Article
Biology
Matthew D'lorio, Ken Dewar
Summary: The structural arrangements of bacterial chromosomes vary widely between closely related species and can result in significant phenotypic outcomes. This study identifies replication-associated structural rearrangements (RASRs) in bacteria and investigates their locations and potential biological mechanisms. The findings suggest that large-scale chromosomal inversions, often symmetric relative to markers for the origin of replication, can occur through repairing breaks formed during the replication process.
LIFE SCIENCE ALLIANCE
(2022)
Review
Microbiology
Erwin C. Stuffle, Mark S. Johnson, Kylie J. Watts
Summary: PAS domains are versatile domains found in proteins across different kingdoms, with a conserved cleft for cofactor or ligand binding. Recent years have seen a significant increase in identified PAS domains and corresponding structures, leading to a better understanding of PAS signaling mechanisms. New bacterial PAS ligands have been discovered, expanding the list of bacterial PAS functions beyond signal sensing to include modulation, transduction, dimerization, protein interaction, and cellular localization.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biology
Peiyi Ye, Xia Li, Binbin Cui, Shihao Song, Fangfang Shen, Xiayu Chen, Gerun Wang, Xiaofan Zhou, Yinyue Deng
Summary: PutA functions not only in proline metabolism, but also as a global regulator in controlling the biological functions and virulence of Ralstonia solanacearum. It regulates target gene expression levels by directly binding to promoter DNA, and its activity is enhanced by L-proline. The cofactors NAD(+) and FAD have contrasting effects, enhancing the enzymatic activity of PutA while inhibiting its regulatory activity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Applied
Tao Zhan, Xiao-Zhen Feng, Yun-Yun Cheng, Guo-Cheng Han, Zhencheng Chen, Heinz-Bernhard Kraatz
Summary: We developed a facile sensor by conjugating heme with gold nanoparticles on a glass carbon electrode for the ultrasensitive detection of biotin. This sensor exhibits a broad detection range and a low detection limit. The mechanism of biotin electrooxidation was elucidated through electrochemical analyses and calculations. The sensor shows excellent selectivity, reproducibility, and stability, making it suitable for practical applications.
Article
Biochemistry & Molecular Biology
Jose Antonio Gavira, Miguel A. Matilla, Matilde Fernandez, Tino Krell
Summary: The PcaY_PP chemoreceptor from Pseudomonas putida KT2440 has an unusually broad signal range, forming a four-helix bundle structure in the ligand binding domain, and interacts with high-affinity ligands through an extensive hydrogen bonding network.
Article
Engineering, Mechanical
Sahil Bansal, Sai Hung Cheung
Summary: This study proposes an optimal Bayesian sensor placement approach for updating linear structural models, involving two stages of identifying modal parameters and updating model parameters, selecting the sensor configuration that maximizes the expected information gain.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2022)
Article
Biochemistry & Molecular Biology
Jakub Vavra, Artur Sergunin, Petr Pompach, Dariya Savchenko, Jakub Hranicek, Ivana Sloufova, Toru Shimizu, Marketa Martinkova
Summary: The interaction between p53 and heme was thoroughly investigated in this study, focusing on the oxidation, spin, coordination, and ligand state of heme iron. The results showed that p53 oligomeric state and zinc binding ability remained unchanged upon heme binding. The conformational dynamics of p53 were significantly affected by heme, leading to increased flexibility and reduced affinity to a specific DNA sequence. The inhibitory effect of heme on DNA binding was found to be partially reversible. Potential heme binding sites in p53 were discussed in relation to the observed conformational changes and perturbed DNA binding ability.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Malgorzata Figiel, Filip Szubert, Enrico Luchinat, Piotr Bonarek, Anna Baranowska, Katarzyna Wajda-Nikiel, Mateusz Wilamowski, Piotr Milek, Marta Dziedzicka-Wasylewska, Lucia Banci, Andrzej Gorecki
Summary: Human protein Yin Yang 1 (YY1) controls transcription of multiple genes through interactions with partner proteins. This study shows that purified YY1 forms dimers via its disordered N-terminal region with zinc-ion concentration dependence, and the YY1 dimer binds DNA sequences with high affinity. These findings suggest that zinc ion concentration can affect YY1 gene regulation and may have implications for pathogenic processes.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Materials Science, Paper & Wood
Raymond Leopold Heydorn, David Lammers, Martina Gottschling, Katrin Dohnt
Summary: The advances in bioprocess design, genetic engineering, and media optimization have enabled enhanced bacterial cellulose (BC) production and its application for diverse purposes. Numerous approaches were conducted to investigate alternative carbon or nitrogen sources from industrial by-products for BC biosynthesis, which not only affect the BC production but also its properties. This study highlights beneficial effects of food industry by-products for BC biosynthesis and elucidates concomitantly occurring structural polymer alterations to enable further studies dealing with alternative substrates for structurally tailored BC production.
