Article
Biology
Raymond N. Burton-Smith, Chihong Song, Hiroshi Ueno, Takeshi Murata, Ryota Iino, Kazuyoshi Murata
Summary: Using cryo-electron microscopy, we have captured six intermediate conformations of the active rotary vacuolar-type ATPase from Enterococcus hirae, revealing a non-uniform rotor rotation.
COMMUNICATIONS BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Farzana Tuli, Patricia M. Kane
Summary: Vacuolar H+-ATPases (V-ATPases) are multi-subunit enzymes that acidify organelles and export protons in eukaryotic cells. The largest membrane subunit, the a-subunit, interacts with other subunits and bridges the V-1 and V-o subcomplexes. Multiple isoforms of the a-subunit exist, allowing for specific interactions and regulation. Understanding the regulatory mechanisms of V-ATPases, specifically the a-subunit isoforms, is important for the treatment of diseases associated with altered V-ATPase function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Plant Sciences
Frederic Chaux, Domitille Jarrige, Marcio Rodrigues-Azevedo, Sandrine Bujaldon, Oliver D. Caspari, Shin-Ichiro Ozawa, Dominique Drapier, Olivier Vallon, Yves Choquet, Catherine de Vitry
Summary: This study isolated ATP synthase mutants in the green alga Chlamydomonas reinhardtii and investigated their impact on the biogenesis of the ATP synthase complex. The findings revealed the crucial role of the nuclear factor MDE1 in stabilizing the chloroplast-encoded atpE mRNA.
Review
Biochemistry & Molecular Biology
Anthony Cheuk, Thomas Meier
Summary: Driven by transmembrane electrochemical ion gradients, F-type ATP synthases are the primary source of ATP across all domains of life. The ATP synthase in thylakoid membranes of photosynthetic organisms has unique features, such as a larger rotor ring and a redox-regulated switch that inhibits ATP hydrolysis activity in the dark. Recent insights into the structure and mechanism of photosynthesis-involved ATP synthases are reviewed, along with exploration of the cellular physiological consequences of these adaptations in both short and long time scales.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Biochemistry & Molecular Biology
Yoon Kyung Shin, Young Rae Jo, Seoung Hoon Lee, Hwan Tae Park, Jung Eun Shin
Summary: After peripheral nerve injury, demyelinating Schwann cells release myelin debris and macrophages degrade myelin, leading to demyelination of degenerating axons, which is necessary for nerve regeneration. This study identifies ATP6V0D2, which is highly upregulated in injured mouse nerves, as a key player in this process. Knockout of ATP6V0D2 delays peripheral nerve demyelination and impairs myelin lipid digestion, while recruitment of macrophages and dedifferentiation of Schwann cells are unaffected. These findings highlight the specific role of ATP6V0D2 in macrophages during the demyelination process of Wallerian degeneration.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Katarzyna Terejko, Michal A. Michalowski, Anna Dominik, Anna Andrzejczak, Jerzy W. Mozrzymas
Summary: Recent studies have shown that the activation of pLGICs is associated with coordinated subunit twisting in the membrane plane, indicating a crucial role of intersubunit interactions in receptor activation, especially in preactivation and opening processes. The underlying mechanisms of this intersubunit cross-talk outside the top-down pathway remain largely unknown.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anh Chu, Yeqi Yao, Golam T. Saffi, Ji Hyun Chung, Roberto J. Botelho, Miroslawa Glibowicka, Charles M. Deber, Morris F. Manolson
