51
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Mönnich M, Eller S, Karagiannis T, Perkams L, Luber T, Ott D, Niemietz M, Hoffman J, Walcher J, Berger L, Pischl M, Weishaupt M, Wirkner C, Lichtenstein RG, Unverzagt C. Hocheffiziente Synthese von multiantennären “bisected” N-Glycanen über Imidate. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Manuel Mönnich
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Steffen Eller
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | | | - Lukas Perkams
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Thomas Luber
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Dimitri Ott
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Mathäus Niemietz
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Joanna Hoffman
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Janika Walcher
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Lukas Berger
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Matthias Pischl
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Markus Weishaupt
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Cathrin Wirkner
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
| | - Rachel G. Lichtenstein
- Department of Biotechnology Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Carlo Unverzagt
- Bioorganische Chemie, Gebäude NW1; Universität Bayreuth; 95440 Bayreuth Deutschland
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52
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Mönnich M, Eller S, Karagiannis T, Perkams L, Luber T, Ott D, Niemietz M, Hoffman J, Walcher J, Berger L, Pischl M, Weishaupt M, Wirkner C, Lichtenstein RG, Unverzagt C. Highly Efficient Synthesis of Multiantennary Bisected N-glycans Based on Imidates. Angew Chem Int Ed Engl 2016; 55:10487-92. [PMID: 27443163 DOI: 10.1002/anie.201604190] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/11/2022]
Abstract
The occurrence of N-glycans with a bisecting GlcNAc modification on glycoproteins has many implications in developmental and immune biology. However, these particular N-glycans are difficult to obtain either from nature or through synthesis. We have developed a flexible and general method for synthesizing bisected N-glycans of the complex type by employing modular TFAc-protected donors for all antennae. The TFAc-protected N-glycans are suitable for the late introduction of a bisecting GlcNAc. This integrated strategy permits for the first time the use of a single approach for multiantennary N-glycans as well as their bisected derivatives via imidates, with unprecedented yields even in a one-pot double glycosylation. With this new method, rare N-glycans of the bisected type can be obtained readily, thereby providing defined tools to decipher the biological roles of bisecting GlcNAc modifications.
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Affiliation(s)
- Manuel Mönnich
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Steffen Eller
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | | | - Lukas Perkams
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Thomas Luber
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Dimitri Ott
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Mathäus Niemietz
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Joanna Hoffman
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Janika Walcher
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Lukas Berger
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Matthias Pischl
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Markus Weishaupt
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Cathrin Wirkner
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany
| | - Rachel G Lichtenstein
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Carlo Unverzagt
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440, Bayreuth, Germany.
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53
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Only the complex N559-glycan in the synaptic vesicle glycoprotein 2C mediates high affinity binding to botulinum neurotoxin serotype A1. Biochem J 2016; 473:2645-54. [PMID: 27313224 DOI: 10.1042/bcj20160439] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/16/2016] [Indexed: 11/17/2022]
Abstract
The extraordinary potency of botulinum neurotoxins (BoNTs) is mediated by their high neurospecificity, targeting peripheral cholinergic motoneurons leading to flaccid paralysis and successive respiratory failure. Complex polysialo gangliosides accumulate BoNTs on the plasma membrane and facilitate subsequent binding to synaptic vesicle membrane proteins which results in toxin endocytosis. The luminal domain 4 (LD4) of the three synaptic vesicle glycoprotein 2 (SV2) isoforms A-C mediates uptake of the clinically most relevant serotype BoNT/A1. SV2C-LD4 exhibits the strongest protein-protein interaction and comprises five putative N-glycosylation sites (PNG sites). Here, we expressed human SV2C-LD4 fused to human IgG-Fc in prokaryotic and eukaryotic expression systems to analyse the effect of N-glycosylation of SV2C on the interaction with BoNT/A1. Mass spectrometric analysis of gSV2CLD-Fc demonstrates glycosylation of N534, N559 and N565, the latter two residing at the BoNT/A interface. Mutational analysis demonstrates that only the N559-glycan, but not N565-glycan increases affinity of BoNT/A for human gSV2C-LD4. The N559-glycan was characterised as a complex core-fucosylated type with a heterogeneity ranging up to tetra-antennary structure with bisecting N-acetylglucosamine which can establish extensive interactions with BoNT/A. The mutant gSV2CLD-Fc N559A displayed a 50-fold increased dissociation rate kd resulting in an overall 12-fold decreased binding affinity in surface plasmon resonance (SPR) experiments. The delayed dissociation might provide BoNT/A more time for endocytosis into synaptic vesicles. In conclusion, we show the importance of the complex N559-glycan of SV2C-LD4, adding a third anchor point beside a ganglioside and the SV2C-LD4 peptide, for BoNT/A neuronal cell surface binding and uptake.
