349 results on '"Michio Murata"'
Search Results
2. LnDOTA ‐d 8 , a versatile chemical‐shift thermometer for 2 H solid‐state NMR
- Author
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Yuichi Umegawa, Takeshi Shimonishi, Hiroshi Tsuchikawa, and Michio Murata
- Subjects
General Materials Science ,General Chemistry - Published
- 2022
3. A New Pathway for CO2 Reduction Relying on the Self-Activation Mechanism of Boron-Doped Diamond Cathode
- Author
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Jinglun Du, Andrea Fiorani, Taichi Inagaki, Atsushi Otake, Michio Murata, Miho Hatanaka, and Yasuaki Einaga
- Published
- 2022
4. Dynamic assembly and interaction of glycosphingolipids in cholesterol-containing model membranes
- Author
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Shinya Hanashima, Mikito Nakano, and Michio Murata
- Subjects
General Chemical Engineering ,General Chemistry - Abstract
Glycosphingolipids (GSLs) in the mammalian plasma membrane are essential for various biological events that occur on cell membranes by forming glycolipid-rich membrane domains, such as lipid rafts. Lactosylceramide (LacCer) forms a highly ordered phase in model and biological membranes. However, the details of this domain remain unclear. We examined the dynamic assembly of LacCer in cholesterol-containing phase-separated membranes by fluorescence imaging and solid-state NMR. Solid-state 2H NMR of the deuterated LacCer probes in the membranes indicated that the potent LacCer–LacCer interaction significantly reduced the incorporation of cholesterol in the LacCer domains. Moreover, increasing the amount of cholesterol induced the formation of nanometer-scale LacCer domains, which can be biologically relevant. The lateral interaction of ganglioside GM3 with the epidermal growth factor receptor (EGFR) transmembrane segment was examined using fluorescence spectroscopy under membrane conditions. Lateral FRET between the NBD fluorophore on the EGFR transmembrane segment and the ATTO594 fluorophore on the GM3 head group suggested that GM3 interacts with the transmembrane segment and partially inhibits the EGFR dimerization by stabilizing the peptide monomer. More precise investigations of GSL–GSL and GSL-protein interactions occurring in membrane environments can lead to the elucidation of the cellular functions of GSL from structural points of view.
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- 2023
5. Depth-Dependent Segmental Melting of the Sphingomyelin Alkyl Chain in Lipid Bilayers
- Author
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Hiroshi Tsuchikawa, Mami Monji, Yuichi Umegawa, Tomokazu Yasuda, J. Peter Slotte, and Michio Murata
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Membrane Microdomains ,Calorimetry, Differential Scanning ,Lipid Bilayers ,Phosphatidylcholines ,Temperature ,Electrochemistry ,General Materials Science ,Surfaces and Interfaces ,Deuterium ,Condensed Matter Physics ,Spectroscopy ,Sphingomyelins - Abstract
The chain melting of lipid bilayers has often been investigated in detail using calorimetric methods, such as differential scanning calorimetry (DSC), and the resultant main transition temperature is regarded as one of the most important parameters in model membrane experiments. However, it is not always clear whether the hydrocarbon chains of lipids are gradually melting along the depth of the lipid bilayer or whether they all melt concurrently in a very narrow temperature range, as implied by DSC. In this study, we focused on stearoyl-d-sphingomyelin (SSM) as an example of raft-forming lipids. We synthesized deuterium-labeled SSMs at the 4', 10', and 16' positions, and their depth-dependent melting was measured using solid-state deuterium NMR by changing the temperature by 1.0 °C, and comparing with that observed from a saturated lipid, palmitoylstearoylphosphatidylcholine (PSPC). The results showed that SSM exhibited a characteristic depth-dependent melting, which was not observed for PSPC. The strong intermolecular hydrogen bonds between the sphingomyelin amide moiety probably caused the chain melting to start from the chain terminus through the middle part and end in the upper part. This depth-dependent melting implies that the small gel-like domains of SSM remain at temperatures slightly above the main transition temperature. These sphingomyelin features may be responsible for the biological properties of SM-based lipid rafts.
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- 2022
6. Effect of cholesterol on the lactosylceramide domains in phospholipid bilayers
- Author
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Shinya Hanashima, Ryuji Ikeda, Yuki Matsubara, Tomokazu Yasuda, Hiroshi Tsuchikawa, J. Peter Slotte, and Michio Murata
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Cholesterol ,Antigens, CD ,Lipid Bilayers ,Lactosylceramides ,Phosphatidylcholines ,Biophysics ,Articles ,Phospholipids - Abstract
Lactosylceramide (LacCer) in the plasma membranes of immune cells is an important lipid for signaling in innate immunity through the formation of LacCer-rich domains together with cholesterol (Cho). However, the properties of the LacCer domains formed in multicomponent membranes remain unclear. In this study, we examined the properties of the LacCer domains formed in Cho-containing 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) membranes by deuterium solid-state NMR and fluorescence lifetimes. The potent affinity of LacCer-LacCer (homophilic interaction) is known to induce a thermally stable gel phase in the unitary LacCer bilayer. In LacCer/Cho binary membranes, Cho gradually destabilized the LacCer gel phase to form the liquid-ordered phase by its potent order effect. In the LacCer/POPC binary systems without Cho, the (2)H NMR spectra of 10′,10′-d(2)-LacCer and 18′,18′,18′-d(3)-LacCer probes revealed that LacCer was poorly miscible with POPC in the membranes and formed stable gel phases without being distributed in the liquid crystalline domain. The lamellar structure of the LacCer/POPC membrane was gradually disrupted at around 60°C, whereas the addition of Cho increased the thermal stability of the lamellarity. Furthermore, the area of the LacCer gel phase and its chain order were decreased in the LacCer/POPC/Cho ternary membranes, whereas the liquid-ordered domain, which was observed in the LacCer/Cho binary membrane, was not observed. Cho surrounding the LacCer gel domain liberated LacCer and facilitated forming the submicron to nano-scale small domains in the liquid crystalline domain of the LacCer/POPC/Cho membranes, as revealed by the fluorescence lifetimes of trans-parinaric acid and trans-parinaric acid-LacCer. Our findings on the membrane properties of the LacCer domains, particularly in the presence of Cho, would help elucidate the properties of the LacCer domains in biological membranes.
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- 2022
7. Simultaneous electrochemical detection of ozone and free chlorine with a boron-doped diamond electrode
- Author
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Zhen Peng, null Irkham, Kazumi Akai, Michio Murata, Mai Tomisaki, and Yasuaki Einaga
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Ozone ,Electrochemistry ,Environmental Chemistry ,Chlorine ,Electrodes ,Oxidation-Reduction ,Biochemistry ,Spectroscopy ,Boron ,Analytical Chemistry - Abstract
O3 and free chlorine play significant roles in disinfection and organic degradation.
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- 2022
8. Lipid chain-driven interaction of a lipidated Src-family kinase Lyn with the bilayer membrane
- Author
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Shinya Hanashima, Kanako Mito, Yuichi Umegawa, Michio Murata, and Hironobu Hojo
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src-Family Kinases ,Cell Membrane ,Lipid Bilayers ,Organic Chemistry ,Physical and Theoretical Chemistry ,Peptides ,Biochemistry ,Phospholipids - Abstract
S-Palmitoyl and N-myristoyl chains of Lyn cooperatively facilitate binding to the anionic lipids in membranes by extending the hydrocarbon chains deeper into the membrane interior.