Summary: Vacuolar ATPases (V-ATPases) are essential for cellular functions and their interaction with phosphoinositides (PIPs) is crucial for membrane binding. This study identified a lipid binding domain within the N-terminal domain of the human a4 isoform and found a basic motif critical for PIP interaction. Mutations in this motif reduced membrane association and decreased plasma membrane localization of the a4NT protein. Depletion of PI(4,5)P-2 also led to reduced membrane binding of the wildtype protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Yoshiaki Kawano, Masahide Hikita, Naohiro Matsugaki, Masaki Yamamoto, Toshiya Senda
Summary: Native SAD phasing is a promising method for next-generation crystallography, but it requires high-quality diffraction data using long-wavelength X-rays. Optimizing crystal size and shape, as well as removing noncrystalline sample portions, can improve data quality. A crystal-processing machine using a deep-UV laser has been developed and significantly improved diffraction data quality and the success rate of experimental phasing.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Mrinal Shekhar, Chitrak Gupta, Kano Suzuki, Chun Kit Chan, Takeshi Murata, Abhishek Singharoy
Summary: The mechanism of rotatory catalysis in ATP hydrolyzing molecular motors is still poorly understood. In this study, a complete 4-step conformational cycle model of rotatory catalysis is proposed using vacuolar or V-1-type hexameric ATPase as an example. A new intermediate or dwell is identified and a putative cyclic rotation path is derived. Free-energy simulations estimate the rate of protein transformations and reveal the role of arginine-finger residues in coupling chemical and mechanical information. Analysis indicates that overcoming the ADP interactions with V-1-ATPase is the rate-limiting step of motor action.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Kumarevel Thirumananseri, Karthe Ponnuraj
Summary: This study reports the crystal structure of arginase from Thermus thermophilus (TtArginase), and compares it with other homologous structures. The results show that TtArginase is more stable compared to its mesophilic counterpart, Bacillus subtilis arginase (BsArginase). Additionally, the study reveals the critical role of metal ions in both the catalytic function and maintenance of proper active site geometry. These findings are important for optimizing the enzymatic action of arginase in various conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Yu Sakurai, Nodoka Abe, Keito Yoshikawa, Ryotaro Oyama, Satoshi Ogasawara, Takeshi Murata, Yuta Nakai, Kota Tange, Hiroki Tanaka, Hidetaka Akita
Summary: This study developed a method for selective delivery of siRNA to LECs using LNPs. The method of modifying LNPs used in the study shows promise for expanding the delivery of nucleic acids in the future.
JOURNAL OF CONTROLLED RELEASE
(2022)
Article
Multidisciplinary Sciences
Akihiro Otomo, Tatsuya Iida, Yasuko Okuni, Hiroshi Ueno, Takeshi Murata, Ryota Iino
Summary: V-ATPases are rotary motor proteins that convert ATP chemical energy into the electrochemical potential of ions, and the study of ATP-driven stepping rotation under different conditions provides insights into the effects of Na+ and ATP on rotation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Taisei Yamamoto, Satoshi Yasuda, Rinshi S. Kasai, Ryosuke Nakano, Simon Hikiri, Kanna Sugaya, Tomohiko Hayashi, Satoshi Ogasawara, Mitsunori Shiroishi, Takahiro K. Fujiwara, Masahiro Kinoshita, Takeshi Murata
Summary: The study challenged the stabilization of a GPCR in the active state solely by multiple amino-acid mutations, revealing that stabilizing the inactive state leads to a significant increase in thermal denaturation midpoint temperature T-m, but this is not always the case for the active state. The methodology involving statistical thermodynamics and evolutionary molecular engineering was able to identify mutants with higher binding affinity for G protein, shifting structural characteristics towards the active state, although only slight increases in T-m were observed, indicating its unsuitability as a stability measure for the active state.
