Article
Biochemistry & Molecular Biology
He N. Xu, Sarah Gourmaud, Allison Podsednik, Xiaofan Li, Huaqing Zhao, Frances E. Jensen, Delia M. Talos, Lin Z. Li
Summary: The translation above discusses a study on the decline in NAD levels in brain tissue of Alzheimer's disease models and the use of optical redox imaging to explore new biomarkers for AD. The study found that NADH, Fp, and the redox ratio were associated with AD, and suggested that ORI could be used to conveniently study the metabolism of freshly dissected brain tissues.
Article
Biochemistry & Molecular Biology
Giuseppe Silvestri, Federica Arrigoni, Francesca Persico, Luca Bertini, Giuseppe Zampella, Luca De Gioia, Jacopo Vertemara
Summary: Flavodoxins are enzymes containing the redox-active flavin mononucleotide (FMN) cofactor and their redox characteristics are influenced by the molecular environment of the FMN cofactor. Evaluating the interplay between the redox properties and molecular surroundings of flavodoxins is important for both fundamental research and technological advancements, as it is necessary to tune their electrochemical properties for optimal interaction with redox molecules. This study shows that non-equilibrium thermodynamic integration is a reliable tool for predicting the redox potential of flavodoxins.
Article
Biochemistry & Molecular Biology
Erhan Deniz, Michael Oberle, Kristina Ulrich, Werner Maentele, Georg Wille
Summary: The pyruvate oxidases from Escherichia coli (EcPOX) and Lactobacillus plantarum (LpPOX) are similar in sequence and structure, but differ in their activity pattern. The activation mechanism of EcPOX involves proteolysis of the protein's C-terminal 23 residues, while LpPOX is always highly active. Changes in the infrared (IR) difference spectrum of EcPOX indicate major conformational changes and the involvement of cysteines, but the removal of the alpha-peptide results in a similar IR signature to LpPOX, transforming the catalytically complex EcPOX into the simpler LpPOX.
Review
Biochemistry & Molecular Biology
R. Martin Vabulas
Summary: Ferroptosis is an iron-dependent cell death driven by peroxidation of membrane lipids, and can be utilized as a therapeutic approach to kill tumor cells. Understanding the ferroptosis-controlling protein network, especially the involvement of flavoenzymes, is crucial for clinical applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Florencia Tomasina, Jennyfer Martinez, Ari Zeida, Maria Laura Chiribao, Veronica Demicheli, Agustin Correa, Celia Quijano, Laura Castro, Robert H. Carnahan, Paige Vinson, Matt Goff, Tracy Cooper, W. Hayes McDonald, Natalie Castellana, Luciana Hannibal, Paul T. Morse, Junmei Wan, Maik Huttemann, Ronald Jemmerson, Lucia Piacenza, Rafael Radi
Summary: Cytochrome c (cyt c) undergoes reversible conformational changes under biologically relevant conditions, but revealing these alternative conformations at the cell and tissue level is challenging. This study successfully resurrected a monoclonal antibody (mAb) that recognizes a key conformational change in cyt c and showed similar performance to the original mAb. Using this antibody, alternative conformations of cyt c were identified in cells under oxidative or senescence-induced challenge, and these conformations translocated to the nucleus without causing apoptosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Valentina Rabattoni, Loredano Pollegioni, Gabriella Tedeschi, Elisa Maffioli, Silvia Sacchi
Summary: The study identified different isoforms of hDASPO, with the hDASPO_369 isoform found in the hippocampus of female Alzheimer's disease patients. Stable expression of hDASPO isoforms in human glioblastoma cell clones showed lower expression of hDASPO_369 compared to the canonical isoform. Both isoforms are active, localized to peroxisomes, and degraded primarily through the ubiquitin-proteasome system.