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- 2022
9. Urine Protein Quantification in Human Urine on Boron-Doped Diamond Electrodes Based on Electrochemical Reaction of Coomassie Brilliant Blue
- Author
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Hiroshi Aoki, Risa MIYAZAKI, Miho OHAMA, Michio MURATA, Kai ASAI, Genki OGATA, and Yasuaki EINAGA
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- 2023
10. Molecular Dynamics of Glycolipids in Liposomes
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Tomokazu Yasuda, J. Peter Slotte, Michio Murata, and Shinya Hanashima
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- 2023
11. Molecular Dynamics of Glycolipids in Liposomes
- Author
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Tomokazu, Yasuda, J Peter, Slotte, Michio, Murata, and Shinya, Hanashima
- Abstract
Glycosphingolipids (GSLs) in the mammalian plasma membrane are essential for various biological events as they form glycolipid-rich membrane domains, such as lipid rafts. GSLs consist of a certain oligosaccharide head group and a ceramide tail with various lengths of acyl chains. The structure of the head group as well as the carbon number and degree of the unsaturation of the acyl chain are known to regulate the membrane distributions and interleaflet couplings of GSLs by altering physicochemical properties, such as dynamics, interactions, and cluster sizes. This chapter provides the detailed use of time-resolved fluorescence measurement for investigating the membrane properties of lactosylceramide (LacCer)-enriched domains in bilayer membranes. LacCer belongs to the neutral GSLs and is believed in forming a highly ordered phase in model membranes and biological membranes, while the details of the domain remain unclear. Here, we suggest using trans-parinaric acid (tPA) and tPA-LacCer fluorescent probes to reveal the dynamics and size of the GSL domains since they prefer to be distributed in the GSL-rich ordered phase. The fluorescence lifetime in the nanosecond timescale reveals the difference in the surrounding membrane environments, which relates to hydrocarbon chain ordering, membrane hydration, and submicrometer domain size. The fluorescence lifetime of these probes can thus provide important information on submicron- to nano-scale small GSL domains not only in model membranes but also in biological membranes.
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- 2022
12. Boron-Doped Diamond as a Quasi-Reference Electrode
- Author
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Zhen Peng, Andrea Fiorani, Kazumi Akai, Michio Murata, Atsushi Otake, and Yasuaki Einaga
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Electrochemical Techniques ,Diamond ,Electrodes ,Analytical Chemistry ,Boron ,Hydrogen - Abstract
As a working electrode, boron-doped diamond (BDD) has been studied in detail in electrochemical processes because of its superior electrochemical properties. However, these characteristics have rarely been mentioned when BDD is used as a quasi-reference electrode (QRE). Herein, we conducted a systematic investigation on BDD electrodes, with different boron-doping levels (1 and 0.1%) and different surface terminations (hydrogen and oxygen) for their application as a QRE. A BDD electrode with 1% boron and a hydrogen-terminated surface achieved the best stability. Its open-circuit potential (OCP) exhibited less than 100 mV of potential drift over 6000 s and showed a minuscule half-wave potential difference (
- Published
- 2022
13. Author response for 'LnDOTA ‐d 8 , a versatile chemical‐shift thermometer for 2 H solid‐state NMR'
- Author
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null Yuichi Umegawa, null Tsuyoshi Shimonishi, null Hiroshi Tsuchikawa, and null Michio Murata
- Published
- 2022
14. LnDOTA-d
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Yuichi, Umegawa, Takeshi, Shimonishi, Hiroshi, Tsuchikawa, and Michio, Murata
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Membrane Lipids ,Magnetic Resonance Spectroscopy ,Thermometers ,Lipid Bilayers ,Temperature ,Ligands - Published
- 2022
15. Effect of the number of sugar units on the interaction between diosgenyl saponin and membrane lipids
- Author
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Joan Candice Ondevilla, Shinya Hanashima, Akane Mukogawa, Darcy Garza Miyazato, Yuichi Umegawa, and Michio Murata
- Subjects
Biophysics ,Cell Biology ,Biochemistry - Published
- 2023
16. Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study
- Author
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Michio Murata, Hiroshi Tsuchikawa, Shinya Hanashima, Tohru Oishi, Sangjae Seo, Tomoya Yamamoto, Kosuke Funahashi, Taiga Suzuki, Shigeru Matsuoka, Nobuaki Matsumori, Mayank Kumar Dixit, Yuichi Umegawa, Yasuo Nakagawa, and Wataru Shinoda
- Subjects
Ergosterol ,chemistry.chemical_compound ,Molecular dynamics ,Membrane ,Multidisciplinary ,Solid-state nuclear magnetic resonance ,Chemistry ,Antifungal drug ,Biophysics ,Molecule ,Nuclear magnetic resonance spectroscopy ,Ion channel - Abstract
Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of fungal sterol, ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The high-resolution structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.
- Published
- 2022
17. Experimental and theoretical investigations into the mechanism of interactions between membrane-bound fatty acids and their binding protein: A model system to investigate the behavior of lipid acyl chains in contact with proteins
- Author
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Shigeru Sugiyama, Daisuke Matsuoka, Toshiaki Hara, Masashi Sonoyama, Shigeru Matsuoka, and Michio Murata
- Subjects
Organic Chemistry ,Fatty Acids ,Membrane Proteins ,Thermodynamics ,Cell Biology ,Fatty Acid-Binding Proteins ,Ligands ,Molecular Biology ,Biochemistry ,Protein Binding - Abstract
The interaction of proteins with hydrophobic ligands in biological membranes is an important research topic in the life sciences. The hydrophobic nature of ligands, especially their lack of water solubility, often makes it difficult to experimentally investigate their interactions with proteins, thus hampering quantitative evaluation based on thermodynamic parameters. The fatty acid-binding proteins, particularly FABP3, discussed in this review can recognize fatty acids, a primary component of membrane lipids, with high affinity. The precise three-dimensional structure of fatty acids and related ligands bound in FABP3 and their interaction with the binding pocket will contribute to the understanding of accurately determining physicochemical factors that cause the expression of affinity between protein surfaces and lipids in biological membranes. During the research of FABP3, we encountered many of the problems that were widely implicated in experiments dealing with hydrophobic ligands. To address these issues, we developed experimental methodologies using X-ray crystallography, calorimetry, and surface plasmon resonance. Using these methods and computational approaches, we have obtained several insights into the interaction of hydrophobic ligands with protein binding sites. Structural and functional studies of FABP potentially lead to a better understanding of the interaction between lipids and proteins, and thus, this protein may provide one of the model systems for investigating substance transport across cell membranes and inner membrane systems.
- Published
- 2022
18. Molecular substructure of the liquid-ordered phase formed by sphingomyelin and cholesterol: sphingomyelin clusters forming nano-subdomains are a characteristic feature
- Author
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Michio Murata, Nobuaki Matsumori, Masanao Kinoshita, and Erwin London
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Structural Biology ,Biophysics ,Review ,Molecular Biology - Abstract
As a model of lipid rafts, the liquid-ordered (Lo) phase formed by sphingomyelin (SM) and cholesterol (Cho) in bilayer membranes has long attracted the attention of biophysics researchers. New approaches and methodologies have led to a better understanding of the molecular basis of the Lo domain structure. This review summarizes studies on model membrane systems consisting of SM/unsaturated phospholipid/Cho implying that the Lo phase contains SM-based nanodomains (or nano-subdomains). Some of the Lo phase properties may be attributed to these nanodomains. Several studies suggest that the nanodomains contain clustered SM molecules packed densely to form gel-phase-like subdomains of single-digit nanometer size at physiological temperatures. Cho and unsaturated lipids located in the Lo phase are likely to be concentrated at the boundaries between the subdomains. These subdomains are not readily detected in the Lo phase formed by saturated phosphatidylcholine (PC) molecules, suggesting that they are strongly stabilized by homophilic interactions specific to SM, e.g., between SM amide groups. This model for the Lo phase is supported by experiments using dihydro-SM, which is thought to have stronger homophilic interactions than SM, as well as by studies using the enantiomer of SM having opposite stereochemistry to SM at the 2 and 3 positions and by some molecular dynamics (MD) simulations of lipid bilayers containing Lo-lipids. Nanosized gel subdomains seem to play an important role in controlling membrane organization and function in biological membranes.
