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Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C. A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes. J Chem Theory Comput 2023; 19:9077-9092. [PMID: 38091976 PMCID: PMC11145395 DOI: 10.1021/acs.jctc.3c00941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.
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Affiliation(s)
- Marharyta Blazhynska
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332, United States
| | - Haochuan Chen
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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2
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Vosegaard T. Single-crystal NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:51-72. [PMID: 34078537 DOI: 10.1016/j.pnmrs.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Single-crystal (SC) NMR spectroscopy is a solid-state NMR method that has been used since the early days of NMR to study the magnitude and orientation of tensorial nuclear spin interactions in solids. This review first presents the field of SC NMR instrumentation, then provides a survey of software for analysis of SC NMR data, and finally it highlights selected applications of SC NMR in various fields of research. The aim of the last part is not to provide a complete review of all SC NMR literature but to provide examples that demonstrate interesting applications of SC NMR.
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Affiliation(s)
- Thomas Vosegaard
- Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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3
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Mortensen HG, Jensen GV, Hansen SK, Vosegaard T, Pedersen JS. Structure of Phospholipid Mixed Micelles (Bicelles) Studied by Small-Angle X-ray Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14597-14607. [PMID: 30383384 DOI: 10.1021/acs.langmuir.8b02704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mixed phospholipid micelles (bicelles) are widely applied in nuclear magnetic resonance (NMR) studies of membrane proteins in solution, as they can solubilize these proteins and provide a membrane-like environment. In this work, the structure of bicelles of dihexanoyl phosphatidyl choline (DHPC) and dimyristoyl phosphatidyl choline (DMPC) at different ratios was determined by small-angle X-ray scattering (SAXS) at 37 °C. Samples with concentrations as applied for NMR measurements with 28 wt % lipids were diluted to avoid concentration effects in the SAXS data. The DMPC/DHPC ratio within the bicelles was kept constant by diluting with solutions of finite DHPC concentrations, where the concentration of free DHPC is the same as in the original solution. Absolute-scale modeling of the SAXS data using molecular and concentration constraints reveals a relatively complex set of morphologies of the lipid aggregates as a function of the molar ratio Q of DMPC to DHPC. At Q = 0 (pure DHPC lipids), oblate core-shell micelles are present. At Q = 0.5, the bicelles have a tablet-shaped core-shell cylindrical form with an ellipsoidal cross section. For Q = 1, 2, 3.2, and 4, the bicelles have a rectangular cuboidal structure with a core and a shell, for which the overall length and width increase with Q. At Q = ∞ (pure DMPC), there is coexistence between multilamellar structures and free bilayers. For Q = 1-4, the hydrocarbon core is relatively narrow and the headgroup thickness on the flat areas is larger than that of, respectively, pure DHPC and DMPC, suggesting some mixing of DHPC into these areas and staggering of the molecules. This is further supported by comparisons of the ratio of the areas of rim and flat parts and estimates of the composition of the flat areas.
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Affiliation(s)
- Henriette G Mortensen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Grethe V Jensen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Sara K Hansen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Thomas Vosegaard
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
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4
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Ikeda K, Horiuchi A, Egawa A, Tamaki H, Fujiwara T, Nakano M. Nanodisc-to-Nanofiber Transition of Noncovalent Peptide-Phospholipid Assemblies. ACS OMEGA 2017; 2:2935-2944. [PMID: 31457628 PMCID: PMC6641012 DOI: 10.1021/acsomega.7b00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/09/2017] [Indexed: 06/10/2023]
Abstract
We report a novel molecular architecture of peptide-phospholipid coassemblies. The amphiphilic peptide Ac-18A-NH2 (18A), which was designed to mimic apolipoprotein α-helices, has been shown to form nanodisc structures with phospholipid bilayers. We show that an 18A peptide cysteine substitution at residue 11, 18A[A11C], forms fibrous assemblies with 1-palmitoyl-2-oleoyl-phosphatidylcholine at a lipid-to-peptide (L/P) molar ratio of 1, a fiber diameter of 10-20 nm, and a length of more than 1 μm. Furthermore, 18A[A11C] can form nanodiscs with these lipid bilayers at L/P ratios of 4-6. The peptide adopts α-helical structures in both the nanodisc and nanofiber assemblies, although the α-helical bundle structures were evident only in the nanofibers, and the phospholipids of the nanofibers were not lamellar. Fluorescence spectroscopic analysis revealed that the peptide and lipid molecules in the nanofibers exhibited different solvent accessibility and hydrophobicity from those of the nanodiscs. Furthermore, the cysteine substitution at residue 11 did not result in disulfide bond formation, although it was responsible for the nanofiber formation, suggesting that this free sulfhydryl group has an important functional role. Alternatively, the disulfide dimer of 18A[A11C] preferentially formed nanodiscs, even at an L/P ratio of 1. Interconversions of these discoidal and fibrous assemblies were induced by the stepwise addition of free 18A[A11C] or liposomes into the solution. Furthermore, these structural transitions could also be induced by the introduction of oxidative and reductive stresses to the assemblies. Our results demonstrate that heteromolecular lipid-peptide complexes represent a novel approach to the construction of controllable and functional nanoscale assemblies.