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Yang M, Huang J, MacKerell AD. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension. J Chem Theory Comput 2016; 11:2855-67. [PMID: 26082676 PMCID: PMC4463548 DOI: 10.1021/acs.jctc.5b00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 12/17/2022]
Abstract
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Replica exchange (REX) is a powerful
computational tool for overcoming
the quasi-ergodic sampling problem of complex molecular systems. Recently,
several multidimensional extensions of this method have been developed
to realize exchanges in both temperature and biasing potential space
or the use of multiple biasing potentials to improve sampling efficiency.
However, increased computational cost due to the multidimensionality
of exchanges becomes challenging for use on complex systems under
explicit solvent conditions. In this study, we develop a one-dimensional
(1D) REX algorithm to concurrently combine the advantages of overall
enhanced sampling from Hamiltonian solute scaling and the specific
enhancement of collective variables using Hamiltonian biasing potentials.
In the present Hamiltonian replica exchange method, termed HREST-BP,
Hamiltonian solute scaling is applied to the solute subsystem, and
its interactions with the environment to enhance overall conformational
transitions and biasing potentials are added along selected collective
variables associated with specific conformational transitions, thereby
balancing the sampling of different hierarchical degrees of freedom.
The two enhanced sampling approaches are implemented concurrently
allowing for the use of a small number of replicas (e.g., 6 to 8)
in 1D, thus greatly reducing the computational cost in complex system
simulations. The present method is applied to conformational sampling
of two nitrogen-linked glycans (N-glycans) found
on the HIV gp120 envelope protein. Considering the general importance
of the conformational sampling problem, HREST-BP represents an efficient
procedure for the study of complex saccharides, and, more generally,
the method is anticipated to be of general utility for the conformational
sampling in a wide range of macromolecular systems.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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55
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Yang M, MacKerell AD. Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM). J Chem Theory Comput 2016; 11:788-99. [PMID: 25705140 DOI: 10.1021/ct500993h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Oligosaccharides and polysaccharides exert numerous functional roles in biology through their structural diversity and conformational properties. To investigate their conformational properties using computational methods, Hamiltonian replica exchange (H-REX) combined with two-dimensional grid-based correction maps as biasing potentials (bpCMAP) significantly improves the sampling efficiency about glycosidic linkages. In the current study, we extend the application of H-REX with bpCMAP to complex saccharides and establish systematic procedures for bpCMAP construction, determination of replica distribution, and data analysis. Our main findings are that (1) the bpCMAP for each type of glycosidic linkage can be constructed from the corresponding disaccharide using gas-phase umbrella sampling simulations, (2) the replica distribution can be conveniently determined following the exact definition of the average acceptance ratio based on the assigned distribution of biasing potentials, and (3) the extracted free energy surface (or potential of mean force (PMF)) can be improved using the weighted histogram analysis method (WHAM) allowing for the inclusion of data from the excited state replicas in the calculated probability distribution. The method is applied to a branched N-glycan found on the HIV gp120 protein, and a linear N-glycan. Considering the general importance of N-glycans and the wide appreciation of the sampling problem, the present method represents an efficient procedure for the conformational sampling of complex oligo- and polysaccharides under explicit solvent conditions. More generally, the use of WHAM is anticipated to be of general utility for the calculation of PMFs from H-REX simulations in a wide range of macromolecular systems.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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56
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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] [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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57
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Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1635-51. [PMID: 26766517 DOI: 10.1016/j.bbamem.2015.12.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Takaharu Mori
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Miyashita
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Faculty of Biology-Oriented Science and Technology, KINDAI University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Wonpil Im
- Department of Molecular Sciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
| | - Yuji Sugita
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States; Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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58
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Bisecting GlcNAc modification stabilizes BACE1 protein under oxidative stress conditions. Biochem J 2015; 473:21-30. [DOI: 10.1042/bj20150607] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022]
Abstract
BACE1 is a protease essential for amyloid-β production in Alzheimer's disease. We report that bisecting GlcNAc modification on BACE1 stabilizes BACE1 protein under oxidative stress conditions. This suggests that bisecting GlcNAc is a therapeutic target for Alzheimer's disease.
