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Yasuda T, Ueura D, Nakagomi M, Hanashima S, Peter Slotte J, Murata M. Design, synthesis of ceramide 1-phosphate analogs and their affinity for cytosolic phospholipase A 2 as evidenced by surface plasmon resonance. Bioorg Med Chem Lett 2024; 107:129792. [PMID: 38734389 DOI: 10.1016/j.bmcl.2024.129792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Ceramide 1-phosphate (C1P) is a lipid mediator that specifically binds and activates cytosolic phospholipase A2α (cPLA2α). To elucidate the structure-activity relationship of the affinity of C1P for cPLA2α in lipid environments, we prepared a series of C1P analogs containing structural modifications in the hydrophilic parts and subjected them to surface plasmon resonance (SPR). The results suggested the presence of a specific binding site for cPLA2α on the amide, 3-OH and phosphate groups in C1P structure. Especially, dihydro-C1P exhibited enhanced affinity for cPLA2α, suggesting the hydrogen bonding ability of 3-hydroxy group is important for interactions with cPLA2α. This study helps to understand the influence of specific structural moieties of C1P on the interaction with cPLA2α at the atomistic level and may lead to the design of drugs that regulate cPLA2α activation.
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Affiliation(s)
- Tomokazu Yasuda
- Research Foundation ITSUU Laboratory, C1232, Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Daiki Ueura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Madoka Nakagomi
- Research Foundation ITSUU Laboratory, C1232, Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, FIN-20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Watanabe H, Hanashima S, Yano Y, Yasuda T, Murata M. Passive Translocation of Phospholipids in Asymmetric Model Membranes: Solid-State 1H NMR Characterization of Flip-Flop Kinetics Using Deuterated Sphingomyelin and Phosphatidylcholine. Langmuir 2023; 39:15189-15199. [PMID: 37729012 DOI: 10.1021/acs.langmuir.3c01650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Although lateral and inter-leaflet lipid-lipid interactions in cell membranes play roles in maintaining asymmetric lipid bilayers, the molecular basis of these interactions is largely unknown. Here, we established a method to determine the distribution ratio of phospholipids between the outer and inner leaflets of asymmetric large unilamellar vesicles (aLUVs). The trimethylammonium group, (CH3)3N+, in the choline headgroup of N-palmitoyl-sphingomyelin (PSM) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) gave rise to a relatively sharp signal in magic-angle spinning solid-state 1H NMR (MAS-ss-1H NMR). PSM and DOPC have the same headgroup structure, but one phospholipid was selectively observed by deuterating the trimethylammonium group of the other phospholipid. The addition of Pr3+ to the medium surrounding aLUVs selectively shifted the chemical shift of the (CH3)3N+ group in the outer leaflet from that in the inner leaflet, which allowed estimation of the inter-leaflet distribution ratio of the unlabeled lipid in aLUVs. Using this method, we evaluated the translocation of PSM and DOPC between the outer and inner leaflets of the cholesterol-containing aLUVs, with PSM and DOPC mostly distributed in the outer and inner leaflets, respectively, immediately after aLUV preparation; their flip and flop rates were approximately 2.7 and 6.4 × 10-6 s-1, respectively. During the passive symmetrization of aLUVs, the lipid translocation rate was decreased due to changes in the membrane order, probably through the formation of the registered liquid-ordered domains. Comparison of the result with that of symmetric LUVs revealed that lipid asymmetry may not significantly affect the lipid translocation rates, while the lateral lipid-lipid interaction may be a dominant factor in lipid translocation under these conditions. These findings highlight the importance of considering the effects of lateral lipid interactions within the same leaflet on lipid flip-flop rates when evaluating the asymmetry of phospholipids in the cell membrane.
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Affiliation(s)
- Hirofumi Watanabe
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Shinya Hanashima
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8550, Japan
| | - Yo Yano
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Tomokazu Yasuda
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Michio Murata
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan
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3
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Ondevilla JC, Hanashima S, Mukogawa A, Miyazato DG, Umegawa Y, Murata M. Effect of the number of sugar units on the interaction between diosgenyl saponin and membrane lipids. Biochim Biophys Acta Biomembr 2023; 1865:184145. [PMID: 36914020 DOI: 10.1016/j.bbamem.2023.184145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/15/2023]
Abstract
Saponin is the main bioactive component of the Dioscorea species, which are traditionally used for treating chronic diseases. An understanding of the interaction process of bioactive saponins with biomembranes provides insights into their development as therapeutic agents. The biological effects of saponins have been thought to be associated with membrane cholesterol (Chol). To shed light on the exact mechanisms of their interactions, we investigated the effects of diosgenyl saponins trillin (TRL) and dioscin (DSN) on the dynamic behavior of lipids and membrane properties in palmitoyloleolylphosphatidylcholine (POPC) bilayers using solid-state NMR and fluorescence spectroscopy. The membrane effects of diosgenin, a sapogenin of TRL and DSN, are similar to those of Chol, suggesting that diosgenin plays a major role in membrane binding and POPC chain ordering. The amphiphilicity of TRL and DSN enabled them to interact with POPC bilayers, regardless of Chol. In the presence of Chol, the sugar residues more prominently influenced the membrane-disrupting effects of saponins. The activity of DSN, which bears three sugar units, led to perturbation and further disruption of the membrane in the presence of Chol. However, TRL, which bears one sugar residue, increased the ordering of POPC chains while maintaining the integrity of the bilayer. This effect on the phospholipid bilayers is similar to that of cholesteryl glucoside. The influence of the number of sugars in saponin is discussed in more detail.
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Affiliation(s)
- Joan Candice Ondevilla
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan.
| | - Akane Mukogawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Darcy Garza Miyazato
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Forefront Research Centre for Fundamental Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Forefront Research Centre for Fundamental Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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Yasuda T, Slotte JP, Murata M, Hanashima S. Molecular Dynamics of Glycolipids in Liposomes. Methods Mol Biol 2023; 2613:257-270. [PMID: 36587084 DOI: 10.1007/978-1-0716-2910-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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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Affiliation(s)
- Tomokazu Yasuda
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Michio Murata
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shinya Hanashima
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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Yasuda T, Watanabe H, Hirosawa KM, Suzuki KGN, Suga K, Hanashima S. Fluorescence Spectroscopic Analysis of Lateral and Transbilayer Fluidity of Exosome Membranes. Langmuir 2022; 38:14695-14703. [PMID: 36421004 PMCID: PMC9731264 DOI: 10.1021/acs.langmuir.2c02258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Exosomes are small extracellular vesicles (sEVs) involved in distal cell-cell communication and cancer migration by transferring functional cargo molecules. Membrane domains similar to lipid rafts are assumed to occur in exosome membranes and are involved in interactions with target cells. However, the bilayer membrane properties of these small vesicles have not been fully investigated. Therefore, we examined the fluidity, lateral domain separation, and transbilayer asymmetry of exosome membranes using fluorescence spectroscopy. Although there were some differences between the exosomes, TMA-DPH anisotropy showing moderate lipid chain order indicated that ordered phases comprised a significant proportion of exosome membranes. Selective TEMPO quenching of the TMA-DPH fluorescence in the liquid-disordered phase indicated that 40-50% of the exosome membrane area belonged to the ordered phase based on a phase-separated model. Furthermore, NBD-PC in the outer leaflet showed longer fluorescence lifetimes than those in the inner leaflets. Therefore, the exosome membranes maintained transbilayer asymmetry with a topology similar to that of the plasma membranes. In addition, the lateral and transbilayer orders of exosome membranes obtained from different cell lines varied, probably depending on the different membrane lipid components and compositions partially derived from donor cells. As these higher membrane orders and asymmetric topologies are similar to those of cell membranes with lipid rafts, raft-like functional domains are possibly enriched on exosome membranes. These domains likely play key roles in the biological functions and cellular uptake of exosomes by facilitating selective membrane interactions with target organs.