Article
Multidisciplinary Sciences
Rudra Mohan Pradhan, Anand Singh, Arun Kumar Ojha, Tapas Kumar Biswal
Summary: This study investigates the bedrock weathering and groundwater storage in crystalline basement rock terrains by integrating high-resolution subsurface resistivity images with important geological structures. The results show that the presence of foliations, fractures, and faults influence the depth of the weathered zone and groundwater storage. Additionally, the study examines the impact of paleostress and different tectonic structures on the depth of the Critical Zone, highlighting the global applicability of the approach presented in mapping bedrock weathering and groundwater resources.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Kenichi Kitanishi
Summary: Hemerythrin is an oxygen-binding protein found in marine invertebrates, and recent studies have revealed its role as an oxygen and redox sensor in bacteria, regulating cellular physiological processes in response to changes in oxygen concentration and redox status.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Sebastien Alphonse, Imane Djemil, Andrea Piserchio, Ranajeet Ghose
Summary: Bacterial tyrosine kinases (BY-kinases) and their counteracting phosphatases regulate bacterial synthesis and export processes. The structure of the complex between the BY-kinase Wzc and phosphatase Wzb has been determined, providing a mechanistic understanding of the phosphorylation-coupled assembly/disassembly process involved in BY-kinase function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Mingyue Hao, Minghui Wang, Danyu Zhao, Yong Shi, Ye Yuan, Junmei Li, Yunyi Zhai, Xiaofang Liu, Dong Zhou, Huatao Chen, Pengfei Lin, Keqiong Tang, Wei Liu, Yaping Jin, Aihua Wang
Summary: This study found that the alr gene in Brucella suis S2 influences the strain's phenotypic features and triggers the mitochondrial apoptosis pathway during host cell invasion. Deletion of the alr gene resulted in a mutant strain with an unaltered phenotype in acriflavine agglutination tests but lacking the core polysaccharide portion of lipopolysaccharide (LPS). Additionally, the alr deletion strain exhibited reduced intracellular viability and virulence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Applied
Mengshi Xiao, Xinmiao Ren, Jiaying Cheng, Xiaodan Fu, Rong Li, Changliang Zhu, Qing Kong, Haijin Mou
Summary: A fucosylated trisaccharide (GFG) was separated and characterized from exopolysaccharides of Clavibacter michiganensis M1, with glucose, galactose, and fucose as its monosaccharide composition. GFG showed different structure and prebiotic effects compared to 2'-fucosyllactose (2'-FL). GFG could be utilized by more beneficial bacteria and produce more short-chain fatty acids, while it did not promote the growth of Escherichia coli. This study provides a novel fucosylated oligosaccharide as a potential candidate for fucosylated human milk oligosaccharides.
Article
Chemistry, Applied
Tatiya Siripongpreda, Benjawan Somchob, Nadnudda Rodthongkum, Voravee P. Hoven
Summary: The deposition of negatively charged polyelectrolyte CMC within a BC matrix resulted in a re-swellable and biocompatible hydrogel, preserving the original BC's physical and mechanical properties. The BC/CMC-based sensors showed promising features for colorimetric pH sensing and glucose detection, with low detection limits, wide linear detection ranges, and high accuracy, potentially allowing for non-invasive semi-quantitative on-skin health monitoring.