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59
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Jo S, Qi Y, Im W. Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology 2015; 26:19-29. [PMID: 26405106 DOI: 10.1093/glycob/cwv083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
N-linked glycans are on protein surfaces and have direct and water/ion-mediated interactions with surrounding amino acids. Such contacts could restrict their conformational freedom compared to the same glycans free in solution. In this work, we have examined the conformational freedom of the N-glycan core pentasaccharide moiety in solution using standard molecular dynamics (MD) simulations as well as temperature replica-exchange MD simulations. Both simulations yield the comparable conformational variability of the pentasaccharide in solution, indicating the convergence of both simulations. The glycoprotein crystal structures are analyzed to compare the conformational freedom of the N-glycan on the protein surface with the simulation result. Surprisingly, the pentasaccharide free in solution shows more restricted conformational variability than the N-glycan on the protein surface. The interactions between the carbohydrate and the protein side chain appear to be responsible for the increased conformational diversity of the N-glycan on the protein surface. Finally, the transfer entropy analysis of the simulation trajectory also reveals an unexpected causality relationship between intramolecular hydrogen bonds and the conformational states in that the hydrogen bonds play a role in maintaining the conformational states rather than driving the change in glycosidic torsional states.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Center, Argonne National Laboratory, 9700 Cass Ave Bldg. 240, Argonne, IL 60439, USA
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
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60
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Pereira PR, Winter HC, Verícimo MA, Meagher JL, Stuckey JA, Goldstein IJ, Paschoalin VMF, Silva JT. Structural analysis and binding properties of isoforms of tarin, the GNA-related lectin from Colocasia esculenta. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:20-30. [PMID: 25448725 DOI: 10.1016/j.bbapap.2014.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
The lectins, a class of proteins that occur widely in animals, plants, fungi, lichens and microorganisms, are known for their ability to specifically bind to carbohydrates. Plant lectins can be classified into 12 families including the Galanthus nivalis agglutinin (GNA)-related lectin superfamily, which is widespread among monocotyledonous plants and binds specifically to mannose, a behavior that confers remarkable anti-tumor, anti-viral and insecticidal properties on these proteins. The present study characterized a mitogenic lectin from this family, called tarin, which was purified from the crude extract from taro (Colocasia esculenta). The results showed that tarin is a glycoprotein with 2-3% carbohydrate content, composed of least 10 isoforms with pIs ranging from 5.5 to 9.5. The intact protein is a heterotetramer of 47kDa composed of two non-identical and non-covalently associated polypeptides, with small subunits of 11.9kDa and large subunits of 12.6kDa. The tarin structure is stable and recovers or maintains its functional structure following treatments at different temperatures and pH. Tarin showed a complex carbohydrate specificity, binding with high affinity to high-mannose and complex N-glycans. Many of these ligands can be found in viruses, tumor cells and insects, as well as in hematopoietic progenitor cells. Chemical modifications confirmed that both conserved and non-conserved amino acids participate in this interaction. This study determined the structural and ligand binding characteristics of a GNA-related lectin that can be exploited for several different purposes, particularly as a proliferative therapeutic molecule that is able to enhance the immunological response.