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Affiliation(s)
- Tomokazu Yasuda
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
| | - Hirofumi Watanabe
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
| | - Koichiro M. Hirosawa
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu501-1193, Japan
| | - Kenichi G. N. Suzuki
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu501-1193, Japan
| | - Keishi Suga
- Department
of Chemical Engineering, Tohoku University, 6-6-07, Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi980-8579, Japan
| | - Shinya Hanashima
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
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Garza DL, Hanashima S, Umegawa Y, Murata M, Kinoshita M, Matsumori N, Greimel P. Behavior of Triterpenoid Saponin Ginsenoside Rh2 in Ordered and Disordered Phases in Model Membranes Consisting of Sphingomyelin, Phosphatidylcholine, and Cholesterol. Langmuir 2022; 38:10478-10491. [PMID: 35984899 DOI: 10.1021/acs.langmuir.2c01261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ginsenoside Rh2 (Rh2) is a saponin of medicinal ginseng, and it has attracted much attention for its pharmacological activities. In this study, we investigated the interaction of Rh2 with biological membranes using model membranes. We examined the effects of various lipids on the membrane-disrupting activity of Rh2 and found that cholesterol and sphingomyelin (SM) had no significant effect. Furthermore, the effects of Rh2 on acyl chain packing (DPH anisotropy) and water molecule permeability (GP340 values) did not differ significantly between bilayers containing SM and saturated phosphatidylcholine. These results suggest that the formation of the liquid-ordered (Lo) phase affects the behavior of Rh2 in the membrane rather than a specific interaction of Rh2 with a particular lipid. We investigated the effects of Rh2 on the Lo and liquid-disordered (Ld) phases using surface tension measurements and fluorescence experiments. In the surface tension-area isotherms, we compared the monolayers of the Ld and Lo lipid compositions and found that Rh2 is abundantly bound to both monolayers, with the amount being greater in the Ld phase than in the Lo phase. In addition, the hydration state of the bilayers, mainly consisting of the Lo or Ld phase, showed that Rh2 tends to bind to the surface of the bilayer in both phases. At higher concentrations, Rh2 tends to bind more abundantly to the relatively shallow interior of the Ld phase than the Lo phase. The phase-dependent membrane behavior of Rh2 is probably due to the phase-selective affinity and binding mode of Rh2.
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Affiliation(s)
- Darcy Lacanilao Garza
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Peter Greimel
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama 351-0198 Japan
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Hanashima S, Mito K, Umegawa Y, Murata M, Hojo H. Lipid chain-driven interaction of a lipidated Src-family kinase Lyn with the bilayer membrane. Org Biomol Chem 2022; 20:6436-6444. [PMID: 35880995 DOI: 10.1039/d2ob01079h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Myristoylation is a process of ubiquitous protein modification, which promotes the interaction of lipidated proteins on cell surfaces, in conjunction with reversible S-palmitoylation. We report the cooperative lipid-lipid interaction of two acyl chains of proteins, which increases the protein-membrane interaction and facilitates selective targeting of membranes containing anionic lipids. Lyn is a member of the Src family kinases distributed on the membrane surface by N-myristoyl and neighbouring S-palmitoyl chain anchors at the unique N-terminus domain. We prepared N-terminal short segments of lipidated Lyn to investigate the behaviour of each acyl chain in the lipid composition-dependent membrane interaction by solid-state nuclear magnetic resonance (NMR) analysis. Solid-state 31P-NMR studies revealed that S-palmitoylation of N-myristoylated Lyn peptides increased the interaction between peptides and phospholipid head groups, particularly with the anionic phosphatidylserine-containing bilayers. The solid-state 2H-NMR of Lyn peptides with a perdeutero N-myristoyl chain indicated an increase (0.6-0.8 Å) in the extent of the N-myristoyl chain in the presence of nearby S-palmitoyl chains, probably through the interaction via the acyl chains. The cooperative hydrocarbon chain interaction of the two acyl chains of Lyn increased membrane binding by extending the hydrocarbon chains deeper into the membrane interior, thereby promoting the peptide-membrane surface interaction between the cationic peptide side chains and the anionic lipid head groups. This lipid-driven mechanism by S-palmitoylation promotes the partition of the lipidated proteins to the cytoplasmic surface of the cell membranes and may be involved in recruiting Lyn at the signalling domains rich in anionic lipids.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Kanako Mito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan. .,Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hironobu Hojo
- Forefront Research Center, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.,Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
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Umegawa Y, Yamamoto T, Dixit M, Funahashi K, Seo S, Nakagawa Y, Suzuki T, Matsuoka S, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Shinoda W, Murata M. Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. Sci Adv 2022; 8:eabo2658. [PMID: 35714188 PMCID: PMC9205587 DOI: 10.1126/sciadv.abo2658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/04/2022] [Indexed: 05/30/2023]
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 the 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 present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Mayank Dixit
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Kosuke Funahashi
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Yasuo Nakagawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Taiga Suzuki
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Hanashima S, Ikeda R, Matsubara Y, Yasuda T, Tsuchikawa H, Slotte JP, Murata M. Effect of cholesterol on the lactosylceramide domains in phospholipid bilayers. Biophys J 2022; 121:1143-1155. [PMID: 35218738 PMCID: PMC9034317 DOI: 10.1016/j.bpj.2022.02.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/22/2021] [Accepted: 02/22/2022] [Indexed: 11/02/2022] Open
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 (Lo) phase by its potent order effect. In the LacCer/POPC binary systems without Cho, the 2H NMR spectra of 10',10'-d2-LacCer and 18',18',18'-d3-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 (Ld) domain. The lamellar structure of the LacCer/POPC membrane was gradually disrupted at around 60 °C, while 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, while the Lo 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 Ld domain of the LacCer/POPC/Cho membranes, as revealed by the fluorescence lifetimes of trans-parinaric acid (tPA) and tPA-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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Affiliation(s)
- Shinya Hanashima
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan.
| | - Ryuji Ikeda
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Matsubara
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
| | - Tomokazu Yasuda
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6 A, FIN 20520 Turku, Finland
| | - Michio Murata
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan; JST ERATO, Lipid Active Structure Project, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
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10
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Nakano M, Hanashima S, Hara T, Kabayama K, Asahina Y, Hojo H, Komura N, Ando H, Nyholm TKM, Slotte JP, Murata M. FRET detects lateral interaction between transmembrane domain of EGF receptor and ganglioside GM3 in lipid bilayers. Biochim Biophys Acta Biomembr 2021; 1863:183623. [PMID: 33933428 DOI: 10.1016/j.bbamem.2021.183623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/16/2022]
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 Förster 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.
