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Kononova PA, Selyutina OY, Polyakov NE. The Interaction of the Transmembrane Domain of SARS-CoV-2 E-Protein with Glycyrrhizic Acid in Lipid Bilayer. MEMBRANES 2023; 13:membranes13050505. [PMID: 37233566 DOI: 10.3390/membranes13050505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/27/2023]
Abstract
The interaction of the transmembrane domain of SARS-CoV-2 E-protein with glycyrrhizic acid in a model lipid bilayer (small isotropic bicelles) is demonstrated using various NMR techniques. Glycyrrhizic acid (GA) is the main active component of licorice root, and it shows antiviral activity against various enveloped viruses, including coronavirus. It is suggested that GA can influence the stage of fusion between the viral particle and the host cell by incorporating into the membrane. Using NMR spectroscopy, it was shown that the GA molecule penetrates into the lipid bilayer in a protonated state, but localizes on the bilayer surface in a deprotonated state. The transmembrane domain of SARS-CoV-2 E-protein facilitates deeper GA penetration into the hydrophobic region of bicelles at both acidic and neutral pH and promotes the self-association of GA at neutral pH. Phenylalanine residues of the E-protein interact with GA molecules inside the lipid bilayer at neutral pH. Furthermore, GA influences the mobility of the transmembrane domain of SARS-CoV-2 E-protein in the bilayer. These data provide deeper insight into the molecular mechanism of antiviral activity of glycyrrhizic acid.
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Affiliation(s)
- Polina A Kononova
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia
| | - Olga Yu Selyutina
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia
| | - Nikolay E Polyakov
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia
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2
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Nguyen TTT, Haam S, Park JS, Lee SW. Cysteine-Encapsulated Liposome for Investigating Biomolecular Interactions at Lipid Membranes. Int J Mol Sci 2022; 23:ijms231810566. [PMID: 36142476 PMCID: PMC9500635 DOI: 10.3390/ijms231810566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
The development of a strategy to investigate interfacial phenomena at lipid membranes is practically useful because most essential biomolecular interactions occur at cell membranes. In this study, a colorimetric method based on cysteine-encapsulated liposomes was examined using gold nanoparticles as a probe to provide a platform to report an enzymatic activity at lipid membranes. The cysteine-encapsulated liposomes were prepared with varying ratios of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cholesterol through the hydration of lipid films and extrusions in the presence of cysteine. The size, composition, and stability of resulting liposomes were analyzed by scanning electron microscopy (SEM), dynamic light scattering (DLS), nuclear magnetic resonance (NMR) spectroscopy, and UV-vis spectrophotometry. The results showed that the increased cholesterol content improved the stability of liposomes, and the liposomes were formulated with 60 mol % cholesterol for the subsequent experiments. Triton X-100 was tested to disrupt the lipid membranes to release the encapsulated cysteine from the liposomes. Cysteine can induce the aggregation of gold nanoparticles accompanying a color change, and the colorimetric response of gold nanoparticles to the released cysteine was investigated in various media. Except in buffer solutions at around pH 5, the cysteine-encapsulated liposomes showed the color change of gold nanoparticles only after being incubated with Triton X-100. Finally, the cysteine-encapsulated liposomal platform was tested to report the enzymatic activity of phospholipase A2 that hydrolyzes phospholipids in the membrane. The hydrolysis of phospholipids triggered the release of cysteine from the liposomes, and the released cysteine was successfully detected by monitoring the distinct red-to-blue color change of gold nanoparticles. The presence of phospholipase A2 was also confirmed by the appearance of a peak around 690 nm in the UV-vis spectra, which is caused by the cysteine-induced aggregation of gold nanoparticles. The results demonstrated that the cysteine-encapsulated liposome has the potential to be used to investigate biological interactions occurring at lipid membranes.
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Affiliation(s)
- Trang Thi Thuy Nguyen
- Department of Chemical and Biological Engineering, Gachon University, Seongnam-si 13120, Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Korea
| | - Joon-Seo Park
- Department of Chemistry, Eastern University, St. Davids, PA 19087, USA
- Correspondence: (J.-S.P.); (S.-W.L.)
| | - Sang-Wha Lee
- Department of Chemical and Biological Engineering, Gachon University, Seongnam-si 13120, Korea
- Correspondence: (J.-S.P.); (S.-W.L.)