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Affiliation(s)
- Patrícia R Pereira
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
| | - Harry C Winter
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Mauricio A Verícimo
- Instituto de Biologia, Universidade Federal Fluminense, Rio de Janeiro 4020141, Brazil.
| | - Jennifer L Meagher
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jeanne A Stuckey
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Irwin J Goldstein
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Vânia M F Paschoalin
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
| | - Joab T Silva
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
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61
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Ihara H, Okada T, Ikeda Y. Cloning, expression and characterization of Bombyx mori α1,6-fucosyltransferase. Biochem Biophys Res Commun 2014; 450:953-60. [DOI: 10.1016/j.bbrc.2014.06.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 06/17/2014] [Indexed: 01/12/2023]
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Kurimoto A, Kitazume S, Kizuka Y, Nakajima K, Oka R, Fujinawa R, Korekane H, Yamaguchi Y, Wada Y, Taniguchi N. The absence of core fucose up-regulates GnT-III and Wnt target genes: a possible mechanism for an adaptive response in terms of glycan function. J Biol Chem 2014; 289:11704-11714. [PMID: 24619415 DOI: 10.1074/jbc.m113.502542] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycans play key roles in a variety of protein functions under normal and pathological conditions, but several glycosyltransferase-deficient mice exhibit no or only mild phenotypes due to redundancy or compensation of glycan functions. However, we have only a limited understanding of the underlying mechanism for these observations. Our previous studies indicated that 70% of Fut8-deficient (Fut8(-/-)) mice that lack core fucose structure die within 3 days after birth, but the remainder survive for up to several weeks although they show growth retardation as well as emphysema. In this study, we show that, in mouse embryonic fibroblasts (MEFs) from Fut8(-/-) mice, another N-glycan branching structure, bisecting GlcNAc, is specifically up-regulated by enhanced gene expression of the responsible enzyme N-acetylglucosaminyltransferase III (GnT-III). As candidate target glycoproteins for bisecting GlcNAc modification, we confirmed that level of bisecting GlcNAc on β1-integrin and N-cadherin was increased in Fut8(-/-) MEFs. Moreover using mass spectrometry, glycan analysis of IgG1 in Fut8(-/-) mouse serum demonstrated that bisecting GlcNAc contents were also increased by Fut8 deficiency in vivo. As an underlying mechanism, we found that in Fut8(-/-) MEFs Wnt/β-catenin signaling is up-regulated, and an inhibitor against Wnt signaling was found to abrogate GnT-III expression, indicating that Wnt/β-catenin is involved in GnT-III up-regulation. Furthermore, various oxidative stress-related genes were also increased in Fut8(-/-) MEFs. These data suggest that Fut8(-/-) mice adapted to oxidative stress, both ex vivo and in vivo, by inducing various genes including GnT-III, which may compensate for the loss of core fucose functions.
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Affiliation(s)
- Ayako Kurimoto
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Shinobu Kitazume
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Yasuhiko Kizuka
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Kazuki Nakajima
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Ritsuko Oka
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Reiko Fujinawa
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Hiroaki Korekane
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, RIKEN Global Research Cluster, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198
| | - Yoshinao Wada
- Research Institute, Osaka Medical Center for Maternal and Child Health, Izumi, Osaka, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Naoyuki Taniguchi
- Disease Glycomic Team, RIKEN-Max Planck Joint Research Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198.