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Affiliation(s)
- Mikito Nakano
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Toshiaki Hara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Asahina
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Thomas K M Nyholm
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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11
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Ondevilla JC, Hanashima S, Mukogawa A, Umegawa Y, Murata M. Diosgenin-induced physicochemical effects on phospholipid bilayers in comparison with cholesterol. Bioorg Med Chem Lett 2021; 36:127816. [PMID: 33516912 DOI: 10.1016/j.bmcl.2021.127816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
Diosgenin (DGN), which is a sterol occurring in plants of the Dioscorea family, has attracted increasing attention for its various pharmacological activities. DGN has a structural similarity to cholesterol (Cho). In this study we investigated the effects of the common tetracyclic cores and the different side chains on the physicochemical properties of lipid bilayer membranes. Differential scanning calorimetry showed that DGN and Cho reduce the phase transition enthalpy to a similar extent. In 2H NMR, deuterated-DGN/Cho and POPC showed similar ordering in POPC bilayers, which revealed that DGN is oriented parallel to the membrane normal like Cho. It was suggested that the affinity of DGN-Cho in membrane is stronger than that of DGN-DGN or Cho-Cho interaction. 31P NMR of POPC in bilayers revealed that, unlike Cho, DGN altered the interactions of POPC headgroups at 30 mol%. These results suggest that DGN below 30 mol% has similar effects with Cho on basic biomembrane properties.
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Affiliation(s)
- Joan Candice Ondevilla
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Akane Mukogawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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12
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Hanashima S, Fukuda N, Malabed R, Murata M, Kinoshita M, Greimel P, Hirabayashi Y. β-Glucosylation of cholesterol reduces sterol-sphingomyelin interactions. Biochim Biophys Acta Biomembr 2020; 1863:183496. [PMID: 33130096 DOI: 10.1016/j.bbamem.2020.183496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022]
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.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Nanami Fukuda
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Raymond Malabed
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Msanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Peter Greimel
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Yoshio Hirabayashi
- RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan; Institute for Environmental and Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan
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13
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Yano Y, Hanashima S, Tsuchikawa H, Yasuda T, Slotte JP, London E, Murata M. Sphingomyelins and ent-Sphingomyelins Form Homophilic Nano-Subdomains within Liquid Ordered Domains. Biophys J 2020; 119:539-552. [PMID: 32710823 PMCID: PMC7399500 DOI: 10.1016/j.bpj.2020.06.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
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 Förster 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.
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Affiliation(s)
- Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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14
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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.
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Affiliation(s)
- Raymond Malabed
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan
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15
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Kusaka H, Kita S, Tadokoro T, Yoshida K, Kasai Y, Niiyama H, Fujimoto Y, Hanashima S, Murata M, Sugiyama S, Ose T, Kuroki K, Maenaka K. Efficient preparation of human and mouse CD1d proteins using silkworm baculovirus expression system. Protein Expr Purif 2020; 172:105631. [PMID: 32213313 DOI: 10.1016/j.pep.2020.105631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/14/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
CD1d is a major histocompatibility complex (MHC) class I-like glycoprotein and binds to glycolipid antigens that are recognized by natural killer T (NKT) cells. To date, our understanding of the structural basis for glycolipid binding and receptor recognition of CD1d is still limited. Here, we established a preparation method for the ectodomain of human and mouse CD1d using a silkworm-baculovirus expression system. The co-expression of human and mouse CD1d and β2-microglobulin (β2m) in the silkworm-baculovirus system was successful, but the yield of human CD1d was low. A construct of human CD1d fused with β2m via a flexible GS linker as a single polypeptide was prepared to improve protein yield. The production of this single-chained complex was higher (50 μg/larva) than that of the co-expression complex. Furthermore, differential scanning calorimetry revealed that the linker made the CD1d complex more stable and homogenous. These results suggest that the silkworm-baculovirus expression system is useful for structural and biophysical studies of CD1d in several aspects including low cost, easy handling, biohazard-free, rapid, and high yielding.
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Affiliation(s)
- Hiroki Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Kouki Yoshida
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Yoshiyuki Kasai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Harumi Niiyama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yukari Fujimoto
- Department of Chemistry, Faculty of Science and Technology, Keio University, Yokohama, 223-8522, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Shigeru Sugiyama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Faculty of Science & Technology, Kochi University, Kochi, 780-8520, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kimiko Kuroki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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16
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Murata M, Hanashima S, Yano Y, Yasuda T, Tsuchikawa H, Matsumori N, Kinoshita M, Slotte J. Sphingomyelin Nanodomains Mainly Constitute Liquid-Ordered Phase of Ternary Model Membrane. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Hanashima S, Yano Y, Murata M. Enantiomers of phospholipids and cholesterol: A key to decipher lipid‐lipid interplay in membrane. Chirality 2020; 32:282-298. [DOI: 10.1002/chir.23171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
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18
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Takahashi M, Shirasaki J, Komura N, Sasaki K, Tanaka HN, Imamura A, Ishida H, Hanashima S, Murata M, Ando H. Efficient diversification of GM3 gangliosides via late-stage sialylation and dynamic glycan structural studies with 19F solid-state NMR. Org Biomol Chem 2020; 18:2902-2913. [DOI: 10.1039/d0ob00437e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GM3 gangliosides have been synthesized via late-stage α-sialylation using a macro-bicyclic sialyl donor. 19F solid-state NMR analysis of the C5-NHTFAc GM3 analog on a model membrane revealed the influence of cholesterol on glycan dynamics.
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Affiliation(s)
- Maina Takahashi
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Junya Shirasaki
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Katsuaki Sasaki
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hide-Nori Tanaka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Akihiro Imamura
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Hideharu Ishida
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
| | - Shinya Hanashima
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Michio Murata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
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19
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Yamamoto T, Umegawa Y, Tsuchikawa H, Hanashima S, Matsumori N, Funahashi K, Seo S, Shinoda W, Murata M. The Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly. Biochemistry 2019; 58:5188-5196. [PMID: 31793296 DOI: 10.1021/acs.biochem.9b00835] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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 Mn2+ residing near the surface of lipid bilayers induced the depth-dependent decay of 13C NMR signals for individual carbon atoms of AmB. We found that both terminal segments, the 41-COOH group and C38-C40 methyl groups, come close to the lipid bilayer surfaces, suggesting that the AmB-Erg complex spans a palmitoyloleoylphosphatidylcholine (POPC) bilayer with a single-molecule length. Molecular dynamics simulation experiments further confirmed the stabilization of the AmB-Erg complex as a single-length spanning complex. These results provide experimental evidence of the single-length complex incorporated in the membrane by making thinner a POPC-Erg bilayer that mimics fungal membranes.
