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Cardiac Remodeling: Novel Pathophysiological Mechanisms and Therapeutic Strategies J. Biochem. (IF 2.7) Pub Date : 2024-03-20 Motohiro Nishida, Xinya Mi, Yukina Ishii, Yuri Kato, Akiyuki Nishimura
Morphological and structural remodeling of the heart, including cardiac hypertrophy and fibrosis, has been considered a therapeutic target for heart failure for approximately three decades. Groundbreaking heart failure medications demonstrating reverse remodeling effects have contributed significantly to medical advancements. However, nearly 50% of heart failure patients still exhibit drug resistance
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Essential dextrin structure as donor substrate for 4-α-glucanotransferase in glycogen debranching enzyme J. Biochem. (IF 2.7) Pub Date : 2024-03-18 Rentaro Uno, Yasushi Makino, Hiroshi Matsubara
Summary Glycogen debranching enzyme is a single polypeptide with distinct catalytic sites for 4-α-glucanotransferase and amylo-α-1,6-glucosidase. To allow phosphorylase to degrade the inner tiers of highly branched glycogen, 4-α-glucanotransferase converts the phosphorylase-limit biantennary branch G-G-G-G-(G-G-G-G↔)G-G- (G: D-glucose, hyphens: α-1,4-linkages; double-headed arrow: α-1,6-linkage) into
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Cryo-EM advances in GPCR structure determination J. Biochem. (IF 2.7) Pub Date : 2024-03-18 Wataru Shihoya, Aika Iwama, Fumiya K Sano, Osamu Nureki
G-protein-coupled receptors (GPCRs) constitute a prominent superfamily in humans, and are categorized into six classes (A through F) that play indispensable roles in cellular communication and therapeutics. Nonetheless, their structural comprehension has been limited by challenges in high-resolution data acquisition. This review highlights the transformative impact of cryogenic electron microscopy
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Structure-based design, biophysical characterization, and biochemical application of the heterodimeric affinity purification tag based on the Schistosoma japonicum glutathione-S-transferase (SjGST) homodimer J. Biochem. (IF 2.7) Pub Date : 2024-03-12 Yan Du, Yoshihiro Kobashigawa, Kyo Okazaki, Mizuki Ogawa, Tomoyuki Kawaguchi, Takashi Sato, Hiroshi Morioka
Summary Schistosoma japonicum glutathione-S-transferase (SjGST), so-called GST-tag, is one of the most widely used protein tags for the purification of recombinant proteins by affinity chromatography. Attachment of SjGST enables the purification of a protein of interest (POI) using commercially available glutathione-immobilizing resins. Here we produced an SjGST mutant pair that forms heterodimers
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G protein-coupled receptor 84 gene expression is regulated by the ER stress response in the liver J. Biochem. (IF 2.7) Pub Date : 2024-03-12 Soshi Kanemoto
G protein-coupled receptor 84 (Gpr84) is reportedly activated by medium-chain fatty acids and is involved in the pathology of liver fibrosis. Inflammatory stimulants such as lipopolysaccharide and tumor necrosis factor-α upregulate Gpr84 expression. However, the detailed molecular mechanism by which Gpr84 is induced remains unknown. Inflammatory stimulation also evokes endoplasmic reticulum (ER) stress
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SdrR, a LysR-Type Regulator, responds to the mycobacterial antioxidant defense J. Biochem. (IF 2.7) Pub Date : 2024-03-04 Chen Zhu, Wen-ping Wei, Jing-ning An, Jia-ling Hu, Chun-hui Gao, Min Yang
Protection against oxidative stress is a vital defense mechanism for Mycobacterium tuberculosis within the host. However, few transcription factors that control bacterial antioxidant defense are known. Here, we present evidence that SdrR, encoded by the MSMEG_5712 (Ms5712) gene, functions as an oxidative stress response regulator in Mycobacterium smegmatis. SdrR recognizes an 11-bp motif sequence in
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Structure of cytotoxic amyloid oligomers generated during disaggregation J. Biochem. (IF 2.7) Pub Date : 2024-03-02 Toshisuke Kaku, Kazunori Ikebukuro, Kaori Tsukakoshi
Amyloidosis is characterized by the abnormal accumulation of amyloid proteins. The causative proteins aggregate from monomers to oligomers and fibrils, among which some intermediate oligomers considered as major toxins. Cytotoxic oligomers are generated not only by aggregation but also via fibril disaggregation. However, little is known about the structural characteristics and generation conditions
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Structure-specific DNA endonuclease T7 endonuclease I cleaves DNA containing UV-induced DNA lesions J. Biochem. (IF 2.7) Pub Date : 2024-02-28 Kazuki Matsubara, Shouta Ueda, Junpei Yamamoto, Shigenori Iwai, Narumi Shioi-Aoki, Arato Takedachi, Isao Kuraoka