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Zhang Y, Yamaguchi T, Kato K. New NMR Tools for Characterizing the Dynamic Conformations and Interactions of Oligosaccharides. CHEM LETT 2013. [DOI: 10.1246/cl.130789] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ying Zhang
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- The Glycoscience Institute, Ochanomizu University
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65
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Canales A, Mallagaray A, Pérez-Castells J, Boos I, Unverzagt C, André S, Gabius HJ, Cañada FJ, Jiménez-Barbero J. Breaking Pseudo-Symmetry in Multiantennary Complex N-Glycans Using Lanthanide-Binding Tags and NMR Pseudo-Contact Shifts. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307845] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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66
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Canales A, Mallagaray A, Pérez-Castells J, Boos I, Unverzagt C, André S, Gabius HJ, Cañada FJ, Jiménez-Barbero J. Breaking Pseudo-Symmetry in Multiantennary Complex N-Glycans Using Lanthanide-Binding Tags and NMR Pseudo-Contact Shifts. Angew Chem Int Ed Engl 2013; 52:13789-93. [DOI: 10.1002/anie.201307845] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Indexed: 01/24/2023]
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67
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Nagae M, Yamanaka K, Hanashima S, Ikeda A, Morita-Matsumoto K, Satoh T, Matsumoto N, Yamamoto K, Yamaguchi Y. Recognition of bisecting N-acetylglucosamine: structural basis for asymmetric interaction with the mouse lectin dendritic cell inhibitory receptor 2. J Biol Chem 2013; 288:33598-33610. [PMID: 24108122 DOI: 10.1074/jbc.m113.513572] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Dendritic cell inhibitory receptor 2 (DCIR2) is a C-type lectin expressed on classical dendritic cells. We recently identified the unique ligand specificity of mouse DCIR2 (mDCIR2) toward biantennary complex-type glycans containing bisecting N-acetylglucosamine (GlcNAc). Here, we report the crystal structures of the mDCIR2 carbohydrate recognition domain in unliganded form as well as in complex with an agalactosylated complex-type N-glycan unit carrying a bisecting GlcNAc residue. Bisecting GlcNAc and the α1-3 branch of the biantennary oligosaccharide asymmetrically interact with canonical and non-canonical mDCIR2 residues. Ligand-protein interactions occur directly through mDCIR2-characteristic amino acid residues as well as via a calcium ion and water molecule. Our structural and biochemical data elucidate for the first time the unique binding mode of mDCIR2 for bisecting GlcNAc-containing glycans, a mode that contrasts sharply with that of other immune C-type lectin receptors such as DC-SIGN.
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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, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kousuke Yamanaka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Shinya Hanashima
- 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
- 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
| | - Kana Morita-Matsumoto
- 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
| | - Tadashi Satoh
- 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
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yoshiki Yamaguchi
- 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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68
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Ihara H, Hanashima S, Tsukamoto H, Yamaguchi Y, Taniguchi N, Ikeda Y. Difucosylation of chitooligosaccharides by eukaryote and prokaryote α1,6-fucosyltransferases. Biochim Biophys Acta Gen Subj 2013; 1830:4482-90. [PMID: 23688399 DOI: 10.1016/j.bbagen.2013.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/24/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND The synthesis of eukaryotic N-glycans and the rhizobia Nod factor both involve α1,6-fucosylation. These fucosylations are catalyzed by eukaryotic α1,6-fucosyltransferase, FUT8, and rhizobial enzyme, NodZ. The two enzymes have similar enzymatic properties and structures but display different acceptor specificities: FUT8 and NodZ prefer N-glycan and chitooligosaccharide, respectively. This study was conducted to examine the fucosylation of chitooligosaccharides by FUT8 and NodZ and to characterize the resulting difucosylated chitooligosaccharides in terms of their resistance to hydrolysis by glycosidases. METHODS The issue of whether FUT8 or NodZ catalyzes the further fucosylation of chitooligosaccharides that had first been monofucosylated by the other. The oligosaccharide products from the successive reactions were analyzed by normal-phase high performance liquid chromatography, mass spectrometry and nuclear magnetic resonance. The effect of difucosylation on sensitivity to glycosidase digestion was also investigated. RESULTS Both FUT8 and NodZ are able to further fucosylate the monofucosylated chitooligosaccharides. Structural analyses of the resulting oligosaccharides showed that the reducing terminal GlcNAc residue and the third GlcNAc residue from the non-reducing end are fucosylated via α1,6-linkages. The difucosylation protected the oligosaccharides from extensive degradation to GlcNAc by hexosamidase and lysozyme, and also even from defucosylation by fucosidase. CONCLUSIONS The sequential actions of FUT8 and NodZ on common substrates effectively produce site-specific-difucosylated chitooligosaccharides. This modification confers protection to the oligosaccharides against various glycosidases. GENERAL SIGNIFICANCE The action of a combination of eukaryotic and bacterial α1,6-fucosyltransferases on chitooligosaccharides results in the formation of difucosylated products, which serves to stabilize chitooligosaccharides against the action of glycosidases.
