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Shigeki Kiyonaka, Seiji Sakamoto, Sho Wakayama, Yuma Morikawa, Muneo Tsujikawa, Itaru Hamachi
AMPA-type glutamate receptors (AMPARs) mediate fast excitatory synaptic transmission in the central nervous system. Disregulation of AMPAR function is associated with many kinds of neurological, neurodegenerative and psychiatric disorders. As a result, molecules capable of controlling AMPAR functions are potential therapeutic agents. Fluorescent semisynthetic biosensors have attracted considerable interest for the discovery of ligands selectively acting on target proteins. Given the large protein complex formation of AMPARs in live cells, biosensors using full-length AMPARs retaining original functionality are ideal for drug screening...
February 13, 2018: ACS Chemical Biology
Tsuyoshi Ueda, Tomonori Tamura, Itaru Hamachi
Chemically constructed biosensors consisting of a protein scaffold and an artificial small molecule have recently been recognized as attractive analytical tools for the specific detection and real-time monitoring of various biological substances or events in cells. Conventionally, such semisynthetic biosensors have been prepared in test tubes and then introduced into cells using invasive methods. With the impressive advances seen in bioorthogonal protein conjugation methodologies, however, it is now becoming feasible to directly construct semisynthetic biosensors in living cells, providing unprecedented tools for life-science research...
February 12, 2018: ACS Sensors
Hajime Shigemitsu, Takahiro Fujisaku, Wataru Tanaka, Ryou Kubota, Saori Minami, Kenji Urayama, Itaru Hamachi
In the version of this Article originally published online, in Fig. 4b, in the lower-right image, the value of r was incorrect; it should have read 'r = 0.72'. This has now been corrected in all versions of the Article.
January 29, 2018: Nature Nanotechnology
Hajime Shigemitsu, Takahiro Fujisaku, Wataru Tanaka, Ryou Kubota, Saori Minami, Kenji Urayama, Itaru Hamachi
Novel soft materials should comprise multiple supramolecular nanostructures whose responses (for example, assembly and disassembly) to external stimuli can be controlled independently. Such multicomponent systems are present in living cells and control the formation and break-up of a variety of supramolecular assemblies made of proteins, lipids, DNA and RNA in response to external stimuli; however, artificial counterparts are challenging to make. Here, we present a hybrid hydrogel consisting of a self-sorting double network of nanofibres in which each network responds to an applied external stimulus independent of the other...
February 2018: Nature Nanotechnology
Kazuya Matsuo, Yuki Nishikawa, Marie Masuda, Itaru Hamachi
The development of bioorthogonal approaches for labeling of endogenous proteins under the multimolecular crowding conditions of live cells is highly desirable for the analysis and engineering of proteins without using genetic manipulation. N-Sulfonyl pyridone (SP) is reported as a new reactive group for protein sulfonylation. The ligand-directed SP chemistry was able to modify not only purified proteins in vitro, but also endogenous ones on the surface of and inside live cells selectively and rapidly, which allowed to convert endogenous proteins to FRET-based biosensors in situ...
January 15, 2018: Angewandte Chemie
Kazuma Amaike, Tomonori Tamura, Itaru Hamachi
Endogenous protein labeling is one of the most invaluable methods for studying the bona fide functions of proteins in live cells. However, multi-molecular crowding conditions, such as those that occur in live cells, hamper the highly selective chemical labeling of a protein of interest (POI). We herein describe how the efficient coupling of molecular recognition with a chemical reaction is crucial for selective protein labeling. Recognition-driven protein labeling is carried out by a synthetic labeling reagent containing a protein (recognition) ligand, a reporter tag, and a reactive moiety...
November 14, 2017: Chemical Communications: Chem Comm
Tomonori Tamura, Zhining Song, Kazuma Amaike, Shin Lee, Sifei Yin, Shigeki Kiyonaka, Itaru Hamachi
Catalyst-mediated protein modification is a powerful approach for the imaging and engineering of natural proteins. We have previously developed affinity-guided 4-dimethylaminopyridine (AGD) chemistry as an efficient protein modification method using a catalytic acyl transfer reaction. However, because of the high electrophilicity of the thioester acyl donor molecule, AGD chemistry suffers from nonspecific reactions to proteins other than the target protein in crude biological environments, such as cell lysates, live cells, and tissue samples...