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3
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Mandal P, Eswara K, Yerkesh Z, Kharchenko V, Zandarashvili L, Szczepski K, Bensaddek D, Jaremko Ł, Black BE, Fischle W. Molecular basis of hUHRF1 allosteric activation for synergistic histone modification binding by PI5P. SCIENCE ADVANCES 2022; 8:eabl9461. [PMID: 36001657 PMCID: PMC9401617 DOI: 10.1126/sciadv.abl9461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Chromatin marks are recognized by distinct binding modules, many of which are embedded in multidomain proteins. How the different functionalities of such complex chromatin modulators are regulated is often unclear. Here, we delineated the interplay of the H3 amino terminus- and K9me-binding activities of the multidomain hUHRF1 protein. We show that the phosphoinositide PI5P interacts simultaneously with two distant flexible linker regions connecting distinct domains of hUHRF1. The binding is dependent on both, the polar head group, and the acyl part of the phospholipid and induces a conformational rearrangement juxtaposing the H3 amino terminus and K9me3 recognition modules of the protein. In consequence, the two features of the H3 tail are bound in a multivalent, synergistic manner. Our work highlights a previously unidentified molecular function for PI5P outside of the context of lipid mono- or bilayers and establishes a molecular paradigm for the allosteric regulation of complex, multidomain chromatin modulators by small cellular molecules.
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Affiliation(s)
- Papita Mandal
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Karthik Eswara
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Zhadyra Yerkesh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Vladlena Kharchenko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Levani Zandarashvili
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kacper Szczepski
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- Core Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
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Wang H, Falcoz S, Berteau JP. Long-Chain Fatty Acids in Bones and Their Link to Submicroscopic Vascularization Network: NMR Assignment and Relaxation Studies under Magic Angle Spinning Conditions in Intramuscular Bones of Atlantic Herring Fish. J Phys Chem B 2021; 125:4585-4595. [PMID: 33914538 DOI: 10.1021/acs.jpcb.1c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-lasting proton signals in bones are identified as long-chain fatty acids, including saturated, mono-, and di-unsaturated fatty acids, with direct nuclear magnetic resonance evidence. We used intramuscular bones from Atlantic Herring fish to avoid interference from lipid-rich marrows. The key is to recognize that these signals are from mobile phase materials and study them with J-coupled correlation spectroscopies under magic angle spinning conditions. We kept extensive 1H-spin-echo records that allowed us to examine the effect of magic angle spinning on the transverse relaxation time of water and lipids over time. While it is impossible to distinguish based on chemical shifts, the relaxation data suggest that the signals are more consistent with the interpretation of phospholipid membranes than triglycerides in lipid droplets. In particular, the simultaneous T2 changes in water and lipids suggest that the centrifugal impact of magic angle spinning alters the lipid's structure in very tight spaces. Additional evidence of phospholipid membranes came from the choline-γ resonance at 3.2 ppm in fresh samples, which disappears with magic angle spinning. Thus, the fatty acid signals are at least partially from membrane bilayer structures, and we propose that they are linked to the submicroscopic vascularization channels similar to the dense canaliculi network in mammalian bones. Our detection of phospholipids from bones depended critically on two factors: (1) the elimination of the overwhelming triglyceride signals from marrows and (2) the preservation of water that biomembranes require. The relaxation data reveal aspects of lipid fluidity that have not been elucidated by previous order parameter studies on model membranes. Relaxation times have long been considered difficult to interpret. A robust and renewed understanding may be beneficial.