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Affiliation(s)
- Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Department of Chemistry, Graduate School of Science , Kyushu University , Fukuoka 819-0395 , Japan
| | - Kosuke Funahashi
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Sangjae Seo
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Wataru Shinoda
- Department of Materials Chemistry , Nagoya University , Nagoya 464-8603 , Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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20
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Manabe Y, Marchetti R, Takakura Y, Nagasaki M, Nihei W, Takebe T, Tanaka K, Kabayama K, Chiodo F, Hanashima S, Kamada Y, Miyoshi E, Dulal HP, Yamaguchi Y, Adachi Y, Ohno N, Tanaka H, Silipo A, Fukase K, Molinaro A. The Core Fucose on an IgG Antibody is an Endogenous Ligand of Dectin‐1. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Roberta Marchetti
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
| | - Yohei Takakura
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Masahiro Nagasaki
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Wataru Nihei
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Tomoyuki Takebe
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Katsunori Tanaka
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Biofunctional Synthetic Chemistry LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kazuya Kabayama
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Fabrizio Chiodo
- Amsterdam UMCVrije Universiteit AmsterdamDept. of Molecular Cell Biology and ImmunologyAmsterdam Infection and Immunity Institute Amsterdam The Netherlands
| | - Shinya Hanashima
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yoshihiro Kamada
- Department of Molecular Biochemistry & Clinical InvestigationGraduate School of MedicineOsaka University 1–7 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry & Clinical InvestigationGraduate School of MedicineOsaka University 1–7 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Hari Prasad Dulal
- Structural Glycobiology TeamSystems Glycobiology Research GroupRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical ChemistryTohoku Medical and Pharmaceutical University 4-4-1 Komatsushima Aoba-ku, Sendai Miyagi 981-8558 Japan
| | - Yoshiyuki Adachi
- Laboratory for Immunopharmacology of Microbial ProductsSchool of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Naohito Ohno
- Laboratory for Immunopharmacology of Microbial ProductsSchool of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and EngineeringTokyo Institute of Technology 2-12-1-H-101, Ookayama, Meguro Tokyo 152-8552 Japan
| | - Alba Silipo
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
| | - Koichi Fukase
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Antonio Molinaro
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
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21
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Manabe Y, Marchetti R, Takakura Y, Nagasaki M, Nihei W, Takebe T, Tanaka K, Kabayama K, Chiodo F, Hanashima S, Kamada Y, Miyoshi E, Dulal HP, Yamaguchi Y, Adachi Y, Ohno N, Tanaka H, Silipo A, Fukase K, Molinaro A. The Core Fucose on an IgG Antibody is an Endogenous Ligand of Dectin-1. Angew Chem Int Ed Engl 2019; 58:18697-18702. [PMID: 31625659 DOI: 10.1002/anie.201911875] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 01/07/2023]
Abstract
The core fucose, a major modification of N-glycans, is implicated in immune regulation, such as the attenuation of the antibody-dependent cell-mediated cytotoxicity of antibody drugs and the inhibition of anti-tumor responses via the promotion of PD-1 expression on T cells. Although the core fucose regulates many biological processes, no core fucose recognition molecule has been identified in mammals. Herein, we report that Dectin-1, a known anti-β-glucan lectin, recognizes the core fucose on IgG antibodies. A combination of biophysical experiments further suggested that Dectin-1 recognizes aromatic amino acids adjacent to the N-terminal asparagine at the glycosylation site as well as the core fucose. Thus, Dectin-1 appears to be the first lectin-like molecule involved in the heterovalent and specific recognition of characteristic N-glycans on antibodies.
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Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
| | - Yohei Takakura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Masahiro Nagasaki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Wataru Nihei
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Tomoyuki Takebe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Katsunori Tanaka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Biofunctional Synthetic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Fabrizio Chiodo
- Amsterdam UMC, Vrije Universiteit Amsterdam, Dept. of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yoshihiro Kamada
- Department of Molecular Biochemistry & Clinical Investigation, Graduate School of Medicine, Osaka University, 1-7 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry & Clinical Investigation, Graduate School of Medicine, Osaka University, 1-7 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hari Prasad Dulal
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Yoshiyuki Adachi
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Naohito Ohno
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H-101, Ookayama, Meguro, Tokyo, 152-8552, Japan
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Antonio Molinaro
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
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22
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Hanashima S. NMR Study of Glycan Interactions Using Synthetic Oligosaccharides. TRENDS GLYCOSCI GLYC 2019. [DOI: 10.4052/tigg.1932.2se] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University
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23
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Hanashima S. NMR Study of Glycan Interactions Using Synthetic Oligosaccharides. TRENDS GLYCOSCI GLYC 2019. [DOI: 10.4052/tigg.1932.2sj] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University
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24
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Hanashima S, Murakami K, Yura M, Yano Y, Umegawa Y, Tsuchikawa H, Matsumori N, Seo S, Shinoda W, Murata M. Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup. Biophys J 2019; 117:307-318. [PMID: 31303249 DOI: 10.1016/j.bpj.2019.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
Sphingomyelin (SM) and cholesterol (Cho) are the important lipids for the formation of biologically functional membrane domains, lipid rafts. However, the interaction between Cho and the headgroup of SM remains unclear. In this study, we performed solid-state NMR experiments to reveal the Cho effects on the headgroup conformation using 2H-labeled stearoyl-SM (SSM). Deuterated SSMs at the Cα, Cβ, and Cγ positions of a choline moiety were separately prepared and subjected to NMR measurements to determine the quadrupolar splitting of 2H signals in hydrated SSM unitary and SSM/Cho (1:1) bilayers. Using 2H NMR and 13C-31P REDOR data, the conformation and orientation of the choline moiety were deduced and compared with those derived from molecular dynamics simulations. In SSM unitary bilayers, three torsional angles in the phosphocholine moiety, P-O-Cα-Cβ, were found to be consecutive +gauche(g)/+g/+g or -g/-g/-g. The orientation and conformation of the SSM headgroup were consistent with the results of our molecular dynamics simulations and the previous results on phosphatidylcholines. The quadrupolar coupling at the α methylene group slightly increased in the presence of Cho, and those at the Cβ and Cγ decreased more significantly, thus suggesting that Cho reduced the gauche conformation at the Cα-Cβ torsion. The conformational ensemble in the presence of Cho may enhance the so-called umbrella effect of the SSM headgroup, resulting in the stabilization of Cho near the SM molecules by concealing the hydrophobic Cho core from interfacial water. We also examined the effect of the chiral centers at the sphingosine chain to the headgroup conformation by determining the enantiomeric excess between the diastereomeric +g/+g/+g and -g/-g/-g conformers using (S)-Cα-deuterated and (R)-Cα-deuterated SSMs. Their 2H NMR measurements showed that the chiral centers induced the slight diastereomeric excess in the SM headgroup conformation.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Kazuhiro Murakami
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Michihiro Yura
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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25
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Yamamoto T, Umegawa Y, Yamagami M, Suzuki T, Tsuchikawa H, Hanashima S, Matsumori N, Murata M. The Perpendicular Orientation of Amphotericin B Methyl Ester in Hydrated Lipid Bilayers Supports the Barrel-Stave Model. Biochemistry 2019; 58:2282-2291. [PMID: 30973009 DOI: 10.1021/acs.biochem.9b00180] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The clinically important antibiotic amphotericin B (AmB) is a membrane-active natural product that targets membrane sterol. The antimicrobial activity of AmB is generally attributed to its membrane permeabilization, which occurs when a pore is formed across a lipid bilayer. In this study, the molecular orientation of AmB was investigated using solid-state nuclear magnetic resonance (NMR) to better understand the mechanism of antifungal activity. The methyl ester of AmB (AME) labeled with NMR isotopes, d3-AME, and its fluorinated and/or 13C-labeled derivatives were prepared. All of the AmB derivatives showed similar membrane-disrupting activities and ultraviolet spectra in phospholipid liposomes, suggesting that their molecular assemblies in membranes closely mimic those of AmB. Solid-state 2H NMR measurements of d3-AME in a hydrated membrane showed that the mobility of AME molecules depends on concentration and temperature. At a 1:5:45 AME:Erg:dimyristoylphosphatidylcholine ratio, AME became sufficiently mobilized to observe the motional averaging of quadrupole coupling. On the basis of the rotational averaging effect of 19F chemical shift anisotropy, 2H quadrupolar splitting, and 13C-19F dipolar coupling of 14β-F-AMEs, we deduced that the molecular axis of AME is predominantly parallel to the normal of a lipid bilayer. This result supports the barrel-stave model as a molecular assembly of AmB in membranes.