The T7 gene 3 product, T7 endonuclease I, acts on various substrates with DNA structures, including Holliday junctions, heteroduplex DNAs, and single-mismatch DNAs. Genetic analyses have suggested the occurrence of DNA recombination, replication, and repair in E.coli. In this study, T7 endonuclease I digested UV-irradiated covalently closed circular plasmid DNA into linear and nicked plasmid DNA, suggesting
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Cutting-Edge Skin Ageing Research on tissue stem cell J. Biochem. (IF 2.7) Pub Date : 2024-02-26 Ryo Ichijo
In developed economies, the growing number of older individuals is a pressing issue. As a result, research progress into ageing has emphasised the significance of staying healthy in one's later years. Stem cells have a fundamental role to play in fostering diverse cell types and necessary processes for tissue repair and regeneration. Stem cells experience the effects of ageing over time, which is caused
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Therapeutic strategies targeting cellular senescence for cancer and other diseases J. Biochem. (IF 2.7) Pub Date : 2024-02-17 Xuebing Wang, Takeshi Fukumoto, Ken-ichi Noma
Cellular senescence occurs in response to endogenous or exogenous stresses and is characterized by stable cell cycle arrest, alterations in nuclear morphology, and secretion of proinflammatory factors, referred to as the senescence-associated secretory phenotype (SASP). An increase of senescent cells is associated with the development of several types of cancer and aging-related diseases. Therefore
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Photocontrol of small GTPase Ras fused with a photoresponsive protein J. Biochem. (IF 2.7) Pub Date : 2024-02-17 Nobuyuki Nishibe, Shinsaku Maruta
The small GTPase Ras plays an important role in intracellular signal transduction and functions as a molecular switch. In this study, we used a photoresponsive protein as the molecular regulatory device to photoregulate Ras GTPase activity. Photo zipper (PZ), a variant of the photoresponsive protein Aureochrome1 developed by Hisatomi et al. (1-9) was incorporated into the C-terminus of Ras as a fusion
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Relationships between protein degradation, cellular senescence, and organismal aging J. Biochem. (IF 2.7) Pub Date : 2024-02-08 Jun Hamazaki, Shigeo Murata
Summary Aging is a major risk factor for many diseases. Recent studies have shown that age-related disruption of proteostasis leads to the accumulation of abnormal proteins and that dysfunction of the two major intracellular proteolytic pathways, the ubiquitin-proteasome pathway, and the autophagy-lysosome pathway, is largely responsible for this process. Conversely, it has been shown that activation
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Carbohydrate-binding ability of a recombinant protein containing the DM9 motif from Drosophila melanogaster J. Biochem. (IF 2.7) Pub Date : 2024-02-07 Tomomitsu Hatakeyama, Fuki Kojima, Issei Ohkawachi, Hitomi Sawai, Hideaki Unno
Summary Proteins containing DM9 motifs, which were originally identified in the Drosophila melanogaster genome, are widely distributed in various organisms and are assumed to be involved in their innate immune response. In this study, we produced a recombinant protein of CG13321 (rCG13321) from D. melanogaster, which consists of four DM9 motifs, in Escherichia coli cells. In affinity chromatography
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GPCR signaling bias: an emerging framework for opioid drug development J. Biochem. (IF 2.7) Pub Date : 2024-02-02 Ryoji Kise, Asuka Inoue
Biased signaling has emerged as an important concept in drug development targeting G protein-coupled receptors (GPCRs). Drugs that provoke biased signaling are expected to offer an opportunity for enhanced therapeutic effectiveness with minimized side effects. Opioid analgesics, while exerting potent pain-relieving effects, have become a social problem owing to their serious side effects. For the development
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C-terminally truncation is a prominent post-translational modification of human erythrocyte α-synuclein J. Biochem. (IF 2.7) Pub Date : 2024-02-01 Ryosuke Amagai, Riki Otomo, Sakura Yoshioka, Hidekazu Nagano, Naoko Hashimoto, Ryuji Sakakibara, Tomoaki Tanaka, Ayako Okado-Matsumoto
α-Synuclein is a protein related to synucleinopathies with high expression in the central nervous system and erythrocytes which are a major source of peripheral α-synuclein. Recent reports have suggested the presence of α-synuclein within extracellular vesicles derived from erythrocytes, potentially contributing to the pathogenesis of synucleinopathies. While Lewy bodies, intracellular inclusions containing
