Article
Chemistry, Analytical
John G. Pavek, Brian L. Frey, Dustin C. Frost, Ting-Jia Gu, Lingjun Li, Lloyd M. Smith
Summary: Top-down proteomics is a method for characterizing intact proteoforms in complex mixtures, but it may compromise the depth of proteoform coverage on liquid chromatography time scales. We propose a strategy that combines intact mass determination with cysteine count to identify proteoforms in tissue samples.
ANALYTICAL CHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Ilaria Porello, Francesco Cellesi
Summary: Achieving effective delivery of therapeutic proteins to intracellular targets is crucial for advancing human health. Current methods, such as chemical modification and nanocarrier-based approaches, have limitations in efficiency and safety. Developing more versatile delivery tools that trigger endocytosis or directly deliver proteins to the cytosol is essential for successful therapeutic effects. This article provides an overview of current methods for intracellular protein delivery, highlighting challenges and opportunities for future research.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Takaaki Miyamoto, Kousuke Tsuchiya, Keiji Numata
Summary: A strategy utilizing endosome-escaping micelles with dual peptide modification has been developed for efficient intracellular DNA delivery to plants, overcoming vacuolar degradation and enhancing transfection efficiency with minimal cytotoxicity, which could facilitate diverse biotechnological applications in plant bioengineering.
Review
Biochemistry & Molecular Biology
Justin M. Horn, Allie C. Obermeyer
Summary: Protein-based therapeutics are a rapidly growing field in disease treatment, and successful intracellular delivery is crucial for expanding their applications. Various methods for modifying proteins and peptides have been developed to improve their cellular translocation efficiency. General strategies such as chemical supercharging or inclusion of cell-penetrating motifs can facilitate intracellular delivery of proteins.
Review
Engineering, Chemical
Ikuhiko Nakase
Summary: Researchers found that inducing macropinocytosis through modification with biofunctional peptides on exosomal membranes enhances the cellular uptake of exosomes. Arginine-rich cell-penetrating peptides and EGFR activation have been shown to induce macropinocytosis, providing insights for the development of new strategies for exosomes.
Article
Chemistry, Multidisciplinary
Yan Zhao, Haolin Jiang, Jiazhen Yu, Luyao Wang, Juanjuan Du
Summary: Currently, the clinical application of protein/peptide therapeutics is limited to the extracellular spaces, mainly due to the endosomal entrapment of internalized proteins/peptides. This study presents a strategy to design peptides that enable the delivery from endosomes to cytosol by extending the histidine switch principle. By replacing the Arg/Lys residues in cationic cell-penetrating peptides (CPPs) with histidine, the researchers obtained peptides with pH-dependent membrane-perturbation activity, mimicking the endosomal escape of CPPs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Lei Ding, Guangyu Rong, Yiyun Cheng
Summary: Fluorous tagged peptides have shown promising features for biomedical applications such as drug delivery and multimodal imaging. The bioconjugation of fluoroalkyl ligands onto cargo peptides greatly enhances their proteolytic stability and membrane penetration via a proposed fluorine effect. The tagged peptides also efficiently deliver other biomolecules such as DNA and siRNA into cells via a co-assembly strategy.
MACROMOLECULAR BIOSCIENCE
(2023)
Review
Pharmacology & Pharmacy
Shalvi Sinai Kunde, Ritushree Ghosh, Sarika Wairkar
Summary: In comparison with small molecular drugs, the use of biopharmaceuticals as therapeutics has gained popularity due to their higher specificity, selectivity and potency, as well as fewer side effects. The pulmonary route has been investigated as a potential noninvasive method for delivering biopharmaceuticals, offering higher drug concentrations and greater bioavailability than other noninvasive routes. This review focuses on the delivery of various biopharmaceuticals, including peptides, recombinant proteins, enzymes, monoclonal antibodies, and nucleic acids, via the pulmonary route, discussing their advantages and disadvantages.
DRUG DISCOVERY TODAY
(2022)
Article
Pharmacology & Pharmacy
Bareera Qamar, Melani Solomon, Alexander Marin, Thomas R. Fuerst, Alexander K. Andrianov, Silvia Muro
Summary: Achieving intracellular delivery of protein therapeutics is a significant challenge. This study investigated the use of ionic polyphosphazenes to deliver protein cargo intracellularly, finding that PZ-PYR showed faster internalization and higher uptake levels in endothelial cells compared to PZ-PEG, although both polymers achieved similar uptake levels in cancer cells. Uptake was mediated by endocytosis through multiple mechanisms.