- Published
- 2022
19. Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin
- Author
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Yuichi Umegawa, Satoshi Kawatake, Michio Murata, and Shigeru Matsuoka
- Subjects
Organic Chemistry ,Biophysics ,Biochemistry - Published
- 2023
20. A New Pathway for CO
- Author
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Jinglun, Du, Andrea, Fiorani, Taichi, Inagaki, Atsushi, Otake, Michio, Murata, Miho, Hatanaka, and Yasuaki, Einaga
- Abstract
By means of an initial electrochemical carbon dioxide reduction reaction (eCO
- Published
- 2022
21. Sphingomyelins and ent-Sphingomyelins Form Homophilic Nano-Subdomains within Liquid Ordered Domains
- Author
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J. Peter Slotte, Shinya Hanashima, Erwin London, Tomokazu Yasuda, Hiroshi Tsuchikawa, Yo Yano, and Michio Murata
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Lipid Bilayers ,Biophysics ,Cell membrane ,03 medical and health sciences ,0302 clinical medicine ,Membrane Microdomains ,medicine ,otorhinolaryngologic diseases ,Animals ,Lipid bilayer ,Lipid raft ,030304 developmental biology ,0303 health sciences ,Chemistry ,Lipid microdomain ,Cell Membrane ,Biological membrane ,Articles ,Sphingomyelins ,Membrane ,medicine.anatomical_structure ,Förster resonance energy transfer ,Cholesterol ,Phosphatidylcholines ,Sphingomyelin ,030217 neurology & neurosurgery - Abstract
Sphingomyelin (SM), a major component of small domains (or lipid rafts) in mammalian cell membranes, forms a liquid-ordered phase in the presence of cholesterol (Cho). However, the nature of molecular interactions within the ordered SM/Cho phase remains elusive. We previously revealed that stearoyl-SM (SSM) and its enantiomer (ent-SSM) separately form nano-subdomains within the liquid-ordered phase involving homophilic SSM-SSM and ent-SSM-ent-SSM interactions. In this study, the details of the subdomain formation by SSMs at the nanometer range were examined using Forster resonance energy transfer (FRET) measurements in lipid bilayers containing SSM and ent-SSM, dioleoyl-phosphatidylcholine and Cho. Although microscopy detected a stereochemical effect on partition coefficient favoring stereochemically homophilic interactions in the liquid-ordered state, it showed no significant difference in large-scale liquid-ordered domain formation by the two stereoisomers. In contrast to the uniform domains seen microscopy, FRET analysis using fluorescent donor- and acceptor-labeled SSM showed distinct differences in SM and ent-SM colocalization within nanoscale distances. Donor- and acceptor-labeled SSM showed significantly higher FRET efficiency than did donor-labeled SSM and acceptor-labeled ent-SSM in lipid vesicles composed of "racemic" (1:1) mixtures of SSM/ent-SSM with dioleoylphosphatidylcholine and Cho. The difference in FRET efficiency indicated that SSM and ent-SSM assemble to form separate nano-subdomains. The average size of the subdomains decreased as temperature increased, and at physiological temperatures, the subdomains were found to have a single-digit nanometer radius. These results suggest that (even in the absence of ent-SM) SM-SM interactions play a crucial role in forming nano-subdomains within liquid-ordered domains and may be a key feature of lipid microdomains (or rafts) in biological membranes.
- Published
- 2020
22. Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations
- Author
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Wataru Shinoda, Sangjae Seo, and Michio Murata
- Subjects
Phase separation ,010402 general chemistry ,01 natural sciences ,Domain formation ,03 medical and health sciences ,Molecular dynamics ,Phase (matter) ,General Materials Science ,Physical and Theoretical Chemistry ,030304 developmental biology ,0303 health sciences ,Membranes ,Leaflet (botany) ,Chemistry ,Acyls ,Bilayer ,technology, industry, and agriculture ,Lipids ,0104 chemical sciences ,Membrane ,Acyl chain ,cardiovascular system ,Biophysics ,Order ,lipids (amino acids, peptides, and proteins) ,Sphingomyelin - Abstract
The asymmetric lipid composition in plasma membranes within the inner leaflet is not typically suitable for domain formation. Thus elucidation of the likelihood of the formation or stability of a raft-like domain in the inner leaflet is necessary. Herein we investigated the phase behavior of asymmetric membranes using coarse-grained molecular dynamics simulations. The lipid leaflet comprising dioleoylphosphatidylcholine (DOPC) and cholesterol (Chol) does not typically show well-developed domains in symmetric bilayer membranes; however, it does separate into liquid ordered (Lo) and liquid disordered (Ld) phases when the opposing leaflet containing sphingomyelin (SM), DOPC, and Chol demonstrates domain formation. We determine that interdigitated acyl chains modulated the partitioning of Chol in the opposing leaflet, resulting in phase separation. Similarly, the acyl chain length of SM within the opposing leaflet affected the phase behavior of the leaflet. Our results reveal the crucial role of interdigitation in determining the phase status in asymmetric membranes., ファイル公開:2021-07-02
- Published
- 2020
23. Interactions of OSW-1 with Lipid Bilayers in Comparison with Digitonin and Soyasaponin
- Author
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Kaori Sakurai, Raymond S. Malabed, Shinya Hanashima, and Michio Murata
- Subjects
Lipid Bilayers ,Digitonin ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,polycyclic compounds ,Electrochemistry ,Membrane activity ,General Materials Science ,Lipid bilayer ,POPC ,Cholestenones ,Spectroscopy ,Vesicle ,technology, industry, and agriculture ,Surfaces and Interfaces ,Saponins ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,0104 chemical sciences ,Calcein ,Membrane ,chemistry ,Membrane curvature ,Biophysics ,lipids (amino acids, peptides, and proteins) ,0210 nano-technology - Abstract
OSW-1, a unique steroidal saponin isolated from the bulbs of Ornithogalum saundersiae, has potent cell-growth inhibition activity. In this study, we conducted fluorescence measurements and microscopic observations using palmitoyloleoylphosphatidylcholine (POPC)-cholesterol (Chol) bilayers to evaluate the membrane-binding affinity of OSW-1 in comparison with another steroidal saponin, digitonin, and the triterpenoid saponin, soyasaponin Bb(I). The membrane activities of these saponins were evaluated using calcein leakage assays and fitted to the binding isotherm by changing the ratios of saponin-lipids. Digitonin showed the highest binding affinity for the POPC-Chol membrane (Kapp = 0.38 μM-1) and the strongest membrane disruptivity in the bound saponin-lipid ratio at the point of 50% calcein leakage (r50 = 0.47) occurrence. OSW-1 showed slightly lower activity (Kapp = 0.31 μM-1; r50 = 0.78), and the soyasaponin was the lowest in the membrane affinity and the calcein leakage activity (Kapp = 0.017 μM-1; r50 = 1.66). The effect of OSW-1 was further assessed using confocal microscopy in an experiment utilizing DiI and rhodamine 6G as the fluorescence probes. The addition of 30 μM OSW-1 induced inward membrane curvature in some giant unilamellar vesicles (GUVs). At the higher OSW-1 concentration (58 μM, r50 = 0.78) where the 50% calcein leakage was observed, the morphology of some GUVs became elongated. With digitonin at the corresponding concentration (35 μM, r50 = 0.47), membrane disruption and formation of large aggregates in aqueous solution were observed, probably due to a detergent-type mechanism. These saponins, including OSW-1, required Chol to exhibit their potent membrane activity although their mechanisms are thought to be different. At the effective concentration, OSW-1 preferably binds to the bilayers without prominent disruption of vesicles and exerts its activity through the formation of saponin-Chol complexes, probably resulting in membrane permeabilization.
- Published
- 2020
24. Efficient diversification of GM3 gangliosides via late-stage sialylation and dynamic glycan structural studies with 19F solid-state NMR
- Author
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Shinya Hanashima, Hidenori Tanaka, Maina Takahashi, Hiromune Ando, Junya Shirasaki, Michio Murata, Akihiro Imamura, Katsuaki Sasaki, Naoko Komura, and Hideharu Ishida
- Subjects
chemistry.chemical_classification ,Glycan ,biology ,Chemistry ,Glycoconjugate ,Organic Chemistry ,Late stage ,Fluorine-19 NMR ,Biochemistry ,carbohydrates (lipids) ,Glycolipid ,Membrane ,Solid-state nuclear magnetic resonance ,biology.protein ,Moiety ,Physical and Theoretical Chemistry - Abstract
Sialic acid-containing glycoconjugates are involved in important biological processes such as immune response, cancer metastasis, and viral infection. However, their chemical syntheses have been challenging, mainly due to the difficulties in the α-sialylation of oligosaccharides. Very recently, we established a completely stereoselective sialidation method using a macrobicyclic sialyl donor. Herein, we describe a rational and efficient synthesis of sialoglycolipids via direct sialylation of a glycolipid at a late-stage, based on our novel sialidation method. The synthetic method enabled the development of GM3 ganglioside analogs with various C5-modifications of the sialosyl moiety. Furthermore, the synthesized analog was subjected to solid-state 19F NMR analysis on the model membranes and it revealed the influence of cholesterol on glycan dynamics.
