Article
Chemistry, Multidisciplinary
Ji Liu, Jinhan Sheng, Leihou Shao, Qizhen Zheng, Wenting Li, Xianghan Chen, Lanqun Mao, Ming Wang
Summary: Hierarchical self-assembly of TPE-featured metal-organic cages and beta-cyclodextrin-conjugated polyethylenimine generates fluorescent supramolecular nanoparticles (FSNPs) for efficient protein delivery into neural cells, allowing rapid release into the cytosol for subcellular targeting. Delivery of molecular chaperone DJ-1 using FSNPs activates MAPK/ERK signaling in neural cells to protect cells from oxidative stress.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Colman Moore, Yong Cheng, Natalia Tjokro, Brendan Zhang, Matthew Kerr, Mohammed Hayati, Kai Chiao Joe Chang, Nisarg Shah, Casey Chen, Jesse Jokerst
Summary: We report a dual-modal fluorescent and photoacoustic imaging probe for the detection of gingipain proteases secreted by P. gingivalis. The probe showed significant photoacoustic enhancement and fluorescence activation, with low detection limits. It demonstrated good diagnostic efficacy in porcine jaws and gingival crevicular fluid samples from periodontal disease subjects. Additionally, photoacoustic imaging of the probe was achieved in murine brains ex vivo.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Naoya Kawakami, Hiroki Sato, Naohiro Terasaka, Kunio Matsumoto, Hiroaki Suga
Summary: The researchers have developed a ubiquitin-based protein ligand multimer, called U-bodies, as a surrogate agonist for the MET receptor. These U-body constructs have high binding affinity, thermal stability, and proteolytic stability. By assembling them into dimeric, tetrameric, and octameric structures, potent MET activation and cell proliferation-promoting activities are achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Hanrui Liu, Toni A. Baeumler, Kai Nakamura, Yuga Okada, Seojung Cho, Akihiro Eguchi, Daisuke Kuroda, Kouhei Tsumoto, Ryosuke Ueki, Shinsuke Sando
Summary: Cell membrane receptors play a crucial role in regulating cellular responses by detecting and transducing extracellular signals. Receptor engineering allows for directing cells to respond to specific external cues and perform programmed functions. This study introduces an aptamer-based signal transduction system that enables control and customization of engineered receptor functions.
Review
Chemistry, Multidisciplinary
Seungheon Lee, Shivudu Godhulayyagari, Shadler T. Nguyen, Jasmine K. Lu, Sasha B. Ebrahimi, Devleena Samanta
Summary: The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Cell Biology
Sophie Lev, Bethany Bowring, Desmarini Desmarini, Julianne Teresa Djordjevic
Summary: This review provides an overview of the regulation of cellular processes by IPs and PP-IPs in eukaryotes, highlighting their interactions with specific protein targets. Technological advances in genetics have expanded studies to microbial pathogens, showing the significant impact of disrupting PP-IP biosynthesis and PP-IP-protein interactions on pathogenicity. The study also reveals instances of poor conservation in the outcomes of IP-protein interactions despite the presence of conserved IP-binding domains in eukaryotic proteomes.
CELLULAR MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Weibo Wang, Qingpeng Wei, Jiayuan Zhang, Meiqi Zhang, Chuchen Wang, Renyu Qu, Yuan Wang, Guangfu Yang, Jing Wang
Summary: This study developed a genetically encoded fluorescent sensor for ratiometric quantification of LCACoAs in living cells, demonstrating conformational changes of LCACoA molecules and real-time monitoring. The research also revealed the impact of disruptions in ACSL enzymes and ACBP genes on the levels and distribution of LCACoAs in cytosol and mitochondria.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Kevin Ritter, Nikolaus Jork, Anne-Sophie Unmuessig, Maja Koehn, Henning J. J. Jessen
Summary: Inositol phosphates, a family of highly charged messenger molecules, have diverse functions in cellular processes. The phosphorylation patterns result in a vast array of compounds. This study presents a method using NMR measurements for enantiomer assignment, enabling the differentiation of enantiomers. The method was applied to various inositol phosphates and will aid in the assignment of biologically relevant isomers.