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Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus J. Biochem. (IF 2.7) Pub Date : 2024-02-01 Gota Kawai, Kiyoshi Okada, Seiki Baba, Asako Sato, Taiichi Sakamoto, Akio Kanai
Crystal structure of a ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus was determined with the resolution of 2.57 Å in a homo-trimeric form. The monomer structure consists of two domains, N-terminal and C-terminal domains. C-terminal domain forms trimer and each N-terminal domain locates outside of the trimer core. In the obtained crystal, a dinucleotide, pApUp, was bound to the N-terminal
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Extracellular Histones Promote Calcium Phosphate-Dependent Calcification in Mouse Vascular Smooth Muscle Cells J. Biochem. (IF 2.7) Pub Date : 2024-02-01 Tomonori Hoshino, Davood Kharaghani, Shohei Kohno
Summary Vascular calcification, a major risk factor for cardiovascular events, is associated with a poor prognosis in chronic kidney disease (CKD) patients. This process is often associated with the transformation of vascular smooth muscle cells (VSMCs) into cells with osteoblast-like characteristics. Damage-associated molecular patterns (DAMPs), such as extracellular histones released from damaged
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Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms J. Biochem. (IF 2.7) Pub Date : 2024-02-01 Daisuke Yoshioka, Takanori Nakamura, Yuji Kubota, Mutsuhiro Takekawa
Proper regulation of cellular response to environmental stress is crucial for maintaining biological homeostasis and is achieved by the balance between cell death processes, such as the formation of the pyroptosis-inducing NLRP3 inflammasome, and pro-survival processes, such as stress granule (SG) assembly. However, the functional interplay between these two stress-responsive organelles remains elusive
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Protein homeostasis and degradation in quiescent neural stem cells J. Biochem. (IF 2.7) Pub Date : 2024-02-01 Taeko Kobayashi
Tissue stem cells are maintained in the adult body throughout life and are crucial for tissue homeostasis as they supply newly functional cells. Quiescence is a reversible arrest in the G0/G1 phase of the cell cycle and a strategy to maintain the quality of tissue stem cells. Quiescence maintains stem cells in a self-renewable and differentiable state for a prolonged period by suppressing energy consumption
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Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals J. Biochem. (IF 2.7) Pub Date : 2024-01-25 Yu-ichi Aoki, Keiko Taguchi, Hayato Anzawa, Junko Kawashima, Noriko Ishida, Akihito Otuki, Atsushi Hasegawa, Liam Baird, Takafumi Suzuki, Ikuko N Motoike, Kinuko Ohneda, Kazuki Kumada, Fumiki Katsuoka, Kengo Kinoshita, Masayuki Yamamoto
Summary Whole blood transcriptome analysis is a valuable approach in medical research, primarily due to the ease of sample collection and the richness of the information obtained. Since the expression profile of individual genes in the analysis is influenced by medical traits and demographic attributes such as age and gender, there has been a growing demand for a comprehensive database for blood transcriptome
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On the pursuit to reconstitute the Escherichia coli ribosome from purified components J. Biochem. (IF 2.7) Pub Date : 2024-01-18 Hideki Taguchi
The ribosome, the protein synthesizing machinery composed of dozens of proteins and several ribosomal RNAs (rRNAs), is essential for life. In vitro reconstitution of the ribosome holds significance for understanding biosynthesis, applications in biotechnology, and potential contributions to synthetic biology. There is a long history of in vitro reconstitution of bacterial ribosomes, originating in
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Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside J. Biochem. (IF 2.7) Pub Date : 2024-01-16 Junta Tomono, Kosuke Asano, Takuma Chiashi, Masato Suzuki, Masayuki Igarashi, Yoshiaki Takahashi, Yoshikazu Tanaka, Takeshi Yokoyama
The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of
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CdbC: a disulfide bond isomerase involved in the refolding of mycoloyltransferases in Corynebacterium glutamicum cells exposed to oxidative conditions J. Biochem. (IF 2.7) Pub Date : 2024-01-16 Haeri Jeong, Younhee Kim, Heung-Shick Lee
In Corynebacterium glutamicum cells, cdbC, which encodes a protein containing the CysXXCys motif, is regulated by the global redox-responsive regulator OsnR. In this study, we assessed the role of the periplasmic protein CdbC in disulfide bond formation and its involvement in mycomembrane biosynthesis. Purified CdbC efficiently refolded scrambled RNaseA, exhibiting prominent disulfide bond isomerase