- Published
- 2020
25. The Amphotericin B–Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly
- Author
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Wataru Shinoda, Sangjae Seo, Kosuke Funahashi, Shinya Hanashima, Nobuaki Matsumori, Yuichi Umegawa, Tomoya Yamamoto, Hiroshi Tsuchikawa, and Michio Murata
- Subjects
Ergosterol ,Magnetic Resonance Spectroscopy ,Lipid Bilayers ,Antifungal drug ,bacterial infections and mycoses ,Polyene ,Biochemistry ,Sterol ,chemistry.chemical_compound ,Membrane ,chemistry ,Amphotericin B ,polycyclic compounds ,medicine ,lipids (amino acids, peptides, and proteins) ,Lipid bilayer ,Erg ,medicine.drug - Abstract
Amphotericin B (AmB) is a polyene macrolide antibiotic clinically used as an antifungal drug. Its preferential complexation with ergosterol (Erg), the major sterol of fungal membranes, leads to the formation of a barrel-stave-like ion channel across a lipid bilayer. To gain a better understanding of the mechanism of action, the mode of lipid bilayer spanning provides essential information. However, because of the lack of methodologies to observe it directly, it has not been revealed for the Erg-containing channel assembly for many years. In this study, we disclosed that the AmB-Erg complex spans a lipid bilayer with a single-molecule length, using solid-state nuclear magnetic resonance (NMR) experiments. Paramagnetic relaxation enhancement by Mn
- Published
- 2019
26. Impact of Acyl Chain Mismatch on the Formation and Properties of Sphingomyelin-Cholesterol Domains
- Author
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Michio Murata, Kai-Lan Lin, Victor Hautala, Hiroshi Tsuchikawa, J. Peter Slotte, Oskar Engberg, and Thomas K.M. Nyholm
- Subjects
Deuterium NMR ,Magnetic Resonance Spectroscopy ,Lipid Bilayers ,Biophysics ,Phospholipid ,Cholesterol analog ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Fluorescence Resonance Energy Transfer ,Lipid bilayer ,Unilamellar Liposomes ,030304 developmental biology ,0303 health sciences ,Degree of unsaturation ,New and Notable ,Bilayer ,Temperature ,Biological membrane ,Deuterium ,Sterol ,Sphingomyelins ,Cholesterol ,Solubility ,chemistry ,lipids (amino acids, peptides, and proteins) ,030217 neurology & neurosurgery - Abstract
Lateral segregation and the formation of lateral domains are well-known phenomena in ternary lipid bilayers composed of an unsaturated (low gel-to-liquid phase transition temperature (Tm)) phospholipid, a saturated (high-Tm) phospholipid, and cholesterol. The formation of lateral domains has been shown to be influenced by differences in phospholipid acyl chain unsaturation and length. Recently, we also showed that differential interactions of cholesterol with low- and high-Tm phospholipids in the bilayer can facilitate phospholipid segregation. Now, we have investigated phospholipid-cholesterol interactions and their role in lateral segregation in ternary bilayers composed of different unsaturated phosphatidylcholines (PCs) with varying acyl chain lengths, N-palmitoyl-D-erythro-sphingomyelin (PSM), and cholesterol. Using deuterium NMR spectroscopy, we determined how PSM was influenced by the acyl chain composition in surrounding PC environments and correlated this with the affinity of cholestatrienol (a fluorescent cholesterol analog) for PSM in the different PC environments. Results from a combination of time-resolved fluorescence measurements of trans-parinaric acid and Forster resonance energy transfer experiments showed that the relative affinity of cholesterol for phospholipids determined the degree to which the sterol promoted domain formation. From Forster resonance energy transfer, deuterium NMR, and differential scanning calorimetry results, it was clear that cholesterol also influenced both the thermostability of the domains and the degree of order in and outside the PSM-rich domains. The results of this study have shown that the affinity of cholesterol for both low-Tm and high-Tm phospholipids and the effects of low- and high-Tm phospholipids on each other influence both lateral structure and domain properties in complex bilayers. We envision that similar effects also contribute to lateral heterogeneity in even more complex biological membranes.
- Published
- 2019
27. Synthesis of 7,6-Spirocyclic Imine with Butenolide Ring Provides Evidence for the Relative Configuration of Marine Toxin 13-desMe Spirolide C
- Author
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Hiroshi Tsuchikawa, Michio Murata, and Kou Minamino
- Subjects
Natural product ,Cycloaddition Reaction ,Molecular Structure ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Imine ,Diastereomer ,Substituent ,Stereoisomerism ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,4-Butyrolactone ,chemistry ,Marine Toxins ,Spiro Compounds ,Imines ,Physical and Theoretical Chemistry ,Marine toxin ,Butenolide - Abstract
Efficient synthesis of the partial structure of marine toxin 13-desMe spirolide C was achieved via the selective Diels-Alder reaction and C-C bond formation with the use of a silatrane substituent and the subsequent facile formation of a γ-butenolide ring. The comparison of NMR data between the synthesized diastereomers and the natural product strongly suggested that the relative configuration at the C4 position was S configuration with respect to the 7,6-spirocycle.
- Published
- 2019
28. Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes
- Author
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Wataru Shinoda, Hiroshi Tsuchikawa, Yusuke Miyazaki, Yuichi Umegawa, Michio Murata, Masaki Yamagami, Sangjae Seo, and Jin Cui
- Subjects
Salinity ,0303 health sciences ,Hot Temperature ,Magnetic Resonance Spectroscopy ,Chemistry ,Membrane lipids ,Bilayer ,030302 biochemistry & molecular biology ,Molecular Dynamics Simulation ,Archaea ,Biochemistry ,03 medical and health sciences ,Crystallography ,Molecular dynamics ,Membrane ,Purple Membrane ,Chain (algebraic topology) ,Membrane protein ,polycyclic compounds ,lipids (amino acids, peptides, and proteins) ,Thermal stability ,Lipid bilayer ,Phospholipids - Abstract
The average conformation of the methyl-branched chains of archaeal lipid phosphatidyl glycerophosphate methyl ester (PGP-Me) was examined in a hydrated bilayer membrane based on the 2H nuclear magnetic resonance (NMR) of enantioselectively 2H-labeled compounds that were totally synthesized for the first time in this study. The NMR results in combination with molecular dynamics simulations revealed that the PGP-Me chain appeared to exhibit behavior different from that of typical membrane lipids such as dimyristoylphosphatidylcholine (DMPC). The C-C bonds of the PGP-Me chain adopt alternative parallel and tilted orientations to the membrane normal as opposed to a DMPC chain where all of the C-C bonds tilt in the same way on average. This characteristic orientation causes the intertwining of PGP-Me chains, which plays an important role in the excellent thermal and high-salinity stabilities of archaeal lipid bilayers and membrane proteins.
- Published
- 2019
29. Nonlamellar-Phase-Promoting Colipids Enhance Segregation of Palmitoyl Ceramide in Fluid Bilayers
- Author
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Tomoya Yamamoto, Anna Möuts, Thomas K.M. Nyholm, Michio Murata, and J. Peter Slotte
- Subjects
inorganic chemicals ,0303 health sciences ,Ceramide ,Bilayer ,Lipid Bilayers ,technology, industry, and agriculture ,Biophysics ,Articles ,Ceramides ,Sphingolipid ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Membrane ,chemistry ,Membrane curvature ,Phase (matter) ,Cardiolipin ,lipids (amino acids, peptides, and proteins) ,Sphingomyelin ,Phospholipids ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Ceramide is an important intermediate in sphingolipid homeostasis. We examined how colipids, with negative intrinsic curvature and which may induce curvature stress in the bilayers, affected the segregation of palmitoyl ceramide (PCer). Such colipids include 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and tetra-linoleoyl cardiolipin (CL). In 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers, PCer formed ordered, gel-like domains at concentrations above 10 mol% at 23°C, as evidenced by the change in the average lifetime of the trans-parinaric acid emission. When POPE or DOPE were included in the DOPC bilayer (at 20:80 or 40:60 POPE or DOPE to DOPC, by mol), the lateral segregation of PCer was facilitated in a concentration-dependent manner, and less PCer was required for the formation of the ordered ceramide-rich domains. Inclusion of CL in the DOPE bilayer (at 10:90 or 20:80 CL to PC, by mol) also caused a similar facilitation of the lateral segregation of PCer. The PCer-rich domains formed in the presence of POPE, DOPE, or CL in DOPC bilayers were slightly more thermostable (by 2–10°C) when compared to PCer-rich domains in DOPC-only bilayers. Nonlamellar phases were not present in bilayers in which the effects of POPE or DOPE on PCer segregation were the largest, as verified by 31P NMR. When palmitoyl sphingomyelin was added to the different bilayer compositions at 5 mol%, relative to the phospholipids, PCer segregated into gel domains at lower concentrations (2–3 mol% PCer), and the effect of POPE on PCer segregation was eliminated. We suggest that the effects of POPE, DOPE, and CL on PCer segregation was in part influenced by their effects on membrane curvature stress and in part because of unfavorable interactions with PCer due to their unsaturated acyl chains. These lipids are abundant in mitochondrial membranes and are likely to affect functional properties of saturated ceramides in them.