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Affiliation(s)
- Hsin Wang
- Department of Chemistry and Biochemistry, The City College of New York and CUNY Institute for Macromolecular Assemblies, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Steve Falcoz
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, New York 10314, United States
| | - Jean-Philippe Berteau
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, New York 10314, United States.,New York Centre for Biomedical Engineering, City University of New York - City College of New York, New York, New York 10031, United States.,Nanosciences Initiative, City University of New York - Advance Science Research Center, New York, New York 10031, United States
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5
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Lamch Ł, Gancarz R, Tsirigotis-Maniecka M, Moszyńska IM, Ciejka J, Wilk KA. Studying the "Rigid-Flexible" Properties of Polymeric Micelle Core-Forming Segments with a Hydrophobic Phthalocyanine Probe Using NMR and UV Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4316-4330. [PMID: 33794644 PMCID: PMC8154882 DOI: 10.1021/acs.langmuir.1c00328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The aim of the performed studies was to thoroughly examine the internal structure of self-assembled nanocarriers (i.e., polymeric micelles-PMs) by means of a hydrophobic phthalocyanine probe in order to identify the crucial features that are required to enhance the photoactive probe stability and reactivity. PMs of hydrophilic poly(ethylene glycol) and hydrophobic poly(ε-caprolactone) (PCL) or poly(d,l-lactide) (PDLLA) were fabricated and loaded with tetra tert-butyl zinc(II) phthalocyanine (ZnPc-t-but4), a multifunctional spectroscopic probe with a profound ability to generate singlet oxygen upon irradiation. The presence of subdomains, comprising "rigid" and "flexible" regions, in the studied block copolymers' micelles as well as their interactions with the probe molecules, were assessed by various high-resolution NMR measurements [e.g., through-space magnetic interactions by the 1D NOE effect, pulsed field gradient spin-echo, and spin-lattice relaxation time (T1) techniques]. The studies of the impact of the core-type microenvironment on the ZnPc-t-but4 photochemical performance also included photobleaching and reactive oxygen species measurements. ZnPc-t-but4 molecules were found to exhibit spatial proximity effects with both (PCL and PDLLA) hydrophobic polymer chains and interact with both subdomains, which are characterized by different rigidities. It was deduced that the interfaces between particular subdomains constitute an optimal host space for probe molecules, especially in the context of photochemical stability, photoactivity (i.e., for significant enhancement of singlet oxygen generation rates), and aggregation prevention. The present contribution proves that the combination of an appropriate probe, high-resolution NMR techniques, and UV-vis spectroscopy enables one to gain complex information about the subtle structure of PMs essential for their application as nanocarriers for photoactive compounds, for example, in photodynamic therapy, nanotheranostics, combination therapy, or photocatalysis, where the micelles constitute the optimal microenvironment for the desired photoreactions.
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6
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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7
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Primasová H, Vermathen M, Furrer J. Interactions of Cationic Diruthenium Trithiolato Complexes with Phospholipid Membranes Studied by NMR Spectroscopy. J Phys Chem B 2020; 124:8822-8834. [PMID: 32930600 DOI: 10.1021/acs.jpcb.0c05133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To apprehend the possible mechanisms involved in the cellular uptake and the membrane interactions of cytotoxic dinuclear p-cymene trithiolato ruthenium(II) complexes, the interactions of the complexes [(η6-p-MeC6H4Pri)2Ru2(R1)2(R2)]+ (R1 = R2 = SC6H4-m-Pri:1; R1 = SC6H4-p-OMe, R2 = SC6H4-p-OH:2; R1 = SCH2C6H4-p-OMe, R2 = SC6H4-p-OH:3) with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) vesicles and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles were studied using nuclear magnetic resonance (NMR) spectroscopy. 1H NMR, nuclear Overhauser effect (NOE), diffusion ordered spectroscopy (DOSY), and T1 and T2 relaxation data provided information on interactions between the complexes and the model membranes and on the submolecular localization of the complexes at the membrane interface. The results suggest that (a) the interaction takes place without new covalent adduct formation, (b) the cationic diruthenium complexes interact with DOPC head groups most likely involving electrostatic interactions while remaining structurally unchanged, (c) the changes indicating interactions are more pronounced for the most lipophilic complex 1, and (d) the diruthenium complexes remain at the exterior vesicle surface and are unlikely inserted between the phospholipid chains. The complexes also interact with micellar/free DHPC and seem to induce micellization or aggregation in solutions below critical micelle concentration (CMC). Our study suggests high affinity of the Ru complexes for the membrane surface that likely plays a key role in cellular uptake and possibly also in redistribution in mitochondria.