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The ATPase activity of ABCA1 is increased by cholesterol in the presence of anionic lipids J. Biochem. (IF 2.7) Pub Date : 2024-01-11 Kazuki Sakata, Noriyuki Kioka, Kazumitsu Ueda, Yasuhisa Kimura
High-density lipoprotein (HDL) transports excess cholesterol from peripheral tissues back to the liver, and plasma HDL levels are inversely related to cardiovascular disease incidence. ATP-binding cassette A1 (ABCA1) is a member of the ABC protein superfamily, and generates nascent HDL, which consists of several hundreds of phospholipids and cholesterol wrapped by apolipoprotein A-I (apoA-I). However
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Cryo-electron microscopy reveals the impact of the nucleosome dynamics on transcription activity J. Biochem. (IF 2.7) Pub Date : 2024-01-10 Kyohei Arita
The structural biology of nucleosomes and their complexes with chromatin-associated factors contributes to our understanding of fundamental biological processes in the genome. With the advent of cryo-electron microscopy (cryo-EM), several structures are emerging with histone variants, various species, and chromatin-associated proteins that bind to nucleosomes. Cryo-EM enables visualization of the dynamic
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Comparative Analysis of Site-Specific N-glycosylation of LAMP1 from Breast Cancer Tissues J. Biochem. (IF 2.7) Pub Date : 2024-01-10 Shoko Ohashi, Daisuke Takakura, Noritoshi Kobayashi, Motohiko Tokuhisa, Yasushi Ichikawa, Nana Kawasaki
Glycosylation changes in cancer proteins have been associated with malignant transformation. However, techniques for analyzing site-specific glycosylation changes in target proteins obtained from clinical tissue samples are insufficient. To overcome these problems, we developed a targeted N-glycoproteomic approach consisting of immunoprecipitation, glycopeptide enrichment, LC/MS/MS, and structural
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Notch signaling pathway induces expression of type IV collagen in angiogenesis J. Biochem. (IF 2.7) Pub Date : 2024-01-03 Kazuki Kukita, Nanaka Matsuzaka, Mikihisa Takai, Yasutada Imamura, Yongchol Shin
Mural cell adhesion is important for the localization of basement membrane components during angiogenesis, and cell-cell interactions are thought to be critical for basement membrane formation. Type IV collagen, a component of the basement membrane, and non-triple helical type IV collagen α1 chain (NTH α1(IV)) co-localize in the basement membrane of neovascular vessels. However, it remains unclear
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Perturbed collagen metabolism underlies lymphatic recanalization failure in Gata2 heterozygous deficient mice J. Biochem. (IF 2.7) Pub Date : 2024-01-01 Tomomi Watanabe-Asaka, Moyuru Hayashi, Takuya Harada, Satoshi Uemura, Jun Takai, Yasuhiro Nakamura, Takashi Moriguchi, Yoshiko Kawai
Lymphedema has become a global health issue following the growing number of cancer surgeries. Curative or supportive therapeutics have long been awaited for this refractory condition. Transcription factor GATA2 is crucial in lymphatic development and maintenance, as GATA2 haploinsufficient disease often manifests as lymphedema. We recently demonstrated that Gata2 heterozygous deficient mice displayed
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Thermostability optimization of the aspartate/alanine exchange transporter from Tetragenococcus halophilus J. Biochem. (IF 2.7) Pub Date : 2023-12-28 Kota Kunii, Takashi Yamanaka, Akari Miyamoto, Kei Nanatani, Keietsu Abe
Aspartate/alanine exchange transporter (AspT) is a secondary transporter isolated from the lactic acid bacterium Tetragenococcus halophilus D10 strain. This transporter cooperates with aspartate decarboxylase to produce proton-motive force through decarboxylative phosphorylation. A method that successfully analyzes the AspT mechanism could serve as a prototype for elucidating the substrate transport
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DF-Phos: Prediction of Protein Phosphorylation Sites by Deep Forest J. Biochem. (IF 2.7) Pub Date : 2023-12-28 Zeynab Zahiri, Nasser Mehrshad, Maliheh Mehrshad
Phosphorylation is the most important and studied post-translational modification (PTM), which plays a crucial role in protein function studies and experimental design. Many significant studies have been performed to predict phosphorylation sites using various machine-learning methods. Recently, several studies have claimed that deep learning-based methods are the best way to predict the phosphorylation
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Rethinking c-Fos for understanding drug action in the brain J. Biochem. (IF 2.7) Pub Date : 2023-12-28 Katsuyasu Sakurai