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Affiliation(s)
- Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Fundamental Science Research Center, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Masaki Yamagami
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Taiga Suzuki
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Department of Chemistry, Graduate School of Sciences , Kyushu University , Fukuoka 819-0395 , Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Fundamental Science Research Center, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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26
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Yoshida F, Yoshinaka H, Tanaka H, Hanashima S, Yamaguchi Y, Ishihara M, Saburomaru M, Kato Y, Saito R, Ando H, Kiso M, Imamura A, Ishida H. Cover Feature: Synthesis of the Core Oligosaccharides of Lipooligosaccharides from
Campylobacter jejuni
: A Putative Cause of Guillain–Barré Syndrome (Chem. Eur. J. 3/2019). Chemistry 2019. [DOI: 10.1002/chem.201805524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fumi Yoshida
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hiroki Yoshinaka
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hidenori Tanaka
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research GroupRIKEN Global Research Cluster 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research GroupRIKEN Global Research Cluster 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikio Ishihara
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Miyuki Saburomaru
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Yuki Kato
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Risa Saito
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Makoto Kiso
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Akihiro Imamura
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hideharu Ishida
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
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27
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Hanashima S, Ibata Y, Watanabe H, Yasuda T, Tsuchikawa H, Murata M. Side-chain deuterated cholesterol as a molecular probe to determine membrane order and cholesterol partitioning. Org Biomol Chem 2019; 17:8601-8610. [DOI: 10.1039/c9ob01342c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
24dCho, which perfectly retains the cholesterol's membrane properties, was developed to examine cholesterol's interactions and membrane partitions using solid state 2H NMR.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Yuki Ibata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hirofumi Watanabe
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Tomokazu Yasuda
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Michio Murata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
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28
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Yoshida F, Yoshinaka H, Tanaka H, Hanashima S, Yamaguchi Y, Ishihara M, Saburomaru M, Kato Y, Saito R, Ando H, Kiso M, Imamura A, Ishida H. Synthesis of the Core Oligosaccharides of Lipooligosaccharides from
Campylobacter jejuni
: A Putative Cause of Guillain–Barré Syndrome. Chemistry 2018; 25:796-805. [DOI: 10.1002/chem.201804862] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Fumi Yoshida
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hiroki Yoshinaka
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hidenori Tanaka
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research GroupRIKEN Global Research Cluster 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research GroupRIKEN Global Research Cluster 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikio Ishihara
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Miyuki Saburomaru
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Yuki Kato
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Risa Saito
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Makoto Kiso
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Akihiro Imamura
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
| | - Hideharu Ishida
- Department of Applied Bio-organic ChemistryGifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
- Center for Highly Advanced Integration and Nano and Life Sciences, (G-CHAIN)Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan
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29
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Yano Y, Hanashima S, Yasuda T, Tsuchikawa H, Matsumori N, Kinoshita M, Al Sazzad MA, Slotte JP, Murata M. Sphingomyelin Stereoisomers Reveal That Homophilic Interactions Cause Nanodomain Formation. Biophys J 2018; 115:1530-1540. [PMID: 30274830 DOI: 10.1016/j.bpj.2018.08.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/31/2018] [Accepted: 08/27/2018] [Indexed: 01/03/2023] Open
Abstract
Sphingomyelin is an abundant lipid in some cellular membrane domains, such as lipid rafts. Hydrogen bonding and hydrophobic interactions of the lipid with surrounding components such as neighboring sphingomyelin and cholesterol (Cho) are widely considered to stabilize the raft-like liquid-ordered (Lo) domains in membrane bilayers. However, details of their interactions responsible for the formation of Lo domains remain largely unknown. In this study, the enantiomer of stearoyl sphingomyelin (ent-SSM) was prepared, and its physicochemical properties were compared with the natural SSM and the diastereomer of SSM to examine possible stereoselective lipid-lipid interactions. Interestingly, differential scanning calorimetry experiments demonstrated that palmitoyl sphingomyelin, with natural stereochemistry, exhibited higher miscibility with SSM bilayers than with ent-SSM bilayers, indicating that the homophilic sphingomyelin interactions occurred in a stereoselective manner. Solid-state 2H NMR revealed that Cho elicited its ordering effect very similarly on SSM and ent-SSM (and even on the diastereomer of SSM), suggesting that SSM-Cho interactions are not significantly affected by stereospecific hydrogen bonding. SSM and ent-SSM formed gel-like domains with very similar lateral packing in SSM/Cho/palmitoyloleoyl phosphatidylcholine membranes, as shown by fluorescence lifetime experiments. This observation can be explained by a homophilic hydrogen-bond network, which was largely responsible for the formation of gel-like nanodomains of SSMs (or ent-SSM). Our previous study revealed that Cho-poor gel-like domains contributed significantly to the formation of an Lo phase in sphingomyelin/Cho membranes. The results of the study presented here further show that SSM-SSM interactions occur near the headgroup region, whereas hydrophobic SSM-Cho interactions appeared important in the bilayer interior for Lo domain formation. The homophilic interactions of sphingomyelins could be mainly responsible for the formation of the domains of nanometer size, which may correspond to the small sphingomyelin/Cho-based rafts that temporally occur in biological membranes.