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Affiliation(s)
- Hedvika Primasová
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Martina Vermathen
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Julien Furrer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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8
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Formulation of Bicelles Based on Lecithin-Nonionic Surfactant Mixtures. MATERIALS 2020; 13:ma13143066. [PMID: 32659968 PMCID: PMC7412056 DOI: 10.3390/ma13143066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/01/2023]
Abstract
Bicelles have been intensively studied for use as drug delivery carriers and in biological studies, but their preparation with low-cost materials and via a simple process would allow their use for other purposes as well. Herein, bicelles were prepared through a semi-spontaneous method using a mixture of hydrogenated soybean lecithin (SL) and a nonionic surfactant, polyoxyethylene cholesteryl ether (ChEO10), and then we investigated the effect of composition and temperature on the structure of bicelles, which is important to design tailored systems. As the fraction of ChEO10 (XC) was increased, a bimodal particle size distribution with a small particle size of several tens of nanometers and a large particle size of several hundred nanometers was obtained, and only small particles were observed when XC ≥ 0.6, suggesting the formation of significant structure transition (liposomes to bicelles). The small-angle neutron scattering (SANS) spectrum for these particles fitted a core-shell bicelle model, providing further evidence of bicelle formation. A transition from a monomodal to a bimodal size distribution occurred as the temperature was increased, with this transition taking place at lower temperatures when higher SL-ChEO10 concentrations were used. SANS showed that this temperature-dependent size change was reversible, suggesting the SL-ChEO10 bicelles were stable against temperature, hence making them suitable for several applications.
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9
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Ribić R, Manček-Keber M, Chain F, Sinnaeve D, Martins JC, Jerala R, Tomić S, Fehér K. Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface. J Phys Chem B 2020; 124:4132-4145. [PMID: 32283934 DOI: 10.1021/acs.jpcb.0c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.
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Affiliation(s)
- Rosana Ribić
- University Center Varaždin, University North, Jurja Križanića 31b, HR-42 000 Varaždin, Croatia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Fernando Chain
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 - Labex DISTALZ - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, F-59000 Lille, France
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, P.O. Box 660, SI-1001 Ljubljana, Slovenia
| | - Srđanka Tomić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10 000 Zagreb, Croatia
| | - Krisztina Fehér
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre S4, Krijgslaan 281, 9000 Ghent, Belgium.,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, Egyetem tér 1, H-4032 Debrecen, Hungary
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10
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F Dudás E, Wacha A, Bóta A, Bodor A. Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183095. [PMID: 31672542 DOI: 10.1016/j.bbamem.2019.183095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (rH) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). 1H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective rH values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the rG/rH ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using rH and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.
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Affiliation(s)
- E F Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - A Wacha
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bóta
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary.
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11
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Castañar L, Poggetto GD, Colbourne AA, Morris GA, Nilsson M. The GNAT: A new tool for processing NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:546-558. [PMID: 29396867 PMCID: PMC6001793 DOI: 10.1002/mrc.4717] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 05/31/2023]
Abstract
The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T1 /T2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available.
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Affiliation(s)
- Laura Castañar
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | | | - Adam A. Colbourne
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Gareth A. Morris
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mathias Nilsson
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
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12
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Awad TS, Asker D, Romsted LS. Evidence of coexisting microemulsion droplets in oil-in-water emulsions revealed by 2D DOSY 1H NMR. J Colloid Interface Sci 2018; 514:83-92. [DOI: 10.1016/j.jcis.2017.12.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 12/16/2022]
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13
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Neal SL. Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2018; 72:102-113. [PMID: 28805070 DOI: 10.1177/0003702817729347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.