Understanding the mechanisms of drug action in the brain, from the genetic to the neural circuit level, is crucial for the development of new agents that act upon the central nervous system. Determining the brain regions and neurons affected by a drug is essential for revealing its mechanism of action in the brain. c-Fos, a marker of neuronal activation, has been widely used to detect neurons activated
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Protein degraders -from thalidomide to new PROTACs J. Biochem. (IF 2.7) Pub Date : 2023-12-23 Takumi Ito
Recently, the development of protein degraders (protein degrading compounds) has prominently progressed. There are two remarkable classes of protein degraders: proteolysis targeting chimeras (PROTACs) and molecular glue degraders (MGDs). Almost 70 years have passed since thalidomide was initially developed as a sedative-hypnotic drug, which is currently recognized as one of the most well-known MGDs
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Endogenous reductase activities for the generation of ribitol-phosphate, a CDP-ribitol precursor, in mammals. J. Biochem. (IF 2.7) Pub Date : 2023-12-23 Shunsuke Hoshino, Hiroshi Manya, Rieko Imae, Kazuhiro Kobayashi, Motoi Kanagawa, Tamao Endo
The core M3 O-mannosyl glycan on α-dystroglycan serves as the binding epitope for extracellular matrix molecules. Defects in core M3 glycans cause congenital muscular dystrophies that are collectively known as dystroglycanopathies. The core M3 glycan contains a tandem D-ribitol-5-phosphate (Rbo5P) structure, which is synthesized by the Rbo5P-transferases fukutin (FKTN) and fukutin-related protein (FKRP)
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Dephosphorylation of NFAT by Calcineurin inhibits Skp2-mediated degradation J. Biochem. (IF 2.7) Pub Date : 2023-11-30 Shunsuke Hanaki, Makoto Habara, Yuki Sato, Haruki Tomiyasu, Yosei Miki, Shusaku Shibutani, Midori Shimada
Summary The transcription factor NFAT plays key roles in multiple biological activities, such as immune responses, tissue development, and malignant transformation. NFAT is dephosphorylated by calcineurin, which is activated by intracellular calcium levels, and translocated into the nucleus, resulting in transcriptional activation. Calcineurin dephosphorylates various target proteins and regulates
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The Incorporation of Extracellular Vesicle Markers Varies Among Vesicles with Distinct Surface Charges. J. Biochem. (IF 2.7) Pub Date : 2023-11-29 Koki Maeda,Simon Goto,Koya Miura,Koki Saito,Eiji Morita
Extracellular vesicles (EVs) are important mediators of intercellular communication. However, the methods available for distinguishing the heterogeneity of secreted EVs and isolating and purifying them are limited. This study introduced a HiBiT-tag to detect various EV markers, including CD63, CD9, Epidermal Growth Factor Receptor (EGFR), Flotilin1, and Syndecan-1, and investigated whether these marker-containing
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Review title: Mechanisms of mitochondrial reorganization J. Biochem. (IF 2.7) Pub Date : 2023-11-29 Tatsuro Maruyama, Yutaro Hama, Nobuo N Noda
Summary The cytoplasm of eukaryotes is dynamically zoned by membrane-bound and membraneless organelles. Cytoplasmic zoning allows various biochemical reactions to take place at the right time and place. Mitochondrion is a membrane-bound organelle that provides a zone for intracellular energy production and metabolism of lipids and iron. A key feature of mitochondria is their high dynamics: mitochondria
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Supercomplex formation of mitochondrial respiratory chain complexes in leukocytes from patients with neurodegenerative diseases. J. Biochem. (IF 2.7) Pub Date : 2023-11-28 Tsukasa Hara,Ryosuke Amagai,Ryuji Sakakibara,Ayako Okado-Matsumoto
With population aging, cognitive impairments and movement disorders due to neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and dementia with Lewy bodies (DLB), are increasingly considered as key social issues. Clinically, it has remained challenging to diagnose them before the onset of symptoms because of difficulty to observe the progressive loss of neurons
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Molecular Mechanism of Autophagy, Cytoplasmic Zoning by Lipid Membranes J. Biochem. (IF 2.7) Pub Date : 2023-11-20 Tetsuya Kotani, Yuri Yasuda, Hitoshi Nakatogawa
Summary Autophagy is a highly conserved intracellular degradation mechanism. The most distinctive feature of autophagy is the formation of double-membrane structures called autophagosomes, which compartmentalize portions of the cytoplasm. The outer membrane of the autophagosome fuses with the vacuolar/lysosomal membrane, leading to the degradation of the contents of the autophagosome. Approximately
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Comparative study of the steady-state subcellular distribution of lysosome-associated membrane glycoprotein-2 (LAMP-2) isoforms with GYXXΦ-type tyrosine-based motifs that interact differently with four adaptor protein (AP) complexes J. Biochem. (IF 2.7) Pub Date : 2023-11-20 Fumiaki Yamaguchi, Hiroshi Sakane, Kenji Akasaki