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Affiliation(s)
- Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Md Abdullah Al Sazzad
- Biochemistry, Faculty of Science Engineering, Åbo Akademi University, Turku, Finland
| | - J Peter Slotte
- Biochemistry, Faculty of Science Engineering, Åbo Akademi University, Turku, Finland.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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30
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Hanashima S, Suga A, Yamaguchi Y. Bisecting GlcNAc restricts conformations of branches in model N-glycans with GlcNAc termini. Carbohydr Res 2018; 456:53-60. [PMID: 29274553 DOI: 10.1016/j.carres.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023]
Abstract
Bisected N-glycans play significant roles in tumor migration and Alzheimer's disease through modulating the action and localization of their carrier proteins. Such biological functions are often discussed in terms of the conformation of the attached N-glycans with or without bisecting GlcNAc. To obtain insights into the effects of bisecting GlcNAc on glycan conformation, a systematic NMR structural analysis was performed on two pairs of synthetic N-glycans, with and without bisecting GlcNAc. The analysis reveals that terminal GlcNAcs and bisecting GlcNAc cooperate to restrict the conformations of both the α1-3 and α1-6 branches of N-glycans. 1H and 13C chemical shift comparisons suggest that bisecting GlcNAc directly modulates local conformation. Unique NOE correlations between core-mannose and the α1-3 branch mannose as well as the 3JC-H constant of the glycoside linkage indicate that bisecting GlcNAc restricts the conformation of the 1-3 branch. The angles of the glycosidic bonds between core-mannose and α1-6 branch mannose derived from 3JC-H and 3JH-H coupling constants show that terminal GlcNAcs restrict the distribution of the ψ angle to 180° and the bisecting GlcNAc increases the distribution of the ω angle +60° in the presence of terminal GlcNAcs. It is feasible that restriction of branch conformations by bisecting GlcNAc has important consequences for protein-glycan interplay and following biological events.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Akitsugu Suga
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan.
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31
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Satake M, Cornelio K, Hanashima S, Malabed R, Murata M, Matsumori N, Zhang H, Hayashi F, Mori S, Kim JS, Kim CH, Lee JS. Structures of the Largest Amphidinol Homologues from the Dinoflagellate Amphidinium carterae and Structure-Activity Relationships. J Nat Prod 2017; 80:2883-2888. [PMID: 29120640 DOI: 10.1021/acs.jnatprod.7b00345] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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.
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Affiliation(s)
- Masayuki Satake
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kimberly Cornelio
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO Lipid Active Structure Project , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Raymond Malabed
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- JST ERATO Lipid Active Structure Project , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Sciences, Kyushu University , 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Huiping Zhang
- RIKEN Center for Life Science Technology , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Fumiaki Hayashi
- RIKEN Center for Life Science Technology , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences , Sikadai, Seika-cho, Soraku-gun, Kyoto 619-0284 Japan
| | - Jong Souk Kim
- Department of Marine Bio-materials & Aquaculture, Pukyong National University , Busan 608-737, Korea
| | - Chang-Hoon Kim
- Department of Marine Bio-materials & Aquaculture, Pukyong National University , Busan 608-737, Korea
| | - Jong-Soo Lee
- Department of Seafood and Aquaculture Science, College of Marine Science, Gyeongsang National University , Tongyeong, Kyungnam 650-160, Korea
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32
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Nagae M, Mishra SK, Hanashima S, Tateno H, Yamaguchi Y. Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa. Glycobiology 2017; 27:1120-1133. [DOI: 10.1093/glycob/cwx081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sushil K Mishra
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroaki Tateno
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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33
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Malabed R, Hanashima S, Murata M, Sakurai K. Sterol-recognition ability and membrane-disrupting activity of Ornithogalum saponin OSW-1 and usual 3-O-glycosyl saponins. Biochim Biophys Acta Biomembr 2017; 1859:2516-2525. [PMID: 28947142 DOI: 10.1016/j.bbamem.2017.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022]
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.
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Affiliation(s)
- Raymond Malabed
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Kaori Sakurai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan
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34
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Cornelio K, Espiritu RA, Todokoro Y, Hanashima S, Kinoshita M, Matsumori N, Murata M, Nishimura S, Kakeya H, Yoshida M, Matsunaga S. Sterol-dependent membrane association of the marine sponge-derived bicyclic peptide Theonellamide A as examined by 1H NMR. Bioorg Med Chem 2016; 24:5235-5242. [DOI: 10.1016/j.bmc.2016.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 11/29/2022]
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35
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Nakagawa Y, Umegawa Y, Matsushita N, Yamamoto T, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Murata M. The Structure of the Bimolecular Complex between Amphotericin B and Ergosterol in Membranes Is Stabilized by Face-to-Face van der Waals Interaction with Their Rigid Cyclic Cores. Biochemistry 2016; 55:3392-402. [DOI: 10.1021/acs.biochem.6b00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yasuo Nakagawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Naohiro Matsushita
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomoya Yamamoto
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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36
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Hossain MI, Hanashima S, Nomura T, Lethu S, Tsuchikawa H, Murata M, Kusaka H, Kita S, Maenaka K. Synthesis and Th1-immunostimulatory activity of α-galactosylceramide analogues bearing a halogen-containing or selenium-containing acyl chain. Bioorg Med Chem 2016; 24:3687-95. [PMID: 27325450 DOI: 10.1016/j.bmc.2016.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 12/13/2022]
Abstract
A novel series of CD1d ligand α-galactosylceramides (α-GalCers) were synthesized by incorporation of the heavy atoms Br and Se in the acyl chain backbone of α-galactosyl-N-cerotoylphytosphingosine. The synthetic analogues are potent CD1d ligands and stimulate mouse invariant natural killer T (iNKT) cells to selectively enhance Th1 cytokine production. These synthetic analogues would be efficient X-ray crystallographic probes to disclose precise atomic positions of alkyl carbons and lipid-protein interactions in KRN7000/CD1d complexes.