- Published
- 2019
30. Small structural alterations greatly influence the membrane affinity of lipophilic ligands: Membrane interactions of bafilomycin A1 and its desmethyl derivative bearing 19F-labeling
- Author
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Tatsuru Hayashi, Yuichi Umegawa, Michio Murata, and Hiroshi Tsuchikawa
- Subjects
biology ,010405 organic chemistry ,Chemistry ,Bilayer ,ATPase ,Organic Chemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Bafilomycin ,Biological activity ,Desmethyl ,Inhibitory postsynaptic potential ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,chemistry.chemical_compound ,Membrane ,Solid-state nuclear magnetic resonance ,Drug Discovery ,biology.protein ,Biophysics ,Molecular Medicine ,Molecular Biology - Abstract
Molecular behavior under bilayer membrane environments is one of the important research topics concerning how organic molecules exert their biological activities when interacting with cellular membranes. However, chemistry-based approaches to this property have not been successful when compared with the structural biological strategy on ligand-receptor interactions. Here, we investigated the molecular behavior of the lipophilic ATPase inhibitor bafilomycin A1 and its derivatives under a lipid environment from a chemical point of view. Our results revealed significant differences in membrane affinity and dynamics among ligands having different inhibitory potencies, suggesting the specific contribution of ligand-membrane interactions to their biological activity.
- Published
- 2019
31. Theonellamide A, a marine-sponge-derived bicyclic peptide, binds to cholesterol in aqueous DMSO: Solution NMR-based analysis of peptide-sterol interactions using hydroxylated sterol
- Author
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Shinichi Nishimura, Hideaki Kakeya, Raymond S. Malabed, Minoru Yoshida, Shigeki Matsunaga, Kimberly Cornelio, Shinya Hanashima, Masanao Kinoshita, Rafael A. Espiritu, Michio Murata, Yasuto Todokoro, and Nobuaki Matsumori
- Subjects
Models, Molecular ,0301 basic medicine ,Antifungal Agents ,Magnetic Resonance Spectroscopy ,Protein Conformation ,Stereochemistry ,Lipid Bilayers ,Biophysics ,Peptide ,Peptides, Cyclic ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,polycyclic compounds ,Animals ,Dimethyl Sulfoxide ,Solubility ,chemistry.chemical_classification ,Ergosterol ,Aqueous solution ,030102 biochemistry & molecular biology ,010405 organic chemistry ,Chemistry ,Temperature ,Cell Biology ,Sterol ,Cyclic peptide ,Porifera ,0104 chemical sciences ,Dissociation constant ,Kinetics ,Sterols ,Cholesterol ,Phosphatidylcholines ,Solvents ,Proton NMR ,Anisotropy ,lipids (amino acids, peptides, and proteins) ,Protein Binding - Abstract
Theonellamides (TNMs) are antifungal and cytotoxic bicyclic dodecapeptides isolated from the marine sponge Theonella sp. The inclusion of cholesterol (Chol) or ergosterol in the phosphatidylcholine membrane is known to significantly enhance the membrane affinity for theonellamide A (TNM-A). We have previously revealed that TNM-A stays in a monomeric form in dimethylsulfoxide (DMSO) solvent systems, whereas the peptide forms oligomers in aqueous media. In this study, we utilized 1H NMR chemical shift changes (Δδ1H) in aqueous DMSO solution to evaluate the TNM-A/sterol interaction. Because Chol does not dissolve well in this solvent, we used 25-hydroxycholesterol (25-HC) instead, which turned out to interact with membrane-bound TNM-A in a very similar way to that of Chol. We determined the dissociation constant, KD, by NMR titration experiments and measured the chemical shift changes of TNM-A induced by 25-HC binding in the DMSO solution. Significant changes were observed for several amino acid residues in a certain area of the molecule. The results from the solution NMR experiments, together with previous findings, suggest that the TNM-Chol complex, where the hydrophobic cavity of TNM probably incorporates Chol, becomes less polar by Chol interaction, resulting in a greater accumulation of the peptide in membrane. The deeper penetration of TNM-A into the membrane interior enhances membrane disruption. We also demonstrated that hydroxylated sterols, such as 25-HC that has higher solubility in most NMR solvents than Chol, act as a versatile substitute for sterol and could be used in 1H NMR-based studies of sterol-binding peptides.
- Published
- 2019
32. A Synthetic Approach to the Channel Complex Structure of Antibiotic in a Membrane: Backbone 19F-Labeled Amphotericin B for Solid-State NMR Analysis
- Author
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Tohru Oishi, Yuichi Umegawa, Michio Murata, and Hiroshi Tsuchikawa
- Subjects
Membrane ,Channel complex ,Solid-state nuclear magnetic resonance ,medicine.drug_class ,Chemistry ,Amphotericin B ,Organic Chemistry ,Antibiotics ,medicine ,Combinatorial chemistry ,medicine.drug - Published
- 2018
33. FRET detects lateral interaction between transmembrane domain of EGF receptor and ganglioside GM3 in lipid bilayers
- Author
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Naoko Komura, Mikito Nakano, Michio Murata, Toshiaki Hara, Hironobu Hojo, Shinya Hanashima, Kazuya Kabayama, Hiromune Ando, Yuya Asahina, J. Peter Slotte, and Thomas K.M. Nyholm
- Subjects
Lipid Bilayers ,Biophysics ,Phospholipid ,Biochemistry ,Biophysical Phenomena ,03 medical and health sciences ,chemistry.chemical_compound ,Protein Domains ,Fluorescence Resonance Energy Transfer ,G(M3) Ganglioside ,Humans ,Epidermal growth factor receptor ,Phosphorylation ,Lipid bilayer ,030304 developmental biology ,Cell Proliferation ,0303 health sciences ,biology ,Epidermal Growth Factor ,Chemistry ,Bilayer ,030302 biochemistry & molecular biology ,Autophosphorylation ,Cell Cycle ,Cell Biology ,carbohydrates (lipids) ,ErbB Receptors ,Transmembrane domain ,Kinetics ,Membrane ,Förster resonance energy transfer ,biology.protein ,lipids (amino acids, peptides, and proteins) ,Signal Transduction - Abstract
Ganglioside GM3 in the plasma membranes suppresses cell growth by preventing the autophosphorylation of the epidermal growth factor receptor (EGFR). Biological studies have suggested that GM3 interacts with the transmembrane segment of EGFR. Further biophysical experiments are particularly important for quantitative evaluation of the peptide-glycolipid interplay in bilayer membranes using a simple reconstituted system. To examine these interactions in this way, we synthesized the transmembrane segment of EGFR bearing a nitrobenzoxadiazole fluorophore (NBD-TM) at the N-terminus. The affinity between EGFR and GM3 was evaluated based on Forster resonance energy transfer (FRET) between NBD-TM and ATTO594-labeled GM3 in bilayers where their non-specific interaction due to lateral proximity was subtracted by using NBD-labeled phospholipid. This method for selectively detecting the specific lipid-peptide interactions in model lipid bilayers disclosed that the lateral interaction between GM3 and the transmembrane segment of EGFR plays a certain role in disturbing the formation of active EGFR dimers.