Article
Multidisciplinary Sciences
Siyuan Yu, Han Yang, Tingdong Li, Haifeng Pan, Shuling Ren, Guoxing Luo, Jinlu Jiang, Linqi Yu, Binbing Chen, Yali Zhang, Shaojuan Wang, Rui Tian, Tianying Zhang, Shiyin Zhang, Yixin Chen, Quan Yuan, Shengxiang Ge, Jun Zhang, Ningshao Xia
Summary: The authors present an intracellular protein delivery system that overcomes the limitations of ineffective endosomal escape and low serum tolerance associated with cell-penetrating peptide-mediated protein delivery. This system shows efficient delivery and therapeutic efficacy in a liver failure model, highlighting the potential of using multifunctional chimaeric peptides for developing cell-penetrating peptide-based protein delivery systems.
NATURE COMMUNICATIONS
(2021)
Review
Instruments & Instrumentation
Marwa Hasanein Asfour
Summary: Proteins and peptides have great potential as therapeutic agents with higher efficiency and lower toxicity, but face challenges in oral bioavailability and transdermal delivery. Recent advancements in drug delivery systems include aquasomes and microneedles, which aim to enhance stability and efficacy of protein and peptide drugs.
DRUG DELIVERY AND TRANSLATIONAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Diana Valeria Rossetti, Ilaria Inserra, Alessia Nestico, Federica Vincenzoni, Federica Iavarone, Irene Messana, Massimo Castagnola, Luca Massimi, Gianpiero Tamburrini, Massimo Caldarelli, Claudia Desiderio
Summary: The study aimed to explore the intact proteome of pediatric brain tumors of different WHO grades and localizations to understand the molecular mechanisms underlying the onset and progression of these pathologies. Proteomic analysis revealed statistically significant differences in protein/peptide levels between tumor histotypes, as well as the identification of naturally occurring fragments and post-translational modifications. This study contributes to elucidating the molecular profiles of the most common solid tumors affecting children.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Jiaying Song, Christina Cortez-Jugo, Steven J. Shirbin, Zhixing Lin, Shuaijun Pan, Greg G. Qiao, Frank Caruso
Summary: This study introduces two template-mediated strategies for immobilizing SNAPPs in microcapsules, achieving sustained release and high antimicrobial activity, internalization by alveolar macrophages in vitro, with negligible cytotoxicity and potential application in pulmonary delivery of antimicrobials against respiratory bacterial infections.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Rui Zhang, Yuyan Yang, Chao He, Xin Zhang, Vincenzo Torraca, Shen Wang, Nan Liu, Jiaren Yang, Shicheng Liu, Jinglei Yuan, Dongzhi Gou, Shi Li, Xueying Dong, Yufei Xie, Junling He, Hua Bai, Mengyu Hu, Zhiquan Liao, Yuan Huang, Hao Lyu, Shuai Xiao, Dong Guo, Declan William Ali, Marek Michalak, Cong Ma, Xing-Zhen Chen, Jingfeng Tang, Cefan Zhou
Summary: RUNDC1 negatively regulates autophagy by inhibiting the assembly of the ATG14-STX17-SNAP29-VAMP8 complex, which hinders autophagosome fusion with lysosomes.
CELL DEATH AND DIFFERENTIATION
(2023)
Review
Pharmacology & Pharmacy
Sarah Le Saux, Anne Aubert-Pouessel, Khaled Elhady Mohamed, Pierre Martineau, Laurence Guglielmi, Jean-Marie Devoisselle, Philippe Legrand, Joel Chopineau, Marie Morille
Summary: Protein therapeutics offer higher specificity and lower toxicity compared to chemicals, with potential for broad application. Delivery systems are necessary for maximizing their biological potential, and extracellular vesicles (EVs) as natural protein nanocarriers show great promise.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Yan Zhao, Zihong Wu, Lei Chen, Xiong Shu, Juan Guan, Kang Yang, Ruya Shi, Yibin Li, Keiji Numata, Zhengzhong Shao
Summary: Natural fiber-reinforced biocomposites with excellent mechanical and biological properties have attractive prospects for internal medical devices. However, poor interfacial adhesion between natural silk fiber and the polymer matrix has been a disturbing issue for such applications. In this study, rigid-flexible agents, such as polydopamine (PDA) and epoxy soybean oil (ESO), were introduced to enhance the interfacial adhesion between Antheraea pernyi (Ap) silk and polycaprolactone (PCL). The Ap-PDA-ESO strategy exhibited a greater enhancement in interfacial adhesion, and proposed interfacial toughening mechanisms.