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Affiliation(s)
- Md Imran Hossain
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Takuto Nomura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sébastien Lethu
- JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Hiroki Kusaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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37
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Nagae M, Ikeda A, Hanashima S, Kojima T, Matsumoto N, Yamamoto K, Yamaguchi Y. Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan. FEBS Lett 2016; 590:1552. [PMID: 27218798 DOI: 10.1002/1873-3468.12206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Nagae M, Ikeda A, Hanashima S, Kojima T, Matsumoto N, Yamamoto K, Yamaguchi Y. Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan. FEBS Lett 2016; 590:1280-8. [PMID: 27015765 DOI: 10.1002/1873-3468.12162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/19/2016] [Accepted: 03/24/2016] [Indexed: 01/09/2023]
Abstract
Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor expressed in classical dendritic cells and accepts several oligosaccharide ligands including N-glycans. Here, we report the crystal structures of human DCIR C-type lectin domains in the absence and presence of a branched N-glycan unit. The domain has a typical C-type lectin fold and two bound calcium ions. In the ligand-bound form, the disaccharide unit (GlcNAcβ1-2Man) acceptably fits the electron density map, indicating that it forms the main epitope. The recognition of the nonterminal N-glycan unit explains the relatively broad specificity of this lectin.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Akemi Ikeda
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan
| | - Takumi Kojima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
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39
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Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y. Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins. Sci Rep 2016; 6:22973. [PMID: 26971576 PMCID: PMC4789653 DOI: 10.1038/srep22973] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/23/2016] [Indexed: 11/09/2022] Open
Abstract
Glycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylglucosamine (GlcNAc), is potentially a good model for investigating conformational dynamics and glycan-lectin interactions, owing to the unique ability of this sugar residue to alter conformer populations and thus modulate the biological activities. Here we analyzed bisected glycan in complex with two unrelated lectins, Calsepa and PHA-E. The crystal structures of the two complexes show a conspicuous flipped back glycan structure (designated 'back-fold' conformation), and solution NMR analysis also provides evidence of 'back-fold' glycan structure. Indeed, statistical conformational analysis of available bisected and non-bisected glycan structures suggests that bisecting GlcNAc restricts the conformations of branched structures. Restriction of glycan flexibility by certain sugar residues may be more common than previously thought and impinges on the mechanism of glycoform-dependent biological functions.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mayumi Kanagawa
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiko Kizuka
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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40
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Yamamoto T, Umegawa Y, Tsuchikawa H, Matsumori N, Hanashima S, Murata M, Haser R, Rawlings BJ, Caffrey P. Role of polyol moiety of amphotericin B in ion channel formation and sterol selectivity in bilayer membrane. Bioorg Med Chem 2015. [PMID: 26209267 DOI: 10.1016/j.bmc.2015.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Amphotericin B (AmB) is a polyene macrolide antibiotic widely used to treat mycotic infections. In this paper, we focus on the role of the polyol moiety of AmB in sterol selectivity using 7-oxo-AmB, 7α-OH-AmB, and 7β-OH-AmB. The 7-OH analogs were prepared from 7-oxo-AmB. Their K(+) flux activity in liposomes showed that introduction of an additional ketone or hydroxy group on the polyol moiety reduces the original activity. Conformational analyses of these derivatives indicated that intramolecular hydrogen-bonding network possibly influenced the conformational rigidity of the macrolactone ring, and stabilized the active conformation in the membrane. Additionally, the flexible polyol leads to destabilization of the whole macrolactone ring conformation, resulting in a loss of sterol selectivity.
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Affiliation(s)
- Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; JST, ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Resul Haser
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, England, United Kingdom
| | - Bernard J Rawlings
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, England, United Kingdom
| | - Patrick Caffrey
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland
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41
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Hanashima S, Götze S, Liu Y, Ikeda A, Kojima-Aikawa K, Taniguchi N, Varón Silva D, Feizi T, Seeberger PH, Yamaguchi Y. Defining the Interaction of Human Soluble Lectin ZG16p and Mycobacterial Phosphatidylinositol Mannosides. Chembiochem 2015; 16:1502-11. [PMID: 25919894 PMCID: PMC5896728 DOI: 10.1002/cbic.201500103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/11/2022]
Abstract
ZG16p is a soluble mammalian lectin that interacts with mannose and heparan sulfate. Here we describe detailed analysis of the interaction of human ZG16p with mycobacterial phosphatidylinositol mannosides (PIMs) by glycan microarray and NMR. Pathogen-related glycan microarray analysis identified phosphatidylinositol mono- and di-mannosides (PIM1 and PIM2) as novel ligand candidates of ZG16p. Saturation transfer difference (STD) NMR and transferred NOE experiments with chemically synthesized PIM glycans indicate that PIMs preferentially interact with ZG16p by using the mannose residues. The binding site of PIM was identified by chemical-shift perturbation experiments with uniformly (15)N-labeled ZG16p. NMR results with docking simulations suggest a binding mode of ZG16p and PIM glycan; this will help to elucidate the physiological role of ZG16p.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Sebastian Götze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Yan Liu
- Glycosciences Laboratory, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN (UK)
| | - Akemi Ikeda
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Kyoko Kojima-Aikawa
- The Glycoscience Institute, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)
| | - Naoyuki Taniguchi
- Disease Glycomics Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Ten Feizi
- Glycosciences Laboratory, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN (UK)
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan).
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42
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Nakagawa Y, Umegawa Y, Nonomura K, Matsushita N, Takano T, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Murata M. Axial Hydrogen at C7 Position and Bumpy Tetracyclic Core Markedly Reduce Sterol’s Affinity to Amphotericin B in Membrane. Biochemistry 2015; 54:303-12. [DOI: 10.1021/bi5012942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasuo Nakagawa
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kenichi Nonomura
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Naohiro Matsushita
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tetsuro Takano
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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43
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Tanaka K, Pradipta A, Tsutsui A, Ogura A, Hanashima S, Yamaguchi Y, Kurbangalieva A. Microfluidic Mixing of Polyamine with Acrolein Enables the Detection of the [4+4] Polymerization of Intermediary Unsaturated Imines: The Properties of a Cytotoxic 1,5-Diazacyclooctane Hydrogel. Synlett 2014. [DOI: 10.1055/s-0034-1378634] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | | | - Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster
| | - Almira Kurbangalieva
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University
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44
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Hanashima S, Korekane H, Taniguchi N, Yamaguchi Y. Synthesis of N-glycan units for assessment of substrate structural requirements of N-acetylglucosaminyltransferase III. Bioorg Med Chem Lett 2014; 24:4533-4537. [PMID: 25139566 DOI: 10.1016/j.bmcl.2014.07.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 12/27/2022]
Abstract
N-Acetylglucosaminyltransferase (GnT) III is a glycosyltransferase which produces bisected N-glycans by transferring GlcNAc to the 4-position of core mannose. Bisected N-glycans are involved in physiological and pathological processes through the functional regulation of their carrier proteins. An understanding of the biological functions of bisected glycans will be greatly accelerated by use of specific inhibitors of GnT-III. Thus far, however, such inhibitors have not been developed and even the substrate-binding mode of GnT-III is not fully understood. To gain insight into structural features required of the substrate, we systematically synthesized four N-glycan units, the branching parts of the bisected and non-bisected N-glycans. The series of syntheses were achieved from a common core trimannose, giving bisected tetra- and hexasaccharides as well as non-bisected tri- and pentasaccharides. A competitive GnT-III inhibition assay using the synthetic substrates revealed a vital role for the Manβ(1-4)GlcNAc moiety. In keeping with previous reports, GlcNAc at the α1,3-branch is also involved in the interaction. The structural requirements of GnT-III elucidated in this study will provide a basis for rational inhibitor design.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroaki Korekane
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan.