- Published
- 2020
34. Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine
- Author
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Yuichi Umegawa, Wataru Shinoda, Takuya Ono, Hiroshi Tsuchikawa, Michio Murata, and Masaki Yamagami
- Subjects
Chemistry ,Stereochemistry ,Acylation ,Lipid Bilayers ,Phospholipid ,Molecular Conformation ,Water ,Orientation (graph theory) ,Molecular Dynamics Simulation ,Biochemistry ,Archaea ,Permeability ,chemistry.chemical_compound ,Glycerol ,Phosphatidylcholines ,Moiety ,lipids (amino acids, peptides, and proteins) ,Physical stability - Abstract
Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryotic and eubacterial origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaeal membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study, we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in a membrane using
- Published
- 2020
35. β-Glucosylation of cholesterol reduces sterol-sphingomyelin interactions
- Author
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Peter Greimel, Raymond S. Malabed, Nanami Fukuda, Shinya Hanashima, Yoshio Hirabayashi, Msanao Kinoshita, and Michio Murata
- Subjects
0303 health sciences ,Glycosylation ,Calorimetry, Differential Scanning ,030302 biochemistry & molecular biology ,Lipid Bilayers ,Biophysics ,Biological membrane ,Cell Biology ,Biochemistry ,Sterol ,Sphingomyelins ,03 medical and health sciences ,chemistry.chemical_compound ,Glycolipid ,Membrane ,Cholesterol ,Solid-state nuclear magnetic resonance ,chemistry ,Moiety ,lipids (amino acids, peptides, and proteins) ,Sphingomyelin ,Nuclear Magnetic Resonance, Biomolecular ,030304 developmental biology ,Phosphocholine - Abstract
Cholesteryl-β-D-glucoside (ChoGlc) is a mammalian glycolipid that is expressed in brain tissue. The effects of glucosylation on the ordering and lipid interactions of cholesterol (Cho) were examined in membranes composed of N-stearoyl sphingomyelin (SSM), which is abundant in the brain, and to investigate the possible molecular mechanism involved in these interactions. Differential scanning calorimetry revealed that ChoGlc was miscible with SSM in a similar extent of Cho. Solid-state 2H NMR of deuterated SSM and fluorescent anisotropy using 1,6-diphenylhexatriene demonstrated that the glucosylation of Cho significantly reduced the effect of the sterol tetracyclic core on the ordering of SSM chains. The orientation of the sterol core was further examined by solid-state NMR analysis of deuterated and fluorinated ChoGlc analogues. ChoGlc had a smaller tilt angle between the long molecular axis (C3-C17) and the membrane normal than Cho in SSM bilayers, and the fluctuations in the tilt angle were largely unaffected by temperature-dependent mobility changes of SSM acyl chains. This orientation of the sterol core of ChoGlc leads to reduce sterol-SSM interactions. The MD simulation results suggested that the Glc moiety perturbs the SSM-sterol interactions, which reduces the umbrella effect of the phosphocholine headgroup because the hydrophilic glucose moiety resides at the same depth as an SSM amide group. These differences between ChoGlc and Cho also weaken the SSM-ChoGlc interactions. Thus, the distribution and localization of Cho and ChoGlc possibly control the stability of sphingomyelin-based domains that transiently occur at specific locations in biological membranes.
- Published
- 2020
36. Efficient diversification of GM3 gangliosides via late-stage sialylation and dynamic glycan structural studies with
- Author
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Maina, Takahashi, Junya, Shirasaki, Naoko, Komura, Katsuaki, Sasaki, Hide-Nori, Tanaka, Akihiro, Imamura, Hideharu, Ishida, Shinya, Hanashima, Michio, Murata, and Hiromune, Ando
- Abstract
Sialic acid-containing glycoconjugates are involved in important biological processes such as immune response, cancer metastasis, and viral infection. However, their chemical syntheses have been challenging, mainly due to the difficulties in the α-sialylation of oligosaccharides. Very recently, we established a completely stereoselective sialidation method using a macrobicyclic sialyl donor. Herein, we describe a rational and efficient synthesis of sialoglycolipids via direct sialylation of a glycolipid at a late-stage, based on our novel sialidation method. The synthetic method enabled the development of GM3 ganglioside analogs with various C5-modifications of the sialosyl moiety. Furthermore, the synthesized analog was subjected to solid-state 19F NMR analysis on the model membranes and it revealed the influence of cholesterol on glycan dynamics.
- Published
- 2020
37. Evidence of lipid rafts based on the partition and dynamic behavior of sphingomyelins
- Author
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Kenichi G. N. Suzuki, Nobuaki Matsumori, Masanao Kinoshita, and Michio Murata
- Subjects
0301 basic medicine ,Lipid Bilayers ,Raman imaging ,Spectrum Analysis, Raman ,Biochemistry ,Cell Line ,Structure-Activity Relationship ,03 medical and health sciences ,Membrane Microdomains ,Humans ,Image acquisition ,Molecular Biology ,Lipid raft ,Fluorescent Dyes ,Molecular Structure ,Chemistry ,Organic Chemistry ,Direct observation ,Cell Biology ,Raft ,Single Molecule Imaging ,Sphingomyelins ,Kinetics ,Fluorescent labelling ,Cholesterol ,030104 developmental biology ,Cellular Microenvironment ,Phosphatidylcholines ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Sphingomyelin - Abstract
Sphingomyelin (SM)-rich membrane nano-domains, called lipid rafts, have attracted the interest of researchers due to their potential involvement in the formation of signaling platform. Although there are many studies on lipid rafts, the direct observation of lipid rafts is still challenging owing to two critical reasons. One is the lack of an appropriate fluorescent probe mimicking the native behavior of raft lipids; fluorescent labeling often alters the intrinsic disposition of raft lipids. The other is their spatio-temporal stability; the size of lipid rafts is much smaller than the optical resolution of usual microscopy and their lifetime is much shorter than image acquisition duration. These issues are hampering the visualization of lipid rafts. Our review highlights the recent advances in microscopic techniques to visualize the partition and dynamic behavior of SMs, disclosing the detailed structure of lipid rafts. Moreover, we will elucidate the importance of SM-SM interactions in the stabilization of signaling platforms as lipid rafts.
- Published
- 2018
38. Enantiomers of phospholipids and cholesterol: A key to decipher lipid-lipid interplay in membrane
- Author
-
Michio Murata, Shinya Hanashima, and Yo Yano
- Subjects
Membrane lipids ,Glycerophospholipids ,010402 general chemistry ,Ceramides ,01 natural sciences ,Catalysis ,Analytical Chemistry ,Membrane Lipids ,Membrane Microdomains ,Sphingosine ,Drug Discovery ,Lipid raft ,Spectroscopy ,Phospholipids ,Pharmacology ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Biological membrane ,Stereoisomerism ,Sphingolipid ,0104 chemical sciences ,Sphingomyelins ,Sterols ,Membrane ,Cholesterol ,Membrane protein ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Enantiomer ,Sphingomyelin - Abstract
Most phospholipids constituting biological membranes are chiral molecules with a hydrophilic head group and hydrophobic alkyl chains, rendering biphasic property characteristic of membrane lipids. Some lipids assemble into small domains via chirality-dependent homophilic and heterophilic interactions, the latter of which sometimes include cholesterol to form lipid rafts and other microdomains. On the other hand, lipid mediators and hormones derived from chiral lipids are recognized by specific membrane or nuclear receptors to induce downstream signaling. It is crucial to clarify the physicochemical properties of the lipid self-assembly for the study of the functions and behavior of biological membranes, which often become elusive due to effects of membrane proteins and other biological events. Three major lipids with different skeletal structures were discussed: sphingolipids including ceramides, phosphoglycerolipids, and cholesterol. The physicochemical properties of membranes and physiological functions of lipid enantiomers and diastereomers were described in comparison to natural lipids. When each enantiomer formed a self-assembly or interacted with achiral lipids, both lipid enantiomers exhibited identical membrane physicochemical properties, while when the enantiomer interacted with chiral lipids or with the opposite enantiomer, mixed membranes exhibited different properties. For example, racemic membranes comprising native sphingomyelin and its antipode exhibited phase segregation due to their strong homophilic interactions. Therefore, lipid enantiomers and diastereomers can be good probes to investigate stereospecific lipid-lipid and lipid-protein interactions occurring in biological membranes.