Article
Chemistry, Physical
Jie Yang, Yifei Zhang, Yangyi Lu, Lijuan Wang, Faming Lu, Dongping Zhong
Summary: Short-range protein electron transfer is crucial in light-induced biological processes, and this study demonstrates how the dynamics are coupled with protein fluctuations. Comparison with a different flavodoxin shows the importance of electronic coupling in ET rates.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Allison Podsednik, Jinxia Jiang, Annemarie Jacob, Lin Z. Li, He N. Xu
Summary: The study evaluated the therapeutic responses of triple-negative breast cancer cells under different drug treatments using optical redox imaging, showing the effects of different drugs on cells and their synergistic interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Joerg Matysik, Luca Gerhards, Tobias Theiss, Lisa Timmermann, Patrick Kurle-Tucholski, Guzel Musabirova, Ruonan Qin, Frank Ortmann, Ilia A. Solov'yov, Tanja Gulder
Summary: This review summarizes the phenomenon of nuclear hyperpolarization occurring in chemical reactions, known as CIDNP or photo-CIDNP if driven by light. It occurs in both liquid and solid-state, often involving electron transfer systems with flavins as electron acceptors. The article explains the properties of flavins, their occurrence in spin-correlated radical pairs (SCRPs), and the potential involvement of flavin-carrying SCRPs in animal magneto-reception at Earth's magnetic field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Bo Zhuang, Lipsa Nag, Pierre Sournia, Anastasia Croitoru, Rivo Ramodiharilafy, Jean-Christophe Lambry, Hannu Myllykallio, Alexey Aleksandrov, Ursula Liebl, Marten H. Vos
Summary: Quenching of flavin fluorescence by electron transfer from neighboring aromatic residues plays a significant role in flavoproteins, and can be used as a probe for the active site configuration and dynamics. Modified amino acid residues in variants can lead to changes in the temporal characteristics, indicating heterogeneous configurations of electron donor-acceptor pairs.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Danny Schnerwitzki, R. Martin Vabulas
Summary: Flavoproteins play important roles in various redox pathways in cells. The flavin cofactors FMN and FAD provide the required chemical reactivity to flavoenzymes. The interaction between proteins and flavins is noncovalent and stronger than other redox-active cofactors. The recent discovery of dynamic association between flavins and flavoenzymes challenges the previous static view.
Article
Chemistry, Multidisciplinary
Bo Zhuang, Marten H. Vos
Summary: An unprecedented photoswitching phenomenon of flavin-inhibitor complexes in a flavoenzyme was revealed by femtosecond transient absorption spectroscopy. The results showed that the charge transfer interactions in the complex vanish upon excitation and re-form in a thermally activated way after a few nanoseconds.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biochemistry & Molecular Biology
Alexander Dupuy, Lining Arnold Ju, Joyce Chiu, Freda H. Passam
Summary: This article discusses how mechanical forces and reduction-oxidation reactions (redox) affect the adhesive function of integrins. Recent research has shown that integrins can sense external forces and enhance signaling under shear stress. The oxidation and reduction of integrin disulfide bonds are regulated by ERp5. Future research directions include investigating the coordination of mechanical and redox events between the extracellular and intracellular compartments, as well as the decoupling of mechanical forces and redox in thromboinflammatory conditions.
ANTIOXIDANTS & REDOX SIGNALING
(2022)
Article
Chemistry, Multidisciplinary
Chao-Lai Tong, Xiu-Hua Xu, Feng-Ling Qing
Summary: Efficient heptafluoroisopropoxylation reactions were achieved through the invention of a series of redox-active N-OCF(CF3)(2) reagents. Various substrates can undergo direct heptafluoroisopropoxylation to yield products in moderate to excellent yields.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Applied
Amit Kumar, Rojalin Nayak, Soumya Ranjan Purohit, Pavuluri Srinivasa Rao
Summary: This study investigated the effects of UV radiation on wheat flour proteins, finding significant changes in protein concentration and sulfhydryl content after irradiation, as well as variations in viscosity response based on wheat flour variety and irradiation power. Additionally, analyses using SDS-PAGE and FTIR techniques confirmed modifications in protein primary chain and conformational changes, with UV-C radiation showing potential for altering protein solubility and conformations in flour.