Summary Lysosome-associated membrane protein-1 and -2 (LAMP-1 and LAMP-2, respectively) are type I transmembrane proteins. LAMP-2 comprises three splice isoforms (LAMP-2A, -B, and-C) with different cytoplasmic tails (CTs). These three CTs possess different tyrosine-based motifs (GYXXΦ, where Φ is a bulky hydrophobic amino acid) at their C-termini. Interactions between tyrosine-based motifs and μ-subunits
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Correction to: Curcumin analog GO-Y030 inhibits tumor metastasis and glycolysis. J. Biochem. (IF 2.7) Pub Date : 2023-11-18
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Cytoplasmic zoning by protein phase transition after membrane permeabilization J. Biochem. (IF 2.7) Pub Date : 2023-11-15 Shinju Sugiyama, Kojiro Suda, Keiko Kono
Summary Biological membranes, including plasma membrane (PM) and organelle membranes, restrict the flux of ions, molecules, and organelles. However, the barrier function of biological membranes is frequently compromised by various perturbations, including physical membrane damage and protein- or chemical-induced pore formation. Recent evidence suggests that, upon PM damage, protein gelation and solid
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The Largest Subunit of Human TFIIIC Complex, TFIIIC220, a Lysine Acetyltransferase Targets Histone H3K18. J. Biochem. (IF 2.7) Pub Date : 2023-11-14 Moumita Basu,Rohini Bhatt,Anjali Sharma,Ramachandran Boopathi,Sadhan Das,Tapas K Kundu
TFIIIC is a multisubunit complex required for tRNA transcription by RNA polymerase III. Human TFIIIC holo-complex possesses lysine acetyltransferase activity which aids in relieving chromatin- mediated repression for RNA polymerase III-mediated transcription and chromatin assembly. Here we have characterized the acetyltransferase activity of the largest and DNA binding subunit of TFIIIC complex, TFIIIC220
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p62 bodies: cytosolic zoning by phase separation J. Biochem. (IF 2.7) Pub Date : 2023-11-10 Reo Kurusu, Hideaki Morishita, Masaaki Komatsu
Summary Cellular zoning or partitioning is critical in preventing macromolecules from random diffusion and in orchestrating the spatiotemporal dynamics of biochemical reactions. Along with membranous organelles, membrane-less organelles contribute to the precise regulation of biochemical reactions inside cells. In response to environmental cues, membrane-less organelles rapidly form through liquid-liquid
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Involvement of cardiac glycosides targeting Na/K-ATPase in their inhibitory effects on c-Myc expression via its transcription, translation, and proteasomal degradation J. Biochem. (IF 2.7) Pub Date : 2023-11-10 Muneshige Tokugawa, Yasumichi Inoue, Hiromasa Aoki, Chiharu Miyajima, Kan'ichiro Ishiuchi, Kento Tsurumi, Chisane Kujirai, Daisuke Morishita, Michiyo Matsuno, Hajime Mizukami, Masaki Ri, Shinsuke Iida, Toshiaki Makino, Mineyoshi Aoyama, Hidetoshi Hayashi
Cardiac glycosides (CGs) have been used for decades to treat heart failure and arrhythmic diseases. Recent non-clinical and epidemiological findings have suggested that CGs exhibit anti-tumor activities. Therefore, CGs may be repositioned as drugs for the treatment of cancer. A detailed understanding of the anticancer mechanisms of CGs is essential for their application to the treatment of targetable
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An oscillating magnetic field suppresses ice-crystal growth during rapid freezing of muscle tissue of mice J. Biochem. (IF 2.7) Pub Date : 2023-11-10 Kana Okuda, Kunitani Kaori, Aiko Kawauchi, Ishii Miyu, Kentaro Yomogida
Regenerative medicine would benefit from a safe and efficient cryopreservation method to prevent the structural disruption caused by ice-crystal formation in cells and tissue. Various attempts have been made to overcome this problem, one of which is the use of an oscillating magnetic field (OMF). However, the underlying mechanism is unclear. In this study, to evaluate the effect of an OMF on ice-crystal
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Identification of effective CCR2 inhibitors for cancer therapy using humanized mice J. Biochem. (IF 2.7) Pub Date : 2023-11-10 Shigeaki Sugiyama, Kanae Yumimoto, Shun Fujinuma, Keiichi I Nakayama
C-C chemokine receptor type 2 (CCR2) is the receptor for C-C motif chemokine 2 (CCL2) and is associated with various inflammatory diseases and cancer metastasis. Although many inhibitors for CCR2 have been developed, it remains unresolved which inhibitors are the most effective in the clinical setting. In the present study, we compared 10 existing human CCR2 antagonists in a calcium influx assay using