- Published
- 2019
39. Highly Efficient Syntheses of C−N Axially Chiral 1‐( ortho ‐hydroxyaryl)uracil using a Chiral Auxiliary and a Chiral Base
- Author
-
Michio Murata, Yoshifumi Yasukawa, Hiroshi Tsuchikawa, Futoshi Hasegawa, and Kazushi Kawamura
- Subjects
chemistry.chemical_compound ,Chiral auxiliary ,Atropisomer ,chemistry ,010405 organic chemistry ,Organic Chemistry ,Uracil ,010402 general chemistry ,Axial symmetry ,Base (exponentiation) ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences - Published
- 2018
40. Stereoselective Construction of Cisoidal Bisspiroacetal Frameworks through Magnesium Coordination of the Bilateral Acetal Oxygen Atoms
- Author
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Michio Murata, Hiroshi Tsuchikawa, Yoshifumi Yasukawa, and Yasuto Todokoro
- Subjects
010405 organic chemistry ,Magnesium ,Organic Chemistry ,Acetal ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Oxygen atom ,chemistry ,Stereoselectivity ,Chelation ,Isomerization - Published
- 2018
41. Synthesis and Stereochemical Revision of the C31–C67 Fragment of Amphidinol 3
- Author
-
Michio Murata, Tohru Oishi, Yuma Wakamiya, Makoto Ebine, Hiroyuki Omizu, Mariko Murayama, and Nobuaki Matsumori
- Subjects
Biological Products ,Magnetic Resonance Spectroscopy ,Natural product ,010405 organic chemistry ,Stereochemistry ,Chemistry ,Molecular Conformation ,Absolute configuration ,Stereoisomerism ,General Medicine ,General Chemistry ,Nuclear magnetic resonance spectroscopy ,Tetrahydropyran ,Alkenes ,010402 general chemistry ,01 natural sciences ,Chemical synthesis ,Catalysis ,Amphidinol 3 ,0104 chemical sciences ,Stereocenter ,chemistry.chemical_compound ,Fragment (logic) ,Pyrans - Abstract
Amphidinol 3 (AM3) is a marine natural product produced by the dinoflagellate Amphidinium klebsii. Although the absolute configuration of AM3 was determined in 1999 by extensive NMR analysis and degradation of the natural product, it was a daunting task because of the presence of numerous stereogenic centers on the acyclic carbon chain and the limited availability from natural sources. Thereafter, revisions of the absolute configurations at C2 and C51 were reported in 2008 and 2013, respectively. Reported herein is the revised absolute configuration of AM3: 32S, 33R, 34S, 35S, 36S, and 38S based on the chemical synthesis of partial structures corresponding to the C31-C67 fragment of AM3 in combination with degradation of the natural product. The revised structure is unique in that both antipodal tetrahydropyran counterparts exist on a single carbon chain. The structural revision of AM3 may affect proposed structures of congeners related to the amphidinols.
- Published
- 2018
42. Synthesis and Complete Structure Determination of a Sperm-Activating and -Attracting Factor Isolated from the Ascidian Ascidia sydneiensis
- Author
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Michio Murata, Ken Sakai, Kosei Yamauchi, Tomohiro Watanabe, Manabu Yoshida, Nobuaki Matsumori, Hiroshi Tsuchikawa, Shu Lin, Tohru Oishi, Masaaki Morisawa, Makoto Ebine, and Hajime Shibata
- Subjects
Male ,Magnetic Resonance Spectroscopy ,Pinacol coupling reaction ,Ketone ,Stereochemistry ,medicine.medical_treatment ,Pharmaceutical Science ,010402 general chemistry ,01 natural sciences ,Analytical Chemistry ,Steroid ,chemistry.chemical_compound ,Drug Discovery ,medicine ,Side chain ,Animals ,Urochordata ,Pharmacology ,chemistry.chemical_classification ,Biological Products ,Natural product ,010405 organic chemistry ,Organic Chemistry ,Absolute configuration ,Diastereomer ,Spermatozoa ,0104 chemical sciences ,Complementary and alternative medicine ,chemistry ,Molecular Medicine ,Steroids ,Stereoselectivity - Abstract
For the complete structure elucidation of an endogenous sperm-activating and -attracting factor isolated from eggs of the ascidian Ascidia sydneiensis ( Assydn-SAAF), its two possible diastereomers with respect to C-25 were synthesized. Starting from ergosterol, the characteristic steroid backbone was constructed by using an intramolecular pinacol coupling reaction and stereoselective reduction of a hydroxy ketone as key steps, and the side chain was introduced by Julia-Kocienski olefination. Comparison of the NMR data of the two diastereomers with those of the natural product led to the elucidation of the absolute configuration as 25 S; thus the complete structure was determined and the first synthesis of Assydn-SAAF was achieved.
- Published
- 2018
43. Enantioselective Deuteration of β-Substituted α,β-Unsaturated Esters by Rhodium-1,2-Bis(2,5-diphenylphospholano)ethane
- Author
-
Michio Murata, Sébastien Lethu, Shigeru Matsuoka, and Hikaru Ano
- Subjects
Isotopic labeling ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Enantioselective synthesis ,chemistry.chemical_element ,Physical and Theoretical Chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Rhodium - Published
- 2018
44. Sterol-recognition ability and membrane-disrupting activity of Ornithogalum saponin OSW-1 and usual 3-O-glycosyl saponins
- Author
-
Raymond S. Malabed, Kaori Sakurai, Michio Murata, and Shinya Hanashima
- Subjects
Whole membrane ,Membrane lipids ,Biophysics ,Saponin ,Digitonin ,Ornithogalum saundersiae ,010402 general chemistry ,Hemolysis ,01 natural sciences ,Biochemistry ,Membrane Lipids ,chemistry.chemical_compound ,Humans ,Glycosyl ,Oleanolic Acid ,Cholestenones ,Unilamellar Liposomes ,chemistry.chemical_classification ,biology ,010405 organic chemistry ,Chemistry ,Erythrocyte Membrane ,beta-Cyclodextrins ,Biological Transport ,Cell Biology ,Saponins ,Fluoresceins ,Glycyrrhizic Acid ,biology.organism_classification ,Antineoplastic Agents, Phytogenic ,Sterol ,0104 chemical sciences ,Cholesterol ,Membrane ,Phosphatidylcholines ,Ornithogalum ,Dimyristoylphosphatidylcholine - Abstract
OSW-1 is a structurally unique steroidal saponin isolated from the bulbs of Ornithogalum saundersiae, and has exhibited highly potent and selective cytotoxicity in tumor cell lines. This study aimed to investigate the molecular mechanism for the membrane-permeabilizing activity of OSW-1 in comparison with those of other saponins by using various spectroscopic approaches. The membrane effects and hemolytic activity of OSW-1 were markedly enhanced in the presence of membrane cholesterol. Binding affinity measurements using fluorescent cholestatrienol and solid-state NMR spectroscopy of a 3-d-cholesterol probe suggested that OSW-1 interacts with membrane cholesterol without forming large aggregates while 3-O-glycosyl saponin, digitonin, forms cholesterol-containing aggregates. The results suggest that OSW-1/cholesterol interaction is likely to cause membrane permeabilization and pore formation without destroying the whole membrane integrity, which could partly be responsible for its highly potent cell toxicity.
- Published
- 2017
45. Structures of the Largest Amphidinol Homologues from the Dinoflagellate Amphidinium carterae and Structure–Activity Relationships
- Author
-
Huiping Zhang, Jong Souk Kim, Raymond S. Malabed, Fumiaki Hayashi, Shinya Hanashima, Jong-Soo Lee, Kimberly Cornelio, Michio Murata, Shoko Mori, Chang Hoon Kim, Masayuki Satake, and Nobuaki Matsumori
- Subjects
Antifungal ,Antifungal Agents ,medicine.drug_class ,ved/biology.organism_classification_rank.species ,Pharmaceutical Science ,Alkenes ,Biology ,010402 general chemistry ,Hemolysis ,01 natural sciences ,Analytical Chemistry ,Structure-Activity Relationship ,Polyketide ,Japan ,Polyol ,Amphidinium carterae ,Drug Discovery ,medicine ,Animals ,Structure–activity relationship ,Nuclear Magnetic Resonance, Biomolecular ,Pyrans ,Pharmacology ,chemistry.chemical_classification ,Molecular Structure ,010405 organic chemistry ,ved/biology ,Organic Chemistry ,Dinoflagellate ,biology.organism_classification ,0104 chemical sciences ,Complementary and alternative medicine ,chemistry ,Biochemistry ,Polyketides ,Dinoflagellida ,Molecular Medicine ,Drugs, Chinese Herbal - Abstract
Amphidinols are polyketide metabolites produced by marine dinoflagellates and are chiefly composed of a long linear chain with polyol groups and polyolefins. Two new homologues, amphidinols 20 (AM20, 1) and 21 (AM21, 2), were isolated from Amphidinium carterae collected in Korea. Their structures were elucidated by detailed NMR analyses as amphidinol 6-type compounds with remarkably long polyol chains. Amphidinol 21 (2) has the longest linear structure among the amphidinol homologues reported so far. The congeners, particularly amphidinol 21 (2), showed weaker activity in hemolysis and antifungal assays compared to known amphidinols.