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Affiliation(s)
- Sharon L Neal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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Liebau J, Fu B, Brown C, Mäler L. New insights into the membrane association mechanism of the glycosyltransferase WaaG from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:683-690. [PMID: 29225173 DOI: 10.1016/j.bbamem.2017.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Monotopic glycosyltransferases (GTs) interact with membranes via electrostatic interactions. The N-terminal domain is permanently anchored to the membrane while the membrane interaction of the C-terminal domain is believed to be weaker so that it undergoes a functionally relevant conformational change upon donor or acceptor binding. Here, we studied the applicability of this model to the glycosyltransferase WaaG. WaaG is involved in the synthesis of lipopolysaccharides (LPS) in Gram-negative bacteria and was previously categorized as a monotopic GT. We analyzed the binding of WaaG to membranes by stopped-flow fluorescence and NMR diffusion experiments. We find that electrostatic interactions are required to bind WaaG to membranes while mere hydrophobic interactions are not sufficient. WaaG senses the membrane's surface charge density but there is no preferential binding to specific anionic lipids. However, the binding is weaker than expected for monotopic GTs but similar to peripheral GTs. Therefore, WaaG may be a peripheral GT and this could be of functional relevance in vivo since LPS synthesis occurs only when WaaG is membrane-bound. We could not observe a C-terminal domain movement under our experimental conditions.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Biao Fu
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Christian Brown
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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Aramaki K, Iwata C, Mata J, Maehara T, Aburano D, Sakanishi Y, Kitao K. One-step formulation of nonionic surfactant bicelles (NSBs) by a double-tailed polyglycerol-type nonionic surfactant. Phys Chem Chem Phys 2017; 19:23802-23808. [PMID: 28530285 DOI: 10.1039/c7cp02585h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bicelles are generally formed by phospholipid-based systems and are useful for various applications, such as nanocarriers or membrane protein crystallization. The same disc-like assemblies, nonionic surfactant bicelles (NSBs), can also be formed using nonionic amphiphiles, but this has not been reported extensively. We report a novel NSB system that employs the double-tailed nonionic amphiphile, polyglyceryl dialkyl ether (C12CmGn), which has two alkyl chains and a polyglyceryl group. A symmetric-tail molecule, C12C12G13.8, formed vesicles, whereas an asymmetric-tail molecule, C12C14G15.5, formed NSBs through a simple one-step process using ultrasonication. The 1 wt% aqueous solution of C12C14G15.5 was in a two-phase equilibrium of a lamellar phase and a water phase. Transparent dispersion was obtained through ultrasonication treatment. The size distribution in the dispersion was obtained by dynamic light scattering (DLS), resulting in a narrow distribution of around 20 nm in diameter. A negatively-stained transmission electron microscopy (TEM) image showed oblong and spherical shapes, which are typically observed in bicelle-forming systems. A small angle neutron scattering (SANS) measurement well proved bicelle formation by fitting a core-shell bicelle form factor model. The disc thickness and diameter were in agreement with the values obtained by DLS and TEM, respectively. A larger shell thickness at the rim part than at the flat disc part suggested that NSB aggregates have inhomogeneous molecular distribution. Similar to phospholipid systems, the bicelle-forming C12C14G15.5 system produced a defective lamellar phase formation at high surfactant concentrations, whereas a general lamellar phase was formed in the vesicle-forming C12C12G13.8 system.
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Affiliation(s)
- Kenji Aramaki
- Graduate School of Environment and Information Sciences, Yokohama National University, Tokiwadai 79-7, Hodogaya-ku, Yokohama 240-8501, Japan.
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Liebau J, Ye W, Mäler L. Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:395-404. [PMID: 26662467 DOI: 10.1002/mrc.4399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Small isotropic bicelles are versatile membrane mimetics, which, in contrast to micelles, provide a lipid bilayer and are at the same time suitable for solution-state NMR studies. The lipid composition of the bilayer is flexible allowing for incorporation of various head groups and acyl chain types. In bicelles, lipids are solubilized by detergents, which are localized in the rim of the disk-shaped lipid bilayer. Bicelles have been characterized by a broad array of biophysical methods, pulsed-field gradient NMR (PFG NMR) being one of them. PFG NMR can readily be used to measure diffusion coefficients of macromolecules. It is thus employed to characterize bicelle size and morphology. Even more importantly, PFG NMR can be used to study the degree of protein association to membranes. Here, we present the advances that have been made in producing small, fast-tumbling isotropic bicelles from a variety of lipids and detergents, together with insights on the morphology of such mixtures gained from PFG NMR. Furthermore, we review approaches to study protein-membrane interaction by PFG NMR. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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Kiuchi Y, Taguchi Y, Nagasaka Y. Fringe-tunable electrothermal Fresnel mirror for use in compact and high-speed diffusion sensor. OPTICS EXPRESS 2017; 25:758-767. [PMID: 28157964 DOI: 10.1364/oe.25.000758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper reports the development of an electrothermal microelectromechanical systems (MEMS) mirror with serpentine shape actuators. A micro Fresnel mirror with fringe-spacing tunability is required to realize a compact and high-speed diffusion sensor for biological samples whose diffusion coefficient changes significantly because of a conformational change. In this case, the measurement time-constant is dependent on the fringe-spacing and diffusion coefficient of the sample. In this study, a fringe-tunable MEMS mirror with an actuation voltage less than 10 V was developed. The characteristics of the fabricated mirror were investigated experimentally. A high-visibility optical interference fringe was successfully demonstrated using both an ultranarrow-linewidth solid-state laser and a low-cost compact laser diode. The experimental results demonstrated a distinct possibility of developing a measurement device using only simple and low-voltage optical components.