CARBOHYDRATE POLYMERS
(2021)
Article
Oncology
Genta Furuya, Hiroto Katoh, Shinichiro Atsumi, Itaru Hashimoto, Daisuke Komura, Ryo Hatanaka, Shogo Senga, Shuto Hayashi, Shoji Akita, Hirofumi Matsumura, Akihiro Miura, Hideaki Mita, Makoto Nakakido, Satoru Nagatoishi, Akira Sugiyama, Ryohei Suzuki, Hiroki Konishi, Asami Yamamoto, Hiroyuki Abe, Nobuyoshi Hiraoka, Kazunori Aoki, Yasumasa Kato, Yasuyuki Seto, Chihoko Yoshimura, Kazutaka Miyadera, Kouhei Tsumoto, Tetsuo Ushiku, Shumpei Ishikawa
Summary: This study systematically investigates the characteristics of humoral antigens in human cancers and reveals their relationship with intratumor immune reactions. The study finds that these tumor clones have a strong selectivity for negatively charged polymers. Additionally, the study demonstrates a new therapeutic approach using antibody-drug conjugates targeting cell surface antigens for the treatment of multiple cancers.
Article
Chemistry, Multidisciplinary
Kazuto Suzuki, Joshua Kyle Stanfield, Keita Omura, Yuma Shisaka, Shinya Ariyasu, Chie Kasai, Yuichiro Aiba, Hiroshi Sugimoto, Osami Shoji
Summary: Catching the structure of cytochrome P450 enzymes in flagrante is crucial for the development of P450 biocatalysts. We report the crystal structure of P450BM3 mimicking the state in the precise moment preceding epoxidation, which is in perfect agreement with the experimentally observed stereoselectivity. This method serves as a powerful tool for predicting and modelling the stereoselectivity of P450 reactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Hanae Takeda, Kanji Shimba, Masaki Horitani, Tetsunari Kimura, Minoru Kubo, Takashi Nomura, Takehiko Tosha, Yoshitsugu Shiro
Summary: This study demonstrates the trapping of short-lived reaction intermediates of metalloenzymes through the photolysis of a caged compound under cryogenic temperature followed by thermal annealing. This technique is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Atsunori Hirao, Satoru Nagatoishi, Emina Ikeuchi, Tsukushi Yamawaki, Chinatsu Mori, Makoto Nakakido, Kouhei Tsumoto
Summary: Single-domain antibodies, or VHH, nanobodies, are promising tools in biotechnology and pharmaceuticals due to their favorable biophysical properties. In this paper, a generic design strategy of single-domain antibodies for efficient immobilization on a sensing substrate is proposed. The strategy includes mutating the lysine near the antigen binding site, adding a Lys-tag to the C-terminus, and mutating a residue away from the antigen binding site to lysine.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yui Tomioka, Ryo Sato, Ryo Takahashi, Satoru Nagatoishi, Kohei Shiba, Kouhei Tsumoto, Tsutomu Arakawa, Teruo Akuta
Summary: The effects of salting-in and salting-out salts on the solution state of bovine serum albumin (BSA) were examined using gel electrophoresis and mass photometry. Salting-in salts MgCl2, CaCl2, and NaSCN resulted in intermediate structures of BSA upon heating, while salting-out salts NaCl and (NH4)2SO4 resulted in smearing and aggregated bands. Surprisingly, salting-out salt MgSO4 also showed a similar effect. Aggregation-suppressive ArgHCl also showed oligomer aggregates.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yuki Hishikawa, Hiroki Noya, Satoru Nagatoishi, Takashi Yoshidome, Basudev Maity, Kouhei Tsumoto, Satoshi Abe, Takafumi Ueno
Summary: This study investigates the impact of aromatic clusters on protein stability by studying designed aromatic interactions within a protein cage. The results show that inter-subunit phenylalanine clusters enhance interhelix interactions and increase melting temperature. Theoretical calculations suggest that this is due to a transformation from T-shaped geometry to pi-pi stacking and hydration entropic gain at high temperatures. The isolated nanoenvironment within a protein cage allows for detailed analysis of multiple clustering residues, providing insights into biomolecular interactions and potential applications in bionanomaterial design.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Yusui Sato, Satoru Nagatoishi, Shintaro Noguchi, Kouhei Tsumoto
Summary: Antibody drugs in highly-concentrated solutions often form aggregates, leading to loss of efficacy. The physical properties of antibodies at low pH under high concentration conditions are important to understand. Raman spectroscopy was used to investigate the conformational changes of antibodies, and results were validated by colloidal analyses.