- Published
- 2017
46. Growth of protein crystals in high-strength hydrogels with the dialysis membrane
- Author
-
Taichi Naruse, Kenta Hamada, Hiroaki Adachi, Tsugio Nagasawa, Noriaki Kunimune, Michio Murata, Yusuke Mori, and Shigeru Sugiyama
- Subjects
Inorganic Chemistry ,Structural Biology ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry - Published
- 2021
47. Stable C–N axial chirality in 1-aryluracil scaffold and differences in in vitro metabolic clearance between atropisomers of PDE4 inhibitor
- Author
-
Futoshi Hasegawa, Kazushi Kawamura, Michio Murata, and Hiroshi Tsuchikawa
- Subjects
Models, Molecular ,inorganic chemicals ,Scaffold ,Stereochemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Structure-Activity Relationship ,symbols.namesake ,Drug Discovery ,Animals ,Humans ,heterocyclic compounds ,Van der Waals radius ,Uracil ,Molecular Biology ,Racemization ,Atropisomer ,Dose-Response Relationship, Drug ,Molecular Structure ,010405 organic chemistry ,Chemistry ,organic chemicals ,Organic Chemistry ,Diastereomer ,Stereoisomerism ,In vitro ,Cyclic Nucleotide Phosphodiesterases, Type 4 ,Rats ,0104 chemical sciences ,Chiral column chromatography ,Axial chirality ,Microsomes, Liver ,symbols ,Molecular Medicine ,Phosphodiesterase 4 Inhibitors - Abstract
We report herein the stable C-N axial chirality in a 1-phenyl-6-aminouracil scaffold owing to the presence of various functional groups at the ortho-position of the N(1)-phenyl group. Racemic 1-phenyl-6-aminouracils were first separated by chiral HPLC or converting them to the corresponding diastereomers using a chiral resolving agent. We then determined the rotational barrier of each atropisomer by a thermal racemization method and found that these compounds have rotational barriers similar to other C-N axially chiral biaryls. In addition, there was a good correlation between the rotational barriers and van der Waals radii of an ortho-substituent of the N(1)-phenyl group. To explore the possibility of the chiral 1-phenyl-6-aminouracil scaffold as a drug lead, we synthesized both atropisomers as phosphodiesterase-4 inhibitors 10. The atropisomers showed significantly different metabolic stabilities while their PDE4 inhibitory activities were somewhat similar. This finding demonstrates the potential utility of stable C-N bond atropisomers in the development of chiral drugs.
- Published
- 2017
48. Nanosecond pump–probe device for time-resolved serial femtosecond crystallography developed at SACLA
- Author
-
Tomoyuki Tanaka, Michio Murata, Fumitaka Mafuné, Shigeki Owada, Rie Tanaka, Yasumasa Joti, Changyong Song, Takashi Nomura, Yoshihiro Takeda, Naoya Miyauchi, So Iwata, Minoru Kubo, Tetsunari Kimura, Kensuke Tono, Takashi Kameshima, Richard Neutze, Takaki Hatsui, Jun-ya Kohno, Ken Miyajima, Makina Yabashi, Jan Davidsson, Eriko Nango, and Takanori Nakane
- Subjects
0301 basic medicine ,Nuclear and High Energy Physics ,serial femtosecond crystallography ,Materials science ,Atom and Molecular Physics and Optics ,Phase (waves) ,Short Communications ,02 engineering and technology ,pump and probe ,law.invention ,SACLA ,03 medical and health sciences ,Optics ,law ,Instrumentation ,Millisecond ,Radiation ,biology ,business.industry ,XFEL ,time-resolved X-ray crystallography ,Bacteriorhodopsin ,Injector ,Nanosecond ,021001 nanoscience & nanotechnology ,Laser ,Crystallography ,030104 developmental biology ,Femtosecond ,biology.protein ,Atom- och molekylfysik och optik ,0210 nano-technology ,business - Abstract
A nanosecond pump–probe device for time-resolved serial femtosecond crystallography has been developed at SACLA., X-ray free-electron lasers (XFELs) have opened new opportunities for time-resolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TR-SFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.
- Published
- 2017
49. Efficient Access to the Functionalized Bicyclic Pharmacophore of Spirolide C by Using a Selective Diels–Alder Reaction
- Author
-
Sho Hayashi, Michio Murata, Kou Minamino, and Hiroshi Tsuchikawa
- Subjects
Bicyclic molecule ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,010402 general chemistry ,01 natural sciences ,Cycloaddition ,0104 chemical sciences ,Silyl ether ,chemistry.chemical_compound ,chemistry ,Lactam ,Moiety ,Pharmacophore ,Marine toxin ,Diels–Alder reaction - Abstract
A functionalized bicyclic lactam that was used as a key intermediate in an efficient synthesis of the pharmacophore of potent marine toxin spirolide C was synthesized by using a highly selective Diels–Alder reaction. To improve the reactivity of this transformation without loss of selectivity, substrates that contained a silyl ether or silatrane moiety were elaborately designed and converted into the spirobicyclic core structure with stereochemical control over the two asymmetric centers at the C7 and C29 positions. Moreover, a further C−C bond formation by using a Hiyama cross-coupling reaction of the vinyl silatrane derivative facilitated versatile modification at the C5 position with an aryl or alkenyl substituent.
- Published
- 2017
50. Raft-based sphingomyelin interactions revealed by new fluorescent sphingomyelin analogs
- Author
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Takahiro K. Fujiwara, Kenichi G. N. Suzuki, Masanao Kinoshita, Mitsuhiro Abe, Misa Takada, Toshihide Kobayashi, Nobuaki Matsumori, Kenichi Morigaki, Michio Murata, Akihiro Kusumi, Koichiro M. Hirosawa, Hikaru Ano, and Asami Makino
- Subjects
0301 basic medicine ,Fluorophore ,Glycosylphosphatidylinositols ,Swine ,Detergents ,CD59 Antigens ,CHO Cells ,Biology ,Cell Line ,Tools ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Cricetulus ,Membrane Microdomains ,Animals ,Research Articles ,Fluorescent Dyes ,Sphingolipids ,Sphingosine ,Cell Membrane ,Cell Biology ,Raft ,Fluorescence ,Sphingolipid ,Sphingomyelins ,carbohydrates (lipids) ,030104 developmental biology ,Membrane ,Cholesterol ,Biochemistry ,chemistry ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Sphingomyelin ,Linker ,Hydrophobic and Hydrophilic Interactions ,030217 neurology & neurosurgery - Abstract
Sphingomyelin (SM) has been proposed to form cholesterol-dependent raft domains and sphingolipid domains in the plasma membrane (PM). How SM contributes to the formation and function of these domains remains unknown, primarily because of the scarcity of suitable fluorescent SM analogs. We developed new fluorescent SM analogs by conjugating a hydrophilic fluorophore to the SM choline headgroup without eliminating its positive charge, via a hydrophilic nonaethylene glycol linker. The new analogs behaved similarly to the native SM in terms of their partitioning behaviors in artificial liquid order-disorder phase-separated membranes and detergent-resistant PM preparations. Single fluorescent molecule tracking in the live-cell PM revealed that they indirectly interact with each other in cholesterol- and sphingosine backbone{textendash}dependent manners, and that, for ~{}10{textendash}50 ms, they undergo transient colocalization-codiffusion with a glycosylphosphatidylinositol (GPI)-anchored protein, CD59 (in monomers, transient-dimer rafts, and clusters), in CD59-oligomer size{textendash}, cholesterol-, and GPI anchoring{textendash}dependent manners. These results suggest that SM continually and rapidly exchanges between CD59-associated raft domains and the bulk PM., 脂質の挙動をありのままに再現する蛍光プローブでラフトの形成機構を解明. 京都大学プレスリリース. 2017-03-28.
- Published
- 2017
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