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Novel synthetic biological study on intracellular distribution of human GlcNAc-1-phosphotransferase expressed in insect cells J. Biochem. (IF 2.7) Pub Date : 2023-11-10 Kei Kiriyama, Keisuke Fujioka, Kaito Kawai, Teru Mizuno, Yasuo Shinohara, Kohji Itoh
Many lysosomal enzymes contain N-glycans carrying mannose 6-phosphate (M6P) residues. Modifying lysosomal enzymes by M6P residues requires a two-step process in the Golgi apparatus. Then the lysosomal enzymes with M6P residues are transported from the trans-Golgi network to endosomes and lysosomes by M6P receptors. In insect cells, M6P residues are not added to N-glycans. Therefore, many insect lysosomal
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Shaping Transverse-Tubules: Central Mechanisms that Play a Role in the Cytosol Zoning for Muscle Contraction J. Biochem. (IF 2.7) Pub Date : 2023-10-18 Kohei Kawaguchi, Naonobu Fujita
Summary A transverse-tubule (T-tubule) is an invagination of the plasma membrane penetrating deep into muscle cells. An extensive membrane network of T-tubules is crucial for rapid and synchronized signal transmission from the cell surface to the entire sarcoplasmic reticulum for Ca2+ release, leading to muscle contraction. T-tubules are also indispensable for the formation and positioning of other
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Escherichia coli tRNA (Gm18) methyltransferase, TrmH requires the correct localization of its methylation site (G18) in the D-loop for efficient methylation J. Biochem. (IF 2.7) Pub Date : 2023-10-16 Yoh Kohno, Asako Ito, Aya Okamoto, Ryota Yamagami, Akira Hirata, Hiroyuki Hori
TrmH is a eubacterial tRNA methyltransferase responsible for formation of 2’-O-methylguaosine at position 18 (Gm18) in tRNA. In Escherichia coli cells, only 14 tRNA species possess the Gm18 modification. To investigate the substrate tRNA selection mechanism of E. coli TrmH, we performed biochemical and structural studies. E. coli TrmH requires a high concentration of substrate tRNA for efficient methylation
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The Nuclear Cap-Binding Complex, a multitasking binding partner of RNA polymerase II transcripts J. Biochem. (IF 2.7) Pub Date : 2023-10-13 Naoyuki Kataoka
In eukaryotic cells, RNAs transcribed by RNA polymerase-II receives the modification at the 5’ end. This structure is called as the cap structure. The cap structure has a fundamental role for translation initiation by recruiting eukaryotic translation initiation factor 4F(eIF4F). The other important mediator of the cap structure is a nuclear cap binding protein complex (CBC). CBC consists of two proteins
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Access and utilization of host-derived iron by Leishmania parasites J. Biochem. (IF 2.7) Pub Date : 2023-10-13 Yasuyuki Goto, Tatsumi Ito, Souradeepa Ghosh, Budhaditya Mukherjee
Iron is involved in many biochemical processes including oxygen transport, ATP production, DNA synthesis, and antioxidant defense. The importance of iron also applies to Leishmania parasites, an intracellular protozoan pathogen causing leishmaniasis. Leishmania are heme-auxotrophs, devoid of iron storage proteins and the heme synthesis pathway. Acquisition of iron and heme from the surrounding niche
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Degradation of glycosylinositol phosphoceramide during plant tissue homogenization J. Biochem. (IF 2.7) Pub Date : 2023-10-12 Yoshimichi Takai, Rumana Yesmin Hasi, Naoko Matsumoto, Chiho Fujita, Hanif Ali, Junji Hayashi, Ryushi Kawakami, Mutsumi Aihara, Toshiki Ishikawa, Hiroyuki Imai, Mayuko Wakida, Kazuya Ando, Tamotsu Tanaka
Summary A convenient method for the determination of plant sphingolipids (glycosylinositol phosphoceramide, GIPC; glucosylceramide, GluCer; phytoceramide 1-phosphate, PC1P and phytoceramide, PCer) was developed. This method includes the extraction of lipids using 1-butanol, alkali hydrolysis with methylamine and separation by TLC. The amounts of sphingolipids in the sample were determined based on
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PLAAT1 expression triggers fragmentation of mitochondria in an enzyme activity-dependent manner J. Biochem. (IF 2.7) Pub Date : 2023-10-11 Mohammad Mamun Sikder, Toru Uyama, Sumire Sasaki, Katsuhisa Kawai, Nobukazu Araki, Natsuo Ueda
The phospholipase A and acyltransferase (PLAAT) family is a protein family consisting of five members (PLAAT1–5), which acts as phospholipid-metabolizing enzymes with phospholipase A1/A2 and N-acyltransferase activities. Since we previously reported that the overexpression of PLAAT3 in mammalian cells causes the specific disappearance of peroxisomes, in the present study we examined a possible effect