October 11, 2017: Journal of the American Chemical Society
Ales Podgornik, Masataka Hamachi, Yu Isakari, Noriko Yoshimoto, Shuichi Yamamoto
Effect of pore size on the performance of ion-exchange monolith tube chromatography of large biomolecules was investigated. Radial flow 1 mL polymer based monolith tubes of different pore sizes (1.5, 2, and 6 μm) were tested with model samples such as 20 mer poly T-DNA, basic proteins, and acidic proteins (molecular weight 14 000-670 000). Pressure drop, pH transient, the number of binding site, dynamic binding capacity, and peak width were examined. Pressure drop-flow rate curves and dynamic binding capacity values were well correlated with the nominal pore size...
November 2017: Electrophoresis
N Delsuc, S Uchinomiya, A Ojida, I Hamachi
A strategy inspired by tweezer receptors has been employed to develop a new host-guest system. The hybridization into a collagen-like triple helix is the driving force for the recognition that occurs with high affinity and selectivity. Several systems have been screened to find the best host-guest pair and this strategy may be implemented for tag fused protein recognition.
June 22, 2017: Chemical Communications: Chem Comm
Sho Wakayama, Shigeki Kiyonaka, Itaru Arai, Wataru Kakegawa, Shinji Matsuda, Keiji Ibata, Yuri L Nemoto, Akihiro Kusumi, Michisuke Yuzaki, Itaru Hamachi
The location and number of neurotransmitter receptors are dynamically regulated at postsynaptic sites. However, currently available methods for visualizing receptor trafficking require the introduction of genetically engineered receptors into neurons, which can disrupt the normal functioning and processing of the original receptor. Here we report a powerful method for visualizing native α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs) which are essential for cognitive functions without any genetic manipulation...
April 7, 2017: Nature Communications
Akifumi Hamachi, Tomoko Imasaka, Hiroshi Nakamura, Adan Li, Totaro Imasaka
Nerve agent metabolites, i.e., isopropyl methylphosphonic acid (IMPA) and pinacolyl methylphosphonic acid (PMPA), were derivatized by reacting them with 2,3,4,5,6-pentafluorobenzyl bromide (PFBBr) and were determined by mass spectrometry using an ultraviolet femtosecond laser emitting at 267 and 200 nm as the ionization source. The analytes of the derivatized compounds, i.e., IMPA-PFB and PMPA-PFB, contain a large side-chain, and molecular ions are very weak or absent in electron ionization mass spectrometry...
May 2, 2017: Analytical Chemistry
Kei Yamaura, Shigeki Kiyonaka, Itaru Hamachi
Protein-based fluorescent biosensors are powerful tools for quantitative detection of biomolecules or drugs with high sensitivity under physiological conditions. However, conventional methods for construction of biosensors require structural data with high resolution or amino acid sequence information in most cases, which hampers applicability of this method to structurally complicated receptor proteins. To sidestep such limitations, we recently developed a new method that employs ligand-directed chemistry coupled with a bimolecular fluorescence quenching and recovery system, which enabled the conversion of various kinds of membrane-bound receptors to "turn-on" type fluorescent sensors...
2017: Methods in Enzymology
Hajime Shigemitsu, Itaru Hamachi
Stimuli-responsive hydrogels are intriguing biomaterials useful for spatiotemporal controlled release of drugs, cells, and biological cues, cell engineering for various applications, and medical diagnosis. To date, many physical and chemical stimuli-responsive polymer hydrogels have been developed by chemical modification of polymer chains and cross-linking points. In particular, conjugation with biomolecules to polymers produced promising biomolecule-responsive hydrogels. These examples clearly indicate high potentials of stimuli-responsive hydrogels as promising biomaterials...
April 18, 2017: Accounts of Chemical Research
Jirarut Wongkongkatep, Akio Ojida, Itaru Hamachi
The aim of this contribution is to provide an introduction and a brief summary of the principle of fluorescence molecular sensors specific to inorganic phosphate (Pi) and inorganic pyrophosphate (PPi) as well as their applications. In our introduction we describe the impact of both Pi and PPi in the living organism and in the environment, followed by a description of the principle of fluorescence molecular sensors and the sensing mechanism in solution. We then focus on exciting research which has emerged in recent years on the development of fluorescent sensors specific to Pi and PPi, categorized by chemical interactions between the sensor and the target molecule, such as hydrogen bonding, coordination chemistry, displacement assay, aggregation induced emission or quenching, and chemical reactions...