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Key Words
- COSY
- Chitooligosaccharide
- FUT8-monofucosylated chitooligosaccharide
- Fuc
- Fucosylation
- Fucosyltransferase
- GDP
- GN1
- GN2
- GN3
- GN4
- GN5
- GN6
- GNF
- GNFF′
- GNF′
- GlcNAc or N-acetylglucosamine
- Glycosidase
- HPLC
- HSQC
- Lysozyme
- MALDI
- MS
- N,N′,N″,N‴,N‴′,N‴″-hexaacetyl chitohexaose
- N,N′,N″,N‴,N‴′-pentaacetyl chitopentaose
- N,N′,N″,N‴-tetraacetyl chitotetraose
- N,N′,N″-triacetyl chitotriose
- N,N′-diacetyl chitobiose
- NMR
- NodZ-monofucosylated chitooligosaccharide
- TOCSY
- TOF
- correlation spectroscopy
- difucosylated chitooligosaccharide
- fucose
- guanine nucleotide diphosphate
- hetero-nuclear single quantum coherence
- high performance liquid chromatography
- mass spectrometry
- matrix-assisted laser desorption/ionization
- nuclear magnetic resonance
- time of flight
- total correlation spectroscopy
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Affiliation(s)
- Hideyuki Ihara
- Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
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Kötzler MP, Blank S, Bantleon FI, Spillner E, Meyer B. Donor substrate binding and enzymatic mechanism of human core α1,6-fucosyltransferase (FUT8). Biochim Biophys Acta Gen Subj 2012; 1820:1915-25. [PMID: 22982178 DOI: 10.1016/j.bbagen.2012.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND Fucosylation is essential for various biological processes including tumorigenesis, inflammation, cell-cell recognition and host-pathogen interactions. Biosynthesis of fucosylated glycans is accomplished by fucosyltransferases. The enzymatic product of core α1,6-fucosyltransferase (FUT8) plays a major role in a plethora of pathological conditions, e.g. in prognosis of hepatocellular carcinoma and in colon cancer. Detailed knowledge of the binding mode of its substrates is required for the design of molecules that can modulate the activity of the enzyme. METHODS We provide a detailed description of binding interactions of human FUT8 with its natural donor substrate GDP-fucose and related compounds. GDP-Fuc was placed in FUT8 by structural analogy to the structure of protein-O-fucosyltransferase (cePOFUT) co-crystallized with GDP-Fuc. The epitope of the donor substrate bound to FUT8 was determined by STD NMR. The in silico model is further supported by experimental data from SPR binding assays. The complex was optimized by molecular dynamics simulations. RESULTS Guanine is specifically recognized by His363 and Asp453. Furthermore, the pyrophosphate is tightly bound via numerous hydrogen bonds and contributes affinity to a major part. Arg365 was found to bind both the β-phosphate and the fucose moiety at the same time. CONCLUSIONS Discovery of a novel structural analogy between cePOFUT and FUT8 allows the placement of the donor substrate GDP-Fuc. The positioning was confirmed by various experimental and computational techniques. GENERAL SIGNIFICANCE The model illustrates details of the molecular basis of substrate recognition for a human fucosyltransferase for the first time and, thus, provides a basis for structure-based design of inhibitors.
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Re S, Nishima W, Miyashita N, Sugita Y. Conformational flexibility of N-glycans in solution studied by REMD simulations. Biophys Rev 2012; 4:179-187. [PMID: 28510079 DOI: 10.1007/s12551-012-0090-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/21/2012] [Indexed: 01/09/2023] Open
Abstract
Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Wataru Nishima
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoyuki Miyashita
- RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .,RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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