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The SH3 binding site in front of the WH1 domain contributes to the membrane binding of the BAR domain protein endophilin A2 J. Biochem. (IF 2.7) Pub Date : 2023-10-09 Pei Fang Sim, Min Fey Chek, Nhung Thi Hong Nguyen, Tamako Nishimura, Takehiko Inaba, Toshio Hakoshima, Shiro Suetsugu
The Bin-Amphiphysin-Rvs (BAR) domain of endophilin binds to the cell membrane and shapes it into a tubular shape for endocytosis. Endophilin has a Src-homology 3 (SH3) domain at their C-terminal. The SH3 domain interacts with the proline-rich motif (PRM) that is found in proteins such as neural Wiskott-Aldrich syndrome protein (N-WASP). Here, we re-examined the binding sites of the SH3 domain of endophilin
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Characterisation of recombinant photoconverting green fluorescent Akanes J. Biochem. (IF 2.7) Pub Date : 2023-10-05 Mitsuru Jimbo, Mayumi Otake, Haruna Amano, Ko Yasumoto, Shugo Watabe, Daisuke Okada, Hiroshi Kumagai
Summary Akanes are fluorescent proteins that have several fluorescence maxima. In this report, Akane1 and Akane3 from Scleronephthya gracillima were selected, successfully overexpressed in Escherichia coli, and purified by affinity chromatography. Fluorescence spectra of the recombinant Akanes matured in darkness, or ambient light were found to have several fluorescence peaks. SDS-PAGE analysis revealed
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Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis. J. Biochem. (IF 2.7) Pub Date : 2023-10-04 Tomomitsu Hatakeyama,Kazuki Masuda,Mizuki Kudo,Koshi Tanaka,Ayaka Takeuchi,Hideaki Unno
CGL1 is a mannose-specific lectin isolated from the Pacific oyster Crassostrea gigas, and it belongs to the DM9 domain protein family. Each subunit of the CGL1 dimer consists of a tandem repeat of DM9 motifs, which were originally found in the Drosophila melanogaster genome. The CGL1 protomer contains two carbohydrate-binding sites: a high-affinity site A and a low-affinity site B. An assay using dendrimers
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Proline-rich transmembrane protein 2 knock-in mice present dopamine-dependent motor deficits. J. Biochem. (IF 2.7) Pub Date : 2023-10-04 Daisuke Hatta,Kaito Kanamoto,Shiho Makiya,Kaori Watanabe,Tatsuya Kishino,Akira Kinoshita,Koh-Ichiro Yoshiura,Naohiro Kurotaki,Keiro Shirotani,Nobuhisa Iwata
Mutations of proline-rich transmembrane protein 2 (PRRT2) lead to dyskinetic disorders such as paroxysmal kinesigenic dyskinesia (PKD), which is characterized by attacks of involuntary movements precipitated by suddenly initiated motion, and some convulsive disorders. Although previous studies have shown that PKD might be caused by cerebellar dysfunction, PRRT2 has not been sufficiently analyzed in
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Construction of a T7 phage random peptide library by combining seamless cloning with in vitro translation J. Biochem. (IF 2.7) Pub Date : 2023-10-03 Katsuaki Higashi, Sakiho Oda, Mai Fujii, Fumiya Nishida, Hayato Matsumoto, Jyoji Morise, Shogo Oka, Motohiro Nonaka
T7 phage libraries displaying random peptides are powerful tools for screening peptide sequences that bind to various target molecules. The T7 phage system has the advantage of less biased peptide distribution compared to the M13 phage system. However, the construction of T7 phage DNA is challenging due to its long 36 kb linear DNA. Furthermore, the diversity of the libraries depends strongly on the
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Distribution and role of D-glutamate, a novel D-amino acid identified in animals, in the reproductive tissues of male kuruma prawn Marsupenaeus japonicus J. Biochem. (IF 2.7) Pub Date : 2023-10-03 Naoko Yoshikawa, Natsuki Yoshitomi, Kazuki Nakada, Naomi Sawada
Some aquatic invertebrates contain free D-alanine. We previously showed copious amounts of free D-glutamate, a novel D-amino acid, in the tissue of the male reproductive organs of Marsupenaeus japonicus. Herein, we clarified the distribution and potential role of D-glutamate and D-alanine in male reproductive tissues, namely the testis, vas deferens, and seminal receptacle at different growth stages
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Inhibition of human glutathione transferase by catechin and gossypol: comparative structural analysis by kinetic properties, molecular docking and their efficacy on the viability of human MCF-7 cells. J. Biochem. (IF 2.7) Pub Date : 2023-09-29 Rasha Awni Guneidy, Abeer Shokeer, Nevein Salah El-Din Saleh, Eman Ragab Zaki
Glutathione transferase Pi (GSTP1) expression is increased in many cancer types and is associated with multidrug resistance and apoptosis inhibition. Inhibitors of GST P1-1 have the potential to overcome drug resistance and improve chemotherapy efficacy as adjuvant agents. This study investigated the effects of catechin and gossypol on human glutathione transferase Pi (GSTP1-1) activity and their cytotoxic