Article
Plant Sciences
Kazuya Ishikawa, Makoto Kobayashi, Miyako Kusano, Keiji Numata, Yutaka Kodama
Summary: By using the organelle glue technique, we manipulated organelle interactions and controlled the plant metabolome at the pathway level. This study demonstrates the potential for designing plants with desirable metabolic activities by artificially controlling organelle interactions through genetic modification.
PLANT CELL REPORTS
(2023)
Article
Multidisciplinary Sciences
Tomoto Ura, Ako Kagawa, Nanako Sakakibara, Hiromasa Yagi, Naoya Tochio, Takanori Kigawa, Kentaro Shiraki, Tsutomu Mikawa
Summary: The assembly state of enzymes is an important mechanism for regulating enzyme function in living cells. In this study, the activation of L-lactate oxidase (LOX) was demonstrated through the formation of enzyme assemblies. LOX formed nanometer-scale clusters with poly-L-lysine (PLL), which further aggregated into micrometer-scale liquid droplets. The enzyme activities of LOX in clusters and droplets were significantly higher than those in the dispersed state, and the clusters exhibited a higher activation effect than the droplets. Understanding enzyme activation and assembly states is crucial for understanding enzyme function and biotechnology applications.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Nur Alia Oktaviani, Ali D. Malay, Akimasa Matsugami, Fumiaki Hayashi, Keiji Numata
Summary: Spider dragline silk, composed of spidroins MaSp1 and MaSp2, is an incredibly tough biomaterial. The N-terminal domains (NTDs) of spidroins undergo rapid dimerization in response to a pH gradient during fiber self-assembly. In this study, the solution structures of MaSp1 and MaSp2 NTDs from Trichonephila clavipes were determined, and the experimental pKa values of conserved residues involved in dimerization were measured using NMR. The unusual pKa values of specific residues, such as Asp40, Glu119, and Glu79, contribute to the tight spatiotemporal control of spider silk self-assembly.
Article
Biochemistry & Molecular Biology
Naoto Yoshinaga, Ayaka Tateishi, Yasuaki Kobayashi, Tomohiro Kubo, Hitoshi Miyakawa, Kotaro Satoh, Keiji Numata
Summary: Biodegradable polymers are eco-friendly materials that do not accumulate in the environment, making them attractive for use in a sustainable society. However, the chemical toxicities of their degradation products have not been well assessed. This study evaluated the toxic effects of biodegradable polyester, polycaprolactone (PCL), and synthetic oligocaprolactones (OCLs) with different polymerization degrees. The results showed that while PCL did not have adverse effects on organisms, high concentrations of shorter OCLs and the monomer had toxic effects on freshwater microorganisms, marine algae, and mammalian cells. This highlights the importance of understanding the effects of degradation products for ensuring a genuinely sustainable society.
Article
Biochemistry & Molecular Biology
Hiroyuki Nakamura, Nobuaki Kono, Masaru Mori, Hiroyasu Masunaga, Keiji Numata, Kazuharu Arakawa
Summary: This study compares the mechanical properties and water resistance of spider's minor ampullate silk (MI-silk) and major ampullate silk (MA-silk), revealing the unique properties and water resistance of MI-silk. Proteomic analysis shows that MI-silk is composed of minor ampullate spidroin (MiSp), major ampullate spidroin (MaSp1), and spidroin constituting elements (SpiCEs). The absence of MaSp2 in the MI-silk proteome explains the difference in water resistance between MI-silk and MA-silk.
Review
Biochemistry & Molecular Biology
Risa Naka, Kousuke Tsuchiya, Keiji Numata
Summary: Zwitterionic molecules, such as ZILs and ZIPs, can loosen cell wall networks and enhance the penetration of nanocarriers, increasing their transfection efficiency in targeted subcellular organelles in plants.
