Shinya Tsukiji

Bio: Shinya Tsukiji is an academic researcher from Nagoya Institute of Technology. The author has contributed to research in topics: Medicine & Chemical biology. The author has an hindex of 28, co-authored 73 publications receiving 2570 citations. Previous affiliations of Shinya Tsukiji include Tohoku University & University of Tokyo.

Ligand-directed tosyl chemistry for protein labeling in vivo

Abstract: Here we describe a method for the site-selective attachment of synthetic molecules into specific 'endogenous' proteins in vivo using ligand-directed tosyl (LDT) chemistry. This approach was applied not only for chemically labeling proteins in living cells, tissues and mice but also for constructing a biosensor directly inside cells without genetic engineering. These data establish LDT chemistry as a new tool for the study and manipulation of biological systems.

Sortase‐Mediated Ligation: A Gift from Gram‐Positive Bacteria to Protein Engineering

Abstract: A new enzymatic protein ligation tool, sortase, has recently emerged from Gram-positive bacteria. This article outlines the technique, sortase-mediated ligation, and its applications in protein engineering, which include the introduction of unnatural molecules into proteins, protein immobilization, protein–protein conjugation, protein cyclization, as a self-cleavable tag for protein expression, protein–PNA hybrids, neoglycoconjugates, and cell-surface protein labeling, etc.

Self-assembling nanoprobes that display off/on 19F nuclear magnetic resonance signals for protein detection and imaging.

Abstract: Magnetic resonance imaging (MRI) is one of the most promising techniques for the non-invasive visualization of biomarkers and biologically relevant species, both in vivo and ex vivo. Although (1)H MRI with paramagnetic contrast agents, such as Gd(3+) complexes and iron oxide, is widely used, it often suffers from low contrast because of the large background signals caused by the abundant distribution of protons in biological samples. Here we report the use of supramolecular organic nanoparticles to detect specific proteins by (19)F-based MRI in an off/on mode. In NMR spectroscopy these designed probes are silent when aggregated, but in the presence of a target protein they disassemble to produce a sharp signal. This 'turn-on' response allowed us to visualize clearly the protein within live cells by (19)F MRI and construct an in-cell inhibitor assay. This recognition-driven disassembly of nanoprobes for a turn-on (19)F signal is unprecedented and may extend the use of (19)F MRI for specific protein imaging.

Site-Specific Protein Modification on Living Cells Catalyzed by Sortase

Abstract: The use of enzymes is a promising approach for site-specific protein modification on living cells owing to their substrate specificity. Herein we describe a general strategy for the site-specific modification of cell surface proteins with synthetic molecules by using Sortase, a transpeptidase from Staphylococcus aureus. The short peptide tag LPETGG is genetically introduced to the C terminus of the target protein, expressed on the cell surface. Subsequent addition of Sortase and an N-terminal triglycine-containing probe results in the site-specific labeling of the tagged protein. We were successful in the C-terminal-specific labeling of osteoclast differentiation factor (ODF) with a biotin- or fluorophore-containing short peptide on the living cell surface. The labeling reaction occurred efficiently in serum-containing medium, as well as serum-free medium or PBS. The labeled products were detected after incubation for 5 min. In addition, site-specific protein-protein conjugation was successfully demonstrated on a living cell surface by the Sortase-catalyzed reaction. This strategy provides a powerful tool for cell biology and cell surface engineering.

Target-Specific Chemical Acylation of Lectins by Ligand-Tethered DMAP Catalysts

Abstract: Because sugar-binding proteins, so-called lectins, play important roles in many biological phenomena, the lectin-selective labeling should be useful for investigating biological processes involving lectins as well as providing molecular tools for analysis of saccharides and these derivatives. We describe herein a new strategy for lectin-selective labeling based on an acyl transfer reaction directed by ligand-tethered DMAP (4-dimethylaminopyridine). DMAP is an effective acyl transfer catalyst, which can activate an acyl ester for its transfer to a nucleophilic residue. To direct the acyl transfer reaction to a lectin of interest, we attached the DMAP to a saccharide ligand specific for the target lectin. It was clearly demonstrated by biochemical analyses that the target-selective labeling of Congerin II, an animal lectin having selective affinity for Lactose/LacNAc (N-acetyllactosamine), was achieved in the presence of Lac-tethered DMAPs and acyl donors containing probes such as fluorescent molecules or b...

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

Abstract: The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

Fluorescent probes for super-resolution imaging in living cells

Abstract: Recent advances in fluorescent probe technology have improved spatial and temporal resolution, bringing us closer to the ideal of imaging individual cellular features in real time with molecular (1–5 nm) resolution. In parallel, the development of super-resolution imaging techniques has revolutionized fluorescence microscopy. In 1873, Ernst Abbe discovered that features closer than ∼200 nm cannot be resolved by lens-based light microscopy. In recent years, however, several new far-field super-resolution imaging techniques have broken this diffraction limit, producing, for example, video-rate movies of synaptic vesicles in living neurons with 62 nm spatial resolution. Current research is focused on further improving spatial resolution in an effort to reach the goal of video-rate imaging of live cells with molecular (1–5 nm) resolution. Here, we describe the contributions of fluorescent probes to far-field super-resolution imaging, focusing on fluorescent proteins and organic small-molecule fluorophores. We describe the features of existing super-resolution fluorophores and highlight areas of importance for future research and development.

Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy

Abstract: The review covers the knowledge on photoremovable protecting groups and includes all relevant chromophores studied in the time period of 2000–2012; the most relevant earlier works are also discussed.

Fluorescent chemosensors: The past, present and future

Abstract: Fluorescent chemosensors for ions and neutral analytes have been widely applied in many diverse fields such as biology, physiology, pharmacology, and environmental sciences. The field of fluorescent chemosensors has been in existence for about 150 years. In this time, a large range of fluorescent chemosensors have been established for the detection of biologically and/or environmentally important species. Despite the progress made in this field, several problems and challenges still exist. This tutorial review introduces the history and provides a general overview of the development in the research of fluorescent sensors, often referred to as chemosensors. This will be achieved by highlighting some pioneering and representative works from about 40 groups in the world that have made substantial contributions to this field. The basic principles involved in the design of chemosensors for specific analytes, problems and challenges in the field as well as possible future research directions are covered. The application of chemosensors in various established and emerging biotechnologies, is very bright.