PHARMACEUTICAL RESEARCH
(2023)
Article
Chemistry, Physical
Shinya Ariyasu, Kai Yonemura, Chie Kasai, Yuichiro Aiba, Hiroki Onoda, Yuma Shisaka, Hiroshi Sugimoto, Takehiko Tosha, Minoru Kubo, Takashi Kamachi, Kazunari Yoshizawa, Osami Shoji
Summary: This study reports the catalytic oxidation of methane to methanol by wild-type P450BM3 without mutagenesis. The findings have significant implications for the development of biological methane oxidation technology.
Article
Biochemical Research Methods
Satoru Nagatoishi, Toshinobu Toyoshima, Kotohiro Furukawa, Kouhei Tsumoto
Summary: This study introduces a new method called Pinched-Flow Fractionation (PFF)-Coulter for the quantitative analysis of submicron-sized particles. The method combines PFF and Coulter techniques to separate and detect particles, allowing for more accurate particle analysis.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Shunyi Li, Daisuke Murakami, Satoru Nagatoishi, Yiwei Liu, Kouhei Tsumoto, Yoshiki Katayama, Takeshi Mori
Summary: In this work, mannan-coated protein nanoparticles incorporating antigen proteins were successfully prepared by a one-pot method. The nanoparticles showed the ability for antigen-specific tolerance induction and targeted dendritic cells. The incorporation of rapamycin enhanced the induction of a tolerogenic phenotype. The results suggest that these mannan-coated nanoparticles have potential for effective and safe allergy treatment.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Correction
Biology
Rini H. Pek, Xiaojing Yuan, Nicole Rietzschel, Jianbing Zhang, Laurie Jackson, Eiji Nishibori, Ana Ribeiro, William Simmons, Jaya Jagadeesh, Iqbal Hamza
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
Chemistry, Physical
Hanae Takeda, Kanji Shimba, Masaki Horitani, Tetsunari Kimura, Takashi Nomura, Minoru Kubo, Yoshitsugu Shiro, Takehiko Tosha
Summary: The characterization of short-lived reaction intermediates is crucial for understanding the mechanism of metalloenzyme-catalyzed reactions. In this study, we demonstrated that the photolysis of a caged compound followed by thermal annealing is an effective technique for trapping short-lived reaction intermediates of metalloenzymes. By applying this technique to the study of membrane-integrated nitric oxide reductase (NOR), we were able to trap and characterize the intermediate species involved in the reductive coupling of NO molecules by NOR at its heme/nonheme FeB binuclear center.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Engineering, Biomedical
Shunyi Li, Hiroki Toriumi, Daisuke Takahashi, Tomoko Kamasaki, Yoichiro Fujioka, Satoru Nagatoishi, Jinting Li, Yiwei Liu, Takanatsu Hosokawa, Kouhei Tsumoto, Yusuke Ohba, Yoshiki Katayama, Daisuke Murakami, Koji Hase, Takeshi Mori
Summary: Allergen immunotherapy (AIT) is the only curative treatment for allergic diseases, but it has limitations. In this study, we developed a new approach using MAN-coated ovalbumin (OVA) nanoparticles (MDO) to target dendritic cells (DCs) more effectively and promote higher antigen presentation efficiency. The results showed that DCs exposed to MDO induced Treg cells and MDO had low reactivity and high safety. In a mouse model of allergic asthma, MDO had significant preventative and therapeutic effects.