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45
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Isobe M, Murata M, Hanashima S, Nishida A, Loh TP, Rahman NA, Thasana N, Chittchang M. JSPS Asian Core Program: 7 th& 8 thICCEOCA (Phase II/NICCEOCA-3 & -4), 2 nd& 3 rdJunior ICCEOCA, and Partly IUPAC Asian Project. Chem Asian J 2014; 9:1689-96. [DOI: 10.1002/asia.201402189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Indexed: 11/07/2022]
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46
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Kanagawa M, Liu Y, Hanashima S, Ikeda A, Chai W, Nakano Y, Kojima-Aikawa K, Feizi T, Yamaguchi Y. Structural basis for multiple sugar recognition of Jacalin-related human ZG16p lectin. J Biol Chem 2014; 289:16954-65. [PMID: 24790092 PMCID: PMC4059138 DOI: 10.1074/jbc.m113.539114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ZG16p is a soluble mammalian lectin, the first to be described with a Jacalin-related β-prism-fold. ZG16p has been reported to bind both to glycosaminoglycans and mannose. To determine the structural basis of the multiple sugar-binding properties, we conducted glycan microarray analyses of human ZG16p. We observed that ZG16p preferentially binds to α-mannose-terminating short glycans such as Ser/Thr-linked O-mannose, but not to high mannose-type N-glycans. Among sulfated glycosaminoglycan oligomers examined, chondroitin sulfate B and heparin oligosaccharides showed significant binding. Crystallographic studies of human ZG16p lectin in the presence of selected ligands revealed the mechanism of multiple sugar recognition. Manα1–3Man and Glcβ1–3Glc bound in different orientations: the nonreducing end of the former and the reducing end of the latter fitted in the canonical shallow mannose binding pocket. Solution NMR analysis using 15N-labeled ZG16p defined the heparin-binding region, which is on an adjacent flat surface of the protein. On-array competitive binding assays suggest that it is possible for ZG16p to bind simultaneously to both types of ligands. Recognition of a broad spectrum of ligands by ZG16p may account for the multiple functions of this lectin in the formation of zymogen granules via glycosaminoglycan binding, and in the recognition of pathogens in the digestive system through α-mannose-related recognition.
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Affiliation(s)
- Mayumi Kanagawa
- From the Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yan Liu
- the Department of Medicine, Glycosciences Laboratory, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, United Kingdom,
| | - Shinya Hanashima
- From the Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akemi Ikeda
- From the Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Wengang Chai
- the Department of Medicine, Glycosciences Laboratory, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, United Kingdom
| | - Yukiko Nakano
- the Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and the The Glycoscience Institute, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kyoko Kojima-Aikawa
- the Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and the The Glycoscience Institute, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Ten Feizi
- the Department of Medicine, Glycosciences Laboratory, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, United Kingdom
| | - Yoshiki Yamaguchi
- From the Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan,
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47
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Yamamoto S, Subedi GP, Hanashima S, Satoh T, Otaka M, Wakui H, Sawada KI, Yokota SI, Yamaguchi Y, Kubota H, Itoh H. ATPase activity and ATP-dependent conformational change in the co-chaperone HSP70/HSP90-organizing protein (HOP). J Biol Chem 2014; 289:9880-6. [PMID: 24535459 PMCID: PMC3975032 DOI: 10.1074/jbc.m114.553255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Co-chaperones help to maintain cellular homeostasis by modulating the activities of molecular chaperones involved in protein quality control. The HSP70/HSP90-organizing protein (HOP) is a co-chaperone that cooperates with HSP70 and HSP90 in catalysis of protein folding and maturation in the cytosol. We show here that HOP has ATP-binding activity comparable to that of HSP70/HSP90, and that HOP slowly hydrolyzes ATP. Analysis of deletion mutants revealed that the ATPase domain of HOP is in the N-terminal TPR1-DP1-TPR2A segment. In addition, HOP changes its conformation in the presence of ATP. These results indicate that HOP is a unique co-chaperone that undergoes an ATP-dependent conformational change.
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Affiliation(s)
- Soh Yamamoto
- From the Department of Life Science, Faculty and Graduate School of Engineering and Resource Science, Akita University, Akita 010-8502, Japan
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48
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Nagae M, Soga K, Morita-Matsumoto K, Hanashima S, Ikeda A, Yamamoto K, Yamaguchi Y. Phytohemagglutinin from Phaseolus vulgaris (PHA-E) displays a novel glycan recognition mode using a common legume lectin fold. Glycobiology 2014; 24:368-78. [DOI: 10.1093/glycob/cwu004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Tsutsui A, Imamaki R, Kitazume S, Hanashima S, Yamaguchi Y, Kaneda M, Oishi S, Fujii N, Kurbangalieva A, Taniguchi N, Tanaka K. Polyamine modification by acrolein exclusively produces 1,5-diazacyclooctanes: a previously unrecognized mechanism for acrolein-mediated oxidative stress. Org Biomol Chem 2014; 12:5151-7. [DOI: 10.1039/c4ob00761a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polyamines were found to react with acrolein to produce 1,5-diazacyclooctane.
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Affiliation(s)
- Ayumi Tsutsui
- Biofunctional Synthetic Chemistry Laboratory
- RIKEN
- Saitama 351-0198, Japan
| | - Rie Imamaki
- Systems Glycobiology Research Group
- RIKEN-Max Planck Joint Research Center for Systems Chemical Biology
- RIKEN Global Research Cluster
- RIKEN
- Saitama 351-0198, Japan
| | - Shinobu Kitazume
- Systems Glycobiology Research Group
- RIKEN-Max Planck Joint Research Center for Systems Chemical Biology
- RIKEN Global Research Cluster
- RIKEN
- Saitama 351-0198, Japan
| | - Shinya Hanashima
- Systems Glycobiology Research Group
- RIKEN-Max Planck Joint Research Center for Systems Chemical Biology
- RIKEN Global Research Cluster
- RIKEN
- Saitama 351-0198, Japan
| | - Yoshiki Yamaguchi
- Systems Glycobiology Research Group
- RIKEN-Max Planck Joint Research Center for Systems Chemical Biology
- RIKEN Global Research Cluster
- RIKEN
- Saitama 351-0198, Japan
| | - Masato Kaneda
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501, Japan
| | - Almira Kurbangalieva
- Biofunctional Chemistry Laboratory
- A. Butlerov Institute of Chemistry
- Kazan Federal University
- Kazan 420008, Russia
| | - Naoyuki Taniguchi
- Systems Glycobiology Research Group
- RIKEN-Max Planck Joint Research Center for Systems Chemical Biology
- RIKEN Global Research Cluster
- RIKEN
- Saitama 351-0198, Japan
| | - Katsunori Tanaka
- Biofunctional Synthetic Chemistry Laboratory
- RIKEN
- Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory
- A. Butlerov Institute of Chemistry
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50
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Cho J, Sawaki K, Hanashima S, Yamaguchi Y, Shiro M, Saigo K, Ishida Y. Stabilization of β-peptide helices by direct attachment of trifluoromethyl groups to peptide backbones. Chem Commun (Camb) 2014; 50:9855-8. [DOI: 10.1039/c4cc02136c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct attachment of trifluoromethyl groups to peptide backbones was found to be a novel strategy for peptide folding stabilization, where the intramolecular hydrogen-bonding ability of backbone amides is enhanced.
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Affiliation(s)
- Joonil Cho
- RIKEN Center for Emergent Matter Science
- Wako, Japan
| | - Kyohei Sawaki
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Bunkyo-ku, Japan
| | - Shinya Hanashima
- RIKEN Global Research Cluster
- Structural Glycobiology Team
- Wako, Japan
| | - Yoshiki Yamaguchi
- RIKEN Global Research Cluster
- Structural Glycobiology Team
- Wako, Japan
| | | | - Kazuhiko Saigo
- School of Environmental Science and Engineering
- Kochi University of Technology
- Kochi 782-8502, Japan
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