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Affiliation(s)
- Keisuke Ikeda
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ayame Horiuchi
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ayako Egawa
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hajime Tamaki
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Minoru Nakano
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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5
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Abstract
Many antimicrobial peptides function by forming pores in the plasma membrane of the target cells. Intriguingly, some of these peptides are very short, and thus, it is not known how they can span the membrane, or whether other mechanisms of cell disruption are dominant. Here, the conformation and orientation of the 14-residue peptaibol SPF-5506-A4 (SPF) are investigated in lipid environments by atomistic and coarse grained molecular dynamics (MD) simulations, circular dichroism, and nuclear magnetic resonance (NMR) experiments. The MD simulations show that SPF is inserted spontaneously in a transmembrane orientation in both 1,2-dimyristoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers resulting in thinning of the bilayers near the peptides, which drives the peptide aggregation. Furthermore, the backbone conformation of the peptide in the bilayer bound state is different from that of the NMR model solved in small bicelles. These results demonstrate that mutual adaption between the peptides and the membrane is likely to be important for pore formation.
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Pluhackova K, Kirsch SA, Han J, Sun L, Jiang Z, Unruh T, Böckmann RA. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J Phys Chem B 2016; 120:3888-903. [DOI: 10.1021/acs.jpcb.6b01870] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kristyna Pluhackova
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Sonja A. Kirsch
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Jing Han
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Liping Sun
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Zhenyan Jiang
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Tobias Unruh
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 3, 91058 Erlangen, Germany
| | - Rainer A. Böckmann
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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7
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Vestergaard M, Kraft JF, Vosegaard T, Thøgersen L, Schiøtt B. Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations. J Phys Chem B 2015; 119:15831-43. [PMID: 26610232 DOI: 10.1021/acs.jpcb.5b08463] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small bicelles and the nanodiscs show increased peptide solvation and difference in peptide orientation compared to embedding in a bilayer. The large bicelle imitated a bilayer well with respect to both curvature and peptide solvation, although peripheral binding of short tailed lipids to the embedded proteins is observed, which could hinder ligand binding or multimer formation.
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Affiliation(s)
- Mikkel Vestergaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Johan F Kraft
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Danish Center for Ultrahigh-Field NMR Spectroscopy and Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Lea Thøgersen
- Center for Membrane Pumps in Cells and Disease (PUMPKIN), Bioinformatics Research Centre, Aarhus University , C.F. Møllers Alle 8, DK-8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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8
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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Umegawa Y, Yamaguchi T, Murata M, Matsuoka S. Centerband-only analysis of rotor-unsynchronized spin echo for measurement of lipid (31) P chemical shift anisotropy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:514-519. [PMID: 26017552 DOI: 10.1002/mrc.4247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 03/12/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Structural diversity and molecular flexibility of phospholipids are essential for biological membranes to play key roles in numerous cellular processes. Uncovering the behavior of individual lipids in membrane dynamics is crucial for understanding the molecular mechanisms underlying biological functions of cell membranes. In this paper, we introduce a simple method to investigate dynamics of lipid molecules in multi-component systems by measuring the (31) P chemical shift anisotropy (CSA) under magic angle spinning (MAS) conditions. For achieving both signal separation and CSA determination, we utilized a centerband-only analysis of rotor-unsynchronized spin echo (COARSE). This analysis is based on the curve fitting of periodic modulation of centerband intensity along the interpulse delay time in rotor-unsynchronized spin-echo experiments. The utility of COARSE was examined by using phospholipid vesicles, a three-component lipid raft model system, and archaeal purple membranes. We found that the apparent advantages of this method are high resolution and high sensitivity given by the moderate MAS speed and the one-dimensional acquisition with short spin-echo delays. COARSE provides an alternative method for CSA measurement that is effective in the investigation of lipid polymorphologies.
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Affiliation(s)
- Yuichi Umegawa
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Project Research Centre for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
| | - Toshiyuki Yamaguchi
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Project Research Centre for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
| | - Michio Murata
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Project Research Centre for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
| | - Shigeru Matsuoka
- JST ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
- Project Research Centre for Fundamental Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka Prefecture, 560-0043, Japan
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