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Szpryngiel S, Mäler L. Insights into the Membrane Interacting Properties of the C-Terminal Domain of the Monotopic Glycosyltransferase DGD2 in Arabidopsis thaliana. Biochemistry 2016; 55:6776-6786. [PMID: 27951648 DOI: 10.1021/acs.biochem.6b00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosyltransferases (GTs) are responsible for regulating the membrane composition of plants. The synthesis of one of the main lipids in the membrane, the galactolipid digalactosyldiacylglycerol, is regulated by the enzyme digalactosyldiacylglycerol synthase 2 (atDGD2) under starving conditions, such as phosphate shortage. The enzyme belongs to the GT-B fold, characterized by two β/α/β Rossmann domains that are connected by a flexible linker. atDGD2 has previously been shown to attach to lipid membranes by the N-terminal domain via interactions with negatively charged lipids. The role of the C-terminal domain in the membrane interaction is, however, not known. Here we have used a combination of in silico prediction methods and biophysical experimental techniques to shed light on the membrane interacting properties of the C-terminal domain. Our results demonstrate that there is an amphipathic sequence, corresponding to residues V240-E258, that interacts with lipids in a charge-dependent way. A second sequence was identified as being potentially important, with a high charge density, but no amphipathic character. The features of the plant atDGD2 observed here are similar in prokaryotic glycosyltransferases. On the basis of our results, and by analogy to other glycosyltransferases, we propose that atDGD2 interacts with the membrane through the N-terminus and with parts of the C-terminus acting as a switch, allowing for a dynamic interaction with the membrane.
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Affiliation(s)
- Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
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Fast-tumbling bicelles constructed from native Escherichia coli lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2097-2105. [DOI: 10.1016/j.bbamem.2016.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022]
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Mineev KS, Nadezhdin KD, Goncharuk SA, Arseniev AS. Characterization of Small Isotropic Bicelles with Various Compositions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6624-6637. [PMID: 27285636 DOI: 10.1021/acs.langmuir.6b00867] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural studies of membrane proteins are of great importance and interest, with solution and solid state NMR spectroscopy being very promising tools for that task. However, such investigations are hindered by a number of obstacles, and in the first place by the fact that membrane proteins need an adequate environment that models the cell membrane. One of the most widely used and prospective membrane mimetics is isotropic bicelles. While large anisotropic bicelles are well-studied, the field of small bicelles contains a lot of "white spots". The present work reports the radii of particles and concentration of the detergents in the monomeric state in solutions of isotropic bicelles, formed by 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO), and sodium cholate, as a function of lipid/detergent ratio and temperature. These parameters were measured using (1)H NMR diffusion spectroscopy for the bicelles composed of lipids with saturated fatty chains of different length and lipids, containing unsaturated fatty acid residue. The influence of a model transmembrane protein (membrane domain of rat TrkA) on the properties of bicelles and the effect of the bicelle size and composition on the properties of the transmembrane protein were investigated with heteronuclear NMR and nuclear Overhauser effect spectroscopy. We show that isotropic bicelles that are applicable for solution NMR spectroscopy behave as predicted by the theoretical models and are likely to be bicelles rather than mixed micelles. Using the obtained data, we propose a simple approach to control the size of bicelles at low concentrations. On the basis of our results, we compared different rim-forming agents and selected CHAPS as a detergent of choice for structural studies in bicelles, if the deuteration of the detergent is not required.
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Affiliation(s)
- K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - K D Nadezhdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
| | - S A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Lomonosov Moscow State University , Leninskiye Gory, 1, Moscow, 119991, Russian Federation
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
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Watanabe Y, Aramaki K, Kadomatsu Y, Tanaka K, Konno Y. Preparation of Bicelles Using the Semi-spontaneous Method. CHEM LETT 2016. [DOI: 10.1246/cl.160118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yuki Watanabe
- Graduate School of Environment and Information Science, Yokohama National University
| | - Kenji Aramaki
- Graduate School of Environment and Information Science, Yokohama National University
| | | | - Ken Tanaka
- Research and Development Division, KOSÉ Corporation
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