FOOD HYDROCOLLOIDS
(2021)
Article
Chemistry, Physical
Tomohiko Hayashi, Satoshi Yasuda, Kano Suzuki, Tomoki Akiyama, Kanae Kanehara, Keiichi Kojima, Mikio Tanabe, Ryuichi Kato, Toshiya Senda, Yuki Sudo, Takeshi Murata, Masahiro Kinoshita
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Biochemical Research Methods
Ryuichi Kato, Masahiko Hiraki, Yusuke Yamada, Mikio Tanabe, Toshiy Senda
Summary: The PXS system is a fully automated protein crystallization and monitoring system that can automatically set up crystallization plates, transfer, observe, and monitor crystallization drops. As time has passed, user demands have changed, requiring screening with smaller amounts of proteins, and membrane proteins have become a primary target for X-ray crystallography.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Evdokia-Anastasia Giannopoulou, Miki Senda, Maharani Pertiwi Koentjoro, Naruhiko Adachi, Naoto Ogawa, Toshiya Senda
Summary: LTTRs are a large family of transcriptional regulators in bacteria, typically homo-tetrameric proteins that interact with promoter DNA. Studies show that LTTR binding to promoter DNA bends the DNA, and upon inducer binding, the tetrameric LTTR undergoes structural changes leading to transcription activation. The crystal structure of full-length LTTR CbnR in complex with its promoter DNA reveals the mechanism of quaternary structure changes necessary for promoter region-binding.
Article
Entomology
Kotaro Koiwai, Kana Morohashi, Kazue Inaba, Kana Ebihara, Hirotatsu Kojima, Takayoshi Okabe, Ryunosuke Yoshino, Takatsugu Hirokawa, Taiki Nampo, Yuuta Fujikawa, Hideshi Inoue, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa
Summary: The development of IGRs involves elucidating the molecular mechanisms of insect-specific biological events, with insect molting and metamorphosis controlled by ecdysteroids serving as targets for IGR development. The conserved Nobo plays a crucial role in ecdysteroid biosynthesis, and novel non-steroidal DmNobo inhibitors have been identified as potential seed compounds for IGR development. Crystal structure analysis revealed dynamic alterations in amino acid residues upon inhibitor binding, indicating the potential for developing IGRs with greater Nobo inhibitory activity.
JOURNAL OF PESTICIDE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Yohei Katsuyama, Kaoru Sone, Ayaka Harada, Seiji Kawai, Naoki Urano, Naruhiko Adachi, Toshio Moriya, Masato Kawasaki, Kazuo Shin-ya, Toshiya Senda, Yasuo Ohnishi
Summary: The study determined the structure of FmoA3 using X-ray crystallography and cryogenic electron microscopy, revealing the accommodation of alpha-methyl-l-serine in the active site. The Cy domains of FmoA2 and FmoA3 catalyze different reactions, with the Cy domain of FmoA3 potentially losing its donor PCP binding activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biology
Yoshihisa Hirakawa, Miki Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, Masafumi Taira, Kazushi Kinbara, Toshiya Senda
Summary: COG4337 proteins are a novel metal-independent variant of iota-class carbonic anhydrases, which accelerate CO2 hydration and are localized in organelles for CO2 metabolism. They share structural features with iota-class CAs but exhibit activity without reliance on metals.