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel, Karthe Ponnuraj
Summary: The crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus (TtPCP) was solved and refined at 1.9 angstrom resolution using the molecular replacement method. Comparing TtPCP with its structural homologs, it was found that the putative thermal stability of TtPCP may be attributed to more intra and inter-molecular hydrogen bonds, hydrophobic and ion pair interactions. This structural information of TtPCP can contribute to understanding the intrinsic stability of thermophilic proteins and can be useful for protein engineering.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Engineering, Multidisciplinary
Songshi Li, Daisuke Kawashima, Kennedy Omondi Okeyo, Takeshi Murata, Masahiro Takei
Summary: This study proposes a method combining electrical impedance tomography (EIT) with an ion transport model to evaluate the anisotropic transmembrane transport of ions in a cell-spheroid under inhomogeneous ion concentration fields. The method assesses the transmembrane transport coefficient of each part of the cell membrane by the ion transport model using the average conductivity of the extracellular sector reconstructed by EIT. An anisotropic factor H is introduced to represent the anisotropic transmembrane transport. The results show successful observation of the inhomogeneous ion concentration distribution and agreement with fluorescence ratio measurements.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hidetsugu Asada, Dohyun Im, Yunhon Hotta, Satoshi Yasuda, Takeshi Murata, Ryoji Suno, So Iwata
Summary: The study uncovers the importance of orexin receptors in regulating the sleep-wake cycle and highlights the potential of developing antagonists for these receptors as novel treatments for sleep-related diseases. The determination of the structure of OX2R bound to lemborexant provides valuable insights into the binding mechanism and furthers our understanding of the pharmacophore models and target selectivity to OXRs.
Article
Multidisciplinary Sciences
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Summary: Antimicrobial resistance is a global health problem and there is a rise in drug-resistant species. Our research has identified a new antibiotic compound that can combat drug-resistant Neisseria gonorrhoeae, and our findings on the inhibitory mechanism provide new avenues for modulating protein functions and overcoming antimicrobial resistance.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Mutsuko Kukimoto-Niino, Kentaro Ihara, Chiemi Mishima-Tsumagari, Mio Inoue, Yoshinori Fukui, Shigeyuki Yokoyama, Mikako Shirouzu
Summary: This study reveals the crystal structures of the catalytic DHR2 domain of mouse DOCK10, complexed with either Cdc42 or Rac1, and uncovers the unique dual activation mechanism of DOCK10.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tatsuo Yanagisawa, Eiko Seki, Hiroaki Tanabe, Yoshifumi Fujii, Kensaku Sakamoto, Shigeyuki Yokoyama
Summary: Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) from Methanosarcina mazei and Methanosarcina barkeri are used for site-specific incorporations of non-canonical amino acids into proteins. Mutations in Methanomethylophilus alvus PylRS allow efficient binding with N-e-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys) but not with N-e-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Hiroaki Matsuura, Naoki Sakai, Sachiko Toma-Fukai, Norifumi Muraki, Koki Hayama, Hironari Kamikubo, Shigetoshi Aono, Yoshiaki Kawano, Masaki Yamamoto, Kunio Hirata
Summary: In macromolecular structure determination using X-ray diffraction from multiple crystals, hierarchical clustering analysis (HCA) has been effective in classifying polymorphous data sets with a certain threshold, allowing for the identification of polymorphs in data sets with unknown structural heterogeneity. Additionally, polymorphs can also be detected in single crystals using the continuous helical scheme.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biology
Raymond N. Burton-Smith, Chihong Song, Hiroshi Ueno, Takeshi Murata, Ryota Iino, Kazuyoshi Murata
Summary: Using cryo-electron microscopy, we have captured six intermediate conformations of the active rotary vacuolar-type ATPase from Enterococcus hirae, revealing a non-uniform rotor rotation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Immunology
Seisuke Kusano, Sho Ueda, Daisuke Oryoji, Aya Toyoumi, Akiko Hashimoto-Tane, Hiroyuki Kishi, Hiroshi Hamana, Atsushi Muraguchi, Hui Jin, Hisashi Arase, Hiroko Miyadera, Reiko Kishikawa, Yasunobu Yoshikai, Hisakata Yamada, Ken Yamamoto, Yasuharu Nishimura, Takashi Saito, Takehiko Sasazuki, Shigeyuki Yokoyama
Summary: Cry j 1 is a major allergen in Japanese cedar pollens. The NF region of Cry j 1 peptide plays a role in enhancing T-cell activation. Mutation of Ser and Lys in the NF region to Glu reduces the affinity for HLA-DP5, antigen presentation, and T-cell activation.
INTERNATIONAL IMMUNOLOGY
(2023)
