo state of LBDs from all three subtypes and uncovering a pathway of allosteric communication in LBD dynamics across the dimerization interface.
COMMUNICATIONS BIOLOGY
(2021)
Article
Engineering, Chemical
Jing Zhong, Sen Lin, Jianguo Yu
Summary: A novel granulation method was developed to recover lithium from old brines with ultrahigh Mg2+/Li+ ratios. The granulated Li/Al-LDHs displayed great structure stability and selectivity, achieving high Li+ adsorption capacity and significant reduction in Mg2+/Li+ ratio. The study also found that Li/Al-LDHs could collapse when eluted with strip solutions with Li+ concentration below 150 mg/L.
SEPARATION AND PURIFICATION TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kazuhiro Kobayashi, Kouki Kawakami, Tsukasa Kusakizako, Hirotake Miyauchi, Atsuhiro Tomita, Kan Kobayashi, Wataru Shihoya, Keitaro Yamashita, Tomohiro Nishizawa, Hideaki E. Kato, Asuka Inoue, Osamu Nureki
Summary: This study reports the cryoelectron microscopic structures of the human PTH1R-Gs complex in the presence of endogenous parathyroid hormone and PTH-related peptide, revealing distinct ligand-receptor interactions and signaling durations induced by these two ligands.
Article
Biochemistry & Molecular Biology
Nozomi Sugano-Nakamura, Kyoko Matoba, Mika Hirose, Nasir K. Bashiruddin, Yukiko Matsunaga, Keitaro Yamashita, Kunio Hirata, Masaki Yamamoto, Takao Arimori, Hiroaki Suga, Junichi Takagi
Summary: Signaling by single-pass transmembrane receptors often involves formation of ligand-induced receptor dimers with particular conformation. Bivalent receptor binders can modulate receptor functions by inducing different receptor dimer conformations. In this study, antagonistic and agonistic receptor dimerizers for PlexinB1 were generated by grafting two different PlxnB1-binding peptides onto the human immunoglobulin G1 (IgG1) Fc protein.
Article
Multidisciplinary Sciences
Takafumi Kato, Tsukasa Kusakizako, Chunhuan Jin, Xinyu Zhou, Ryuichi Ohgaki, LiLi Quan, Minhui Xu, Suguru Okuda, Kan Kobayashi, Keitaro Yamashita, Tomohiro Nishizawa, Yoshikatsu Kanai, Osamu Nureki
Summary: EAAT2 plays crucial roles in glutamate homeostasis in the brain and therapy resistance of cancer cells. This study presents the cryo-EM structures of EAAT2 and the inhibitory mechanisms of selective inhibitor WAY213613. The structures reveal the binding sites and disruption of EAAT2 by WAY213613, providing insights for structure-based drug design targeting EAAT2.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ryoya Nakagawa, Soumya Kannan, Han Altae-Tran, Satoru N. Takeda, Atsuhiro Tomita, Hisato Hirano, Tsukasa Kusakizako, Tomohiro Nishizawa, Keitaro Yamashita, Feng Zhang, Hiroshi Nishimasu, Osamu Nureki
Summary: This study reveals the action mechanism and activation mechanism of Cas13bt3, and improves it through engineering, providing a foundation for the development of CRISPR-Cas13 mediated transcriptome modulation technologies.
Article
Biochemistry & Molecular Biology
Ruiliang Jia, Yimeng Zhao, Motoyuki Hattori
Summary: This study determined the crystal structure of the catalytic ATP binding domain of PhoR sensor histidine kinase from Vibrio cholera. The structure was compared with known histidine kinase protein structures and the potential binding interface with MgtC was discussed.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Materials Science, Biomaterials
Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno
Summary: Protein crystals can serve as porous scaffolds for capturing exogenous molecules. Fixing target proteins in the pores of scaffold protein crystals has been challenging due to limited strategies to control protein-protein interactions. This study successfully fixes a miniprotein within a polyhedra crystal scaffold, revealing the potential of modulating intermolecular interactions for trapping various protein conformations.
BIOMATERIALS SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Mengqi Wang, Yimeng Zhao, Yoshiki Hayashi, Koichi Ito, Motoyuki Hattori
Summary: MgtE is a Mg2+-selective channel regulated by intracellular Mg2+ concentration and plays an important role in cellular Mg2+ homeostasis. Multiple Mg2+ binding sites in MgtE family proteins have been identified, showing the conservation and diversity of the cytoplasmic Mg2+ binding site in these proteins.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2023)
Article
Neurosciences
Andrew M. Stern, Yang Yang, Shanxue Jin, Keitaro Yamashita, Angela L. Meunier, Wen Liu, Yuqi Cai, Maria Ericsson, Lei Liu, Michel Goedert, Sjors H. W. Scheres, Dennis J. Selkoe
Summary: A study has found that Aβ fibrils are present in aqueous extracts from AD brains, indicating their pathological nature. This finding has important implications for understanding and treating AD.