Article
Biochemistry & Molecular Biology
Myunghwan Ahn, Seung Eun Park, Jiyeon Choi, Jiahn Choi, Doyoung Choi, Dongju An, Hayoung Jeon, Soowhan Oh, Kiho Lee, Jaehoon Kim, Jaebong Jang, Seyun Kim, Youngjoo Byun
Summary: This study designed, synthesized, and evaluated flavonoid-based compounds as new inhibitors of IP6K2. Compound 20s was identified as the most potent inhibitor, being 5-fold more potent than the reported flavonoid-based IP6K2 inhibitor quercetin.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Iain C. Clark, Bruk Mensa, Christopher J. Ochs, Nathan W. Schmidt, Marco Mravic, Francisco J. Quintana, William F. DeGrado, Adam R. Abate
Summary: Using a hybrid valve- and droplet-based microfluidic system, a combinatorial DNA library encoding an engineered histidine kinase based on bacterial CpxA was successfully constructed. Surprising results were found, such as the different effects on catalytic activity caused by the combinations of the S helix and TM domain. It was concluded that the intervening HAMP domain passively transmits signals and shapes the signaling response depending on subtle changes in neighboring domains, leading to a richness in functional outputs as HKs vary in response to changing evolutionary pressures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Vera S. Ovechkina, Suren M. Zakian, Sergey P. Medvedev, Kamila R. Valetdinova
Summary: Genetically encoded fluorescent biosensors allow visualization of biological processes in real time, providing benefits such as monitoring drug action and screening at the single-cell resolution. Research aims to improve biomedical applications by exploring their potential and addressing challenges.
Article
Chemistry, Multidisciplinary
Xue Tian, Lloyd C. Murfin, Luling Wu, Simon E. Lewis, Tony D. James
Summary: Small-molecule based fluorescent probes play an increasingly important role in detecting and imaging biological signaling molecules due to their simplicity, high selectivity, and real-time analysis capabilities. Various sensing mechanisms, including FRET, ICT, PeT, ESIPT, AIE, as well as dual/triple sensing mechanisms, are highlighted, but challenges remain. Future development should focus on improving small-molecule fluorescent probes for biosensing applications.
Review
Chemistry, Physical
Heejung Kim, Jihye Seong
Summary: This article introduces the importance of autophagy, its relevance to diseases, and research methods, with a focus on the design principles and potential applications of fluorescent protein-based autophagy biosensors.
Article
Biochemical Research Methods
Simon d'Oelsnitz, Vylan Nguyen, Hal S. Alper, Andrew D. Ellington
Summary: Prokaryotic transcription factors have been repurposed as analytical and synthetic tools for precise chemical measurement and regulation. In this study, genetically encoded, generalist monoterpene biosensors were developed by using directed evolution to expand the effector specificity of the camphor-responsive TetR-family regulator CamR. These biosensors can recognize four distinct monoterpenes and have a high signal-to-noise ratio. They can serve as a starting point for the high-throughput screening and dynamic regulation of bicyclic monoterpene production strains.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
John James Mackrill
Summary: It is conventionally believed that myo-D-inositol 1, 4,5-trisphosphate (IP3) exerts its second messenger effects through IP3R Ca2+ release channels. However, there is evidence suggesting that IP3 may interact with other proteins within cells. A search of the Protein Data Bank revealed 35 structures capable of interacting with IP3, including enzymes, signal transducers, ion channels, and growth factors. Exploring the interaction between IP3 and these proteins may provide further insights into IP3 signaling and its impact on cell biology.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Laura Marongiu, Francesca Mingozzi, Clara Cigni, Roberta Marzi, Marco Di Gioia, Massimiliano Garre, Dario Parazzoli, Laura Sironi, Maddalena Collini, Reiko Sakaguchi, Takashi Morii, Mariacristina Crosti, Monica Moro, Stephane Schurmans, Tiziano Catelani, Rany Rotem, Miriam Colombo, Stephen Shears, Davide Prosperi, Ivan Zanoni, Francesca Granucci
Summary: Recognition of LPS by DCs involves the receptor complex CD14 and TLR4, and subsequent Ca2+ mobilization and NFAT activation require IP3R3 and ITPKB. Targeting ITPKB may offer a promising approach for anti-inflammatory therapies aimed at inhibiting specific DC functions.
Article
Biochemistry & Molecular Biology
Arivazhagan Rajendran, Kirankumar Krishnamurthy, Amulya Giridasappa, Eiji Nakata, Takashi Morii
Summary: The low thermal stability of DNA nanostructures hinders their practical applications, but enzymatic ligation of staple strands can improve their stability at higher temperatures. The optimization of ligation conditions, including higher T4 DNA ligase concentration and overnight incubation at 37 degrees C, can lead to more efficient ligation and increased thermal stability in DNA origami structures. Additionally, ligation affects the structure and flexibility of DNA origami, influencing their overall stability and response to chemical intercalation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Arivazhagan Rajendran, Kirankumar Krishnamurthy, Seojeong Park, Eiji Nakata, Youngjoo Kwon, Takashi Morii
Summary: DNA minicircles are important for studying DNA-protein interactions, and their topological features play a significant role in these interactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Editorial Material
Chemistry, Multidisciplinary
Arivazhagan Rajendran, Kirankumar Krishnamurthy, Seojeong Park, Eiji Nakata, Youngjoo Kwon, Takashi Morii
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Zhengxiao Zhang, Eiji Nakata, Yuya Shibano, Takashi Morii
Summary: Fluorescent cathepsin probes were prepared by modifying peptidic substrates and applying fluorophores and quenchers, enabling simultaneous monitoring of CTSB and CTSD activity. Conjugation of the probes with short single-stranded DNA significantly improved their reactivity, possibly by enhancing solubility.