Article
Polymer Science
Kousuke Tsuchiya, Joan Gimenez-Dejoz, Keiji Numata
Summary: This study investigated the process of cationic peptides condensing plasmid DNA through atomic MD simulations. It was found that the peptides bind to the DNA and induce defects, leading to the folding of the DNA into a globule morphology. These findings provide insight into the mechanism of peptide-mediated gene delivery systems.
Article
Multidisciplinary Sciences
Kazuya Ishikawa, Xiaonan Xie, Yasuhide Osaki, Atsushi Miyawaki, Keiji Numata, Yutaka Kodama
Summary: Plants are able to produce bilirubin in chloroplasts through a nonenzymatic reaction, which helps maintain the redox status in chloroplasts.
Article
Chemistry, Multidisciplinary
Masaomi Ikari, Hiromasa Yagi, Takuma Kasai, Kohsuke Inomata, Masahiro Ito, Kae Higuchi, Natsuko Matsuda, Yutaka Ito, Takanori Kigawa
Summary: In this study, in-cell NMR spectroscopy combined with site-specific F-19 labeling was used to investigate the membrane-associated states of H-Ras in living cells. The results revealed that H-Ras exhibits multiple conformational states on the cellular membrane. This study provides valuable insights into the control mechanism of H-Ras.
Article
Chemistry, Multidisciplinary
Simon Sau Yin Law, Masato Asanuma, Jingwen Shou, Yasuyuki Ozeki, Yutaka Kodama, Keiji Numata
Summary: Plants can respond to various stresses by activating multiple signaling and defense pathways. The use of bioorthogonal probes allows for real-time visualization and quantification of these pathways, which has practical applications in characterizing plant responses to stress.
Article
Biochemistry & Molecular Biology
Naoya Abe, Seiya Fujita, Takaaki Miyamoto, Kousuke Tsuchiya, Keiji Numata
Summary: Plant mitochondria are crucial for metabolism and respiration. Mitochondrial transformation has gained interest for developing crops with valuable traits. In this study, a peptide-based carrier called Cytcox/KAibA-Mic was developed for efficient transfection into plant mitochondria. The modification rates of mitochondrial targeting and cell membrane-penetrating peptides were quantified and controlled. The gene carrier size remained constant despite changes in the mitochondrial targeting peptide modification rate. This gene carrier allows for quantitative investigation of peptide modifications and optimization of conditions for mitochondrial transfection.
Article
Materials Science, Biomaterials
Chonprakun Thagun, Tomohiro Suzuki, Yutaka Kodama, Keiji Numata
Summary: A plant cell-based expression platform was developed to produce complete MaSp2 protein, which self-assembles into spider silk nanofibrils. Overexpression of recombinant secretory MaSp2 proteins in transgenic BY-2 cell lines yielded 0.6-1.3 μg L-1 at 22 days, four times higher than cytosolic expressions. Expression of functional domain-truncated MaSp2 proteins lacking the C-terminal domain increased recombinant protein secretion from 0.9 to 2.8 mg L-1 per day within 7 days. These findings demonstrate significant improvement in extracellular production of spider silk spidroins using plant cells and reveal the regulatory roles of the MaSp2 C-terminal domain.
Review
Chemistry, Multidisciplinary
Simon Sau Yin Law, Takaaki Miyamoto, Keiji Numata
Summary: Genetic engineering has revolutionized agriculture and the use of nanomaterials has further enhanced the benefits. Subcellular targeting using nanomaterials has become possible but remains challenging despite its promise in organellar engineering.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biology
Siti Amalia Aisyah Abdul Halim, Muzzalifah Abd Hamid, Izwandy Idris, Ahmad Sofiman Othman, Siti Azizah Mohd Nor
Summary: The taxonomic diversity of penaeid shrimps from the northwest coast of Peninsular Malaysia was investigated using morphometric and molecular approaches. Geometric morphometrics (GM) and mitochondrial COI gene sequences were used to analyze the morphological and phylogenetic differences among species. The results showed that closely related species tend to cluster together based on morphological variations. Molecular phylogeny analysis indicated significant phylogenetic signals and evolutionary significance for the examined species. In conclusion, the combination of morphometric and molecular analyses provides valuable insights into the taxonomic diversity and evolutionary history of penaeid shrimps.