Article
Multidisciplinary Sciences
Ayumi Sumino, Yimeng Zhao, Daichi Mukai, Takashi Sumikama, Leonardo Puppulin, Motoyuki Hattori, Mikihiro Shibata
Summary: The study directly visualized the single-molecule structural fluctuations of TRPV1 channels using high-speed atomic force microscopy. It found that the binding of resiniferatoxin (RTX) enhances structural fluctuations, while the binding of capsazepine (CPZ) suppresses fluctuations. These ligand-dependent differences in structural fluctuation are important for the gating of TRPV1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Andriko von Kugelgen, Sofie van Dorst, Keitaro Yamashita, Danielle L. Sexton, Elitza I. Tocheva, Garib Murshudov, Vikram Alva, Tanmay A. M. Bharat ab
Summary: Using electron cryomicroscopy, we have revealed that the surface layer (S-layer) of the radiotolerant bacterium Deinococcus radiodurans is formed by the Hexagonally Packed Intermediate-layer (HPI) protein. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, resulting in a highly interconnected, stable sheet-like structure. Our study also shows the structure of the cellular S-layer and highlights the similarities between the S-layer of D. radiodurans and immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, which have implications for the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Keitaro Yamashita, Marcin Wojdyr, Fei Long, Robert A. Nicholls, Garib N. Murshudov
Summary: Macromolecular refinement uses experimental data and prior chemical knowledge to fit an atomic structural model into the data, while ensuring chemical plausibility. In CCP4 suite, the Monomer Library stores the chemical knowledge in restraint dictionaries. Recently, this part of CCP4 has been overhauled, allowing for increased flexibility and easier experimentation.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B. Ballard, Arnaud Basle, James Beilsten-Edmands, Rafael J. Borges, David G. Brown, J. Javier Burgos-Marmol, John M. Berrisford, Paul S. Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G. Cook, Kevin D. Cowtan, Tristan I. Croll, Judit E. Debreczeni, Nicholas E. Devenish, Eleanor J. Dodson, Tarik R. Drevon, Paul Emsley, Gwyndaf Evans, Phil R. Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F. Garman, Markus Gerstel, Richard J. Gildea, Kaushik Hatti, Maarten L. Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A. Hough, Huw T. Jenkins, Elisabet Jimenez, Robbie P. Joosten, Ronan M. Keegan, Nicholas Keep, Eugene B. Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S. Lamzin, David M. Lawson, Andrey A. Lebedev, Andrew G. W. Leslie, Bernhard Lohkamp, Fei Long, Martin Maly, Airlie J. McCoy, Stuart J. McNicholas, Ana Medina, Claudia Millan, James W. Murray, Garib N. Murshudov, Robert A. Nicholls, Martin E. M. Noble, Robert Oeffner, Navraj S. Pannu, James M. Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R. Powell, Randy J. Read, Daniel J. Rigden, William Rochira, Massimo Sammito, Filomeno Sanchez Rodriguez, George M. Sheldrick, Kathryn L. Shelley, Felix Simkovic, Adam J. Simpkin, Pavol Skubak, Egor Sobolev, Roberto A. Steiner, Kyle Stevenson, Ivo Tews, Jens M. H. Thomas, Andrea Thorn, Josep Trivino Valls, Ville Uski, Isabel Uson, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Waterman, Keith S. Wilson, Martyn D. Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
Summary: The Collaborative Computational Project No. 4 (CCP4) is an international collective led by the UK, dedicated to the development, testing, distribution, and promotion of software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs, unified by familiar execution routines, common libraries, and graphical interfaces. This article serves as a general literature citation for the use of the CCP4 software suite, providing an overview of its recent changes, new features, and future developments, while also highlighting the individual programs within the suite and providing up-to-date references for crystallographers worldwide.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Seiya Tajima, Yoon Seok Kim, Masahiro Fukuda, Youngju Jo, Peter Y. Wang, Joseph M. Paggi, Masatoshi Inoue, Eamon F. X. Byrne, Koichiro E. Kishi, Seiwa Nakamura, Charu Ramakrishnan, Shunki Takaramoto, Takashi Nagata, Masae Konno, Masahiro Sugiura, Kota Katayama, Toshiki E. Matsui, Keitaro Yamashita, Suhyang Kim, Hisako Ikeda, Jaeah Kim, Hideki Kandori, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, Hideaki E. Kato
Summary: KCR channelrhodopsins exhibit a distinctive mechanism for K+ selectivity, involving the formation of an asymmetric selectivity gate and a distinct dehydration pathway. The discovery of this mechanism provides a framework for studying ion-channel selectivity and advancing optogenetic applications.
Article
Multidisciplinary Sciences
Danyang Zhang, Josip Ivica, James M. Krieger, Hinze Ho, Keitaro Yamashita, Imogen Stockwell, Rozbeh Baradaran, Ondrej Cais, Ingo H. Greger
Summary: This study determines and characterizes the cryo-electron microscopy structures of GluA1/gamma 3, revealing their unique kinetic properties and synaptic signaling efficiency among AMPAR subtypes.
Article
Biochemistry & Molecular Biology
Junko Tanaka, Satoshi Abe, Tohru Hayakawa, Mariko Kojima, Keitaro Yamashita, Kunio Hirata, Takafumi Ueno
Summary: In-cell protein crystals that spontaneously crystallize in living cells have been analyzed to understand their structures and biological functions. However, their small size has made it challenging to determine their structures. In this study, the cross-linked network of disulfide bonds within Cry1Aa crystals, a cysteine-rich protein that crystallizes in Bacillus thuringiensis, was characterized through direct X-ray crystallographic analysis using crystals purified from Bt cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