Article
Endocrinology & Metabolism
Shunsuke Kato, Izumi Otaka, Hanako Toyama, Ryota Kusumi, Kazuyuki Takahashi, Mitsuhiko Nara, Yumi Suganuma, Takehiro Sato, Tsukasa Morii, Hiroki Fujita, Hironori Waki
Summary: HbA1c, commonly used to estimate average blood glucose levels, may not be accurately measured due to factors such as red blood cell lifespan and hemoglobin variants. Two cases of extremely high blood glucose levels were reported, where HbA1c levels were unmeasurable due to increased labile HbA1c levels. This study highlights the importance of considering the effect of extreme hyperglycemia on HbA1c measurements, regardless of the absolute HbA1c level.
DIABETOLOGY INTERNATIONAL
(2022)
Editorial Material
Biochemistry & Molecular Biology
Eiji Nakata, Khongorzul Gerelbaatar, Futa Komatsubara, Takashi Morii
Summary: Fluorescence imaging is a powerful technique for observing dynamic intracellular processes of living cells, and ratiometric fluorescent probes offer advantages over intensity-changing probes. Minimizing extracellular background fluorescence is important in probe design to avoid obscuring intracellular signals.
Review
Biochemistry & Molecular Biology
Peng Lin, Hui Yang, Eiji Nakata, Takashi Morii
Summary: Cells have developed intelligent systems to implement complex and efficient enzyme cascade reactions through organelles, bacterial microcompartments, and enzyme complexes. This review surveys the reactions of a single type of enzyme on the DNA scaffold and discusses the catalytic enhancement mechanisms. It also reviews the progress of enzyme cascade reactions on the DNA scaffold and discusses the factors that enhance the efficiency of these reactions.
Article
Chemistry, Multidisciplinary
Peng Lin, Huyen Dinh, Yuki Morita, Eiji Nakata, Takashi Morii
Summary: Reconfigurable DNA nanostructures can mimic the close spatial arrangement of cascade enzymes within cells, enhancing the efficiency of cascade reactions.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Hiroaki Konishi, Eiji Nakata, Futa Komatsubara, Takashi Morii
Summary: Cellular compartmentalization is crucial for organizing biochemical reactions, but synthesizing compartments to encapsulate materials with precise control remains challenging. This study evaluated a liposome-encapsulated compartment with potential to locate and control materials of interest. A nanoliposome was constructed inside a ring-shaped DNA skeleton, equipped with a double-stranded DNA platform to isolate molecules from the outer environment.
Article
Chemistry, Multidisciplinary
Eiji Nakata, Khongorzul Gerelbaatar, Mashal Asif, Hiroaki Konishi, Yuya Shibano, Peng Lin, Takashi Morii
Summary: In this study, a ratiometric fluorescent pH probe with a wide pH detection range was successfully constructed by assembling three types of fluorophores with different fluorescence properties on a DNA origami nanostructure.
CHEMISTRY-SWITZERLAND
(2023)
Article
Chemistry, Multidisciplinary
Shunsuke Tajima, Eiji Nakata, Reiko Sakaguchi, Masayuki Saimura, Yasuo Mori, Takashi Morii
Summary: In this study, a two-step screening strategy, including in silico and in vitro screening, was used to select AFP-based biosensors with enhanced signal responses for application in mammalian cells.
Article
Chemistry, Multidisciplinary
Peng Lin, Huyen Dinh, Eiji Nakata, Takashi Morii
Summary: This study found that in a dual-enzyme cascade reaction derived from the xylose metabolic pathway, the downstream enzyme with a larger catalytic constant outweighed the importance of inter-enzyme distance in determining cascade efficiency.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Eiji Nakata, Hisaaki Hirose, Khongorzul Gerelbaatar, Jan Vincent V. Arafiles, Zhengxiao Zhang, Shiroh Futaki, Takashi Morii
Summary: Real-time monitoring of cellular environment, such as intracellular pH, in a defined cellular space provides a comprehensive understanding of dynamic processes in living cells. By assembling multiple fluorophores within a space smaller than the spatial resolution of conventional microscopy, a flexible combinatorial design strategy for developing fluorescent probes is enabled. Assembling fluorescein (CF) and tetramethylrhodamine (CR) on a DNA nanostructure with controlled numbers of each fluorophore type allows for controlled fluorescence emission intensity and ratiometric pH monitoring within the defined space.
Article
Chemistry, Multidisciplinary
Peng Lin, Huyen Dinh, Yuki Morita, Zhengxiao Zhang, Eiji Nakata, Masahiro Kinoshita, Takashi Morii
Summary: The study shows that the highly negative charges on the DNA nanostructures can enhance the catalytic activity of the enzymes loaded onto them, but the local pH shift near the DNA scaffold surface may not play a general role in this enhancement.
CHEMICAL COMMUNICATIONS
(2021)