Article
Biology
Miho Watanabe-Takahashi, Masakazu Tamada, Miki Senda, Masahiro Hibino, Eiko Shimizu, Akiko Okuta, Atsuo Miyazawa, Toshiya Senda, Kiyotaka Nishikawa
Summary: The study identified a tetravalent peptide and a monomeric peptide that can inhibit Shiga toxin (Stx) by targeting its receptor-binding and inhibiting catalytic activity, respectively. These peptides demonstrate potent inhibition of two functionally distinct subunits of Stx, providing a potential intervention for the pathogenic mechanism of enterohemorrhagic Escherichia coli.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Takamasa Teramoto, Takeshi Koyasu, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Tomoyuki Numata, Toshiya Senda, Yoshimitsu Kakuta
Summary: The study of Aquifex RNase P homologs showed that Aq880 enzyme consists of nuclease and protruding helical domains, forming dimers and dodecamers. The cryo-EM structure revealed that Aq880's active site is similar to eukaryotic PRORPs, and its mechanism for processing pre-tRNA resembles that of PRORPs and ribonucleoprotein RNase P.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Naruhiko Adachi, Takahide Yamaguchi, Toshio Moriya, Masato Kawasaki, Kotaro Koiwai, Akira Shinoda, Yusuke Yamada, Fumiaki Yumoto, Takamitsu Kohzuma, Toshiya Senda
Summary: Cu-containing nitrite reductases play central roles in denitrification, but structural analysis of their catalytic mechanisms has been impeded by issues such as crystal packing and photoreduction. Cryo-EM structures of Achromobacter cycloclastes NiR at different pH values were obtained, revealing structural changes and crystallographic artifacts in certain residues. The combination of X-ray and cryo-EM structures provides deeper insight into local structural changes of proteins, despite challenges in estimating coordinate errors in cryo-EM structures.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Cagdas Dag, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, Hasan DeMirci
Summary: The oligomerization of Pr55(Gag) is a critical step in the late stage of the HIV life cycle, with the binding of IP6 at the MA domain playing a key role. The crystal structures of the MA domain in complex with IP6 molecules provide insights into the binding mode, while analysis of key residues and interactions with PIP2 reveal a multilayered assembly process involving coordination between IP6 and PIP2 for membrane localization of virion particles. Additionally, a new model is proposed based on the structures, suggesting that IP6 coordinates the oligomerization of MA and CA domains during assembly and budding.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Natsuki Osaka, Yoshihisa Hirota, Doshun Ito, Yoshiki Ikeda, Ryo Kamata, Yuki Fujii, Venkat R. Chirasani, Sharon L. Campbell, Koh Takeuchi, Toshiya Senda, Atsuo T. Sasaki
Summary: The article provides an overview of post-translational modifications in the RAS G4 and G5 motifs, highlighting their role in RAS activation and potential applications in cancer therapy.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Takuto Kumano, Sanae Hori, Satomi Watanabe, Yuzu Terashita, Hong Yang Yu, Yoshiteru Hashimoto, Toshiya Senda, Miki Senda, Michihiko Kobayashi
Summary: The study identified an enzyme named CarA that plays a crucial role in carminic acid metabolism by oxidizing the sugar moiety. Homologs of CarA were found to be widely distributed in soil microorganisms and important for C-glycoside metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Takahiro Mori, Takuto Kumano, Haibing He, Satomi Watanabe, Miki Senda, Toshio Moriya, Naruhiko Adachi, Sanae Hori, Yuzu Terashita, Masato Kawasaki, Yoshiteru Hashimoto, Takayoshi Awakawa, Toshiya Senda, Ikuro Abe, Michihiko Kobayashi
Summary: Through bioinformatics analysis, researchers identified C-glycoside deglycosidase enzymes in intestinal and soil bacteria, characterized them biochemically, determined their structures, and probed catalytic important residues in mutagenesis experiments. These metal-dependent enzymes exhibit broad substrate specificity toward C-glycosides.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Takuo Minato, Takamasa Teramoto, Naruhiko Adachi, Nguyen Khac Hung, Kaho Yamada, Masato Kawasaki, Masato Akutsu, Toshio Moriya, Toshiya Senda, Seiji Ogo, Yoshimitsu Kakuta, Ki-Seok Yoon
Summary: Takuo Minato and colleagues have identified both a conventional hexameric structure and a novel octameric structure in native C-phycocyanin (CPC) from the thermophilic cyanobacterium Thermoleptolyngbya sp. O77. The observation of an unusual dimeric state via analytical ultracentrifugation suggests a key intermediate structure in the assembly of octameric CPC. These findings offer new insights into the assembly processes of CPCs and the mechanism of energy transfer in light-harvesting complexes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Takuya Miyakawa, Jian Yang, Masato Kawasaki, Naruhiko Adachi, Ayumu Fujii, Yumiko Miyauchi, Tomonari Muramatsu, Toshio Moriya, Toshiya Senda, Masaru Tanokura
Summary: This study solves the cryo-EM structures of CphA1 and reveals the aspartate binding mode and protein dynamics required for cyanophycin elongation. The research also suggests a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.
NATURE COMMUNICATIONS
(2022)