April 2017: Topics in Current Chemistry (Journal)
Takayuki Miki, Masashi Awa, Yuki Nishikawa, Shigeki Kiyonaka, Masaki Wakabayashi, Yasushi Ishihama, Itaru Hamachi
Zinc signaling and dynamics play significant roles in many physiological responses and diseases. To understand the physiological roles of zinc in detail, comprehensive identification of proteins under high concentration of mobile zinc ion is crucial. We developed a 'conditional proteomics' approach to identify proteins involved in zinc homeostasis based on a chemical proteomic strategy that utilizes designer zinc-responsive labeling reagents to tag such proteins and quantitative mass spectrometry for their identification...
November 2016: Nature Methods
Hajime Shigemitsu, Takahiro Fujisaku, Shoji Onogi, Tatsuyuki Yoshii, Masato Ikeda, Itaru Hamachi
Hydrogelators are small, self-assembling molecules that form supramolecular nanofiber networks that exhibit unique dynamic properties. Development of supramolecular hydrogels that degrade in response to various biomolecules could potentially be used for applications in areas such as drug delivery and diagnostics. Here we provide a synthetic procedure for preparing redox-responsive supramolecular hydrogelators that are used to create hydrogels that degrade in response to oxidizing or reducing conditions. The synthesis takes ∼2-4 d, and it can potentially be carried out in parallel to prepare multiple hydrogelator candidates...
September 2016: Nature Protocols
Maria Aurineide Rodrigues, Leonardo Hamachi, Paulo Tamaso Mioto, Eduardo Purgatto, Helenice Mercier
Guzmania monostachia is an epiphytic heteroblastic bromeliad that exhibits rosette leaves forming water-holding tanks at maturity. Different portions along its leaf blades can display variable degrees of crassulacean acid metabolism (CAM) up-regulation under drought. Since abscisic acid (ABA) can act as an important long-distance signal, we conducted a joint investigation of ontogenetic and drought impacts on CAM intensity and ABA levels in different leaf groups within the G. monostachia rosette. For this, three groups of leaves were analysed according to their position within the mature-tank rosette (i...
November 2016: Plant Physiology and Biochemistry: PPB
Kei Yamaura, Shigeki Kiyonaka, Tomohiro Numata, Ryuji Inoue, Itaru Hamachi
The fast inhibitory actions of γ-aminobutyric acid (GABA) are mainly mediated by GABAA receptors (GABAARs) in the brain. The existence of multiple ligand-binding sites and a lack of structural information have hampered the efficient screening of drugs capable of acting on GABAARs. We have developed semisynthetic fluorescent biosensors for orthosteric and allosteric GABAAR ligands on live cells via coupling of affinity-based chemical labeling reagents to a bimolecular fluorescence quenching and recovery system...
October 2016: Nature Chemical Biology
Shoji Onogi, Hajime Shigemitsu, Tatsuyuki Yoshii, Tatsuya Tanida, Masato Ikeda, Ryou Kubota, Itaru Hamachi
Self-sorted supramolecular nanofibres-a multicomponent system that consists of several types of fibre, each composed of distinct building units-play a crucial role in complex, well-organized systems with sophisticated functions, such as living cells. Designing and controlling self-sorting events in synthetic materials and understanding their structures and dynamics in detail are important elements in developing functional artificial systems. Here, we describe the in situ real-time imaging of self-sorted supramolecular nanofibre hydrogels consisting of a peptide gelator and an amphiphilic phosphate...
August 2016: Nature Chemistry
Koichiro Sueyoshi, Yuka Sumi, Yoshiaki Inoue, Yoko Kuroda, Kumiko Ishii, Hitoshi Nakayama, Kazuhisa Iwabuchi, Yasutaka Kurishita, Hajime Shigemitsu, Itaru Hamachi, Hiroshi Tanaka
BACKGROUND: The activation of polymorphonuclear neutrophils (PMNs) plays an important role in sepsis. Previously, we showed that ATP release and feedback via ATP receptors are essential for PMN activation; however, the dynamics remain poorly understood. Two new fluorescent chemosensors, PMAP-1 and MitoAP-1, were developed to detect ATP in the plasma membrane and mitochondria of living cells, respectively. In this study, we aimed to evaluate ATP localization using these chemosensors in PMNs of sepsis patients...
December 2016: Annals of Intensive Care
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