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Leite WC, Wu Y, Pingali SV, Lieberman RL, Urban VS. Change in Morphology of Dimyristoylphosphatidylcholine/Bile Salt Derivative Bicelle Assemblies with Dodecylmaltoside in the Disk and Ribbon Phases. J Phys Chem Lett 2022; 13:9834-9840. [PMID: 36250687 DOI: 10.1021/acs.jpclett.2c02445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bicelles, composed of a mixture of long and short chain lipids, form nanostructured molecular assemblies that are attractive lipid-membrane mimics for in vitro studies of integral membrane proteins. Here we study the effect of a third component, the single chain detergent n-dodecyl-β-d-maltoside (DDM) on the morphology of bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) below (10 °C) and above (38 °C) the phase transition. In the absence of DDM, bicelles convert from ellipsoidal disks at 10 °C to extended ribbon-like structures at 38 °C. The addition of DDM reshapes the ellipsoidal disc to a circular one and the flattened ribbon to a circular-cylinder worm-like micelle. Knowledge of the influence of the single chain detergent DDM on bicelle nanoscale morphology contributes toward comprehending lipid membrane self-organization and to the goal of optimizing lipid mimics for membrane biology research.
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Affiliation(s)
- Wellington C Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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2
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De Angelis A, Park SH, Opella SJ. Magnetically Aligned Lipid Bilayers with High Cholesterol for Solid-State NMR of Membrane Proteins. Biochemistry 2022; 61:1561-1571. [PMID: 35849647 DOI: 10.1021/acs.biochem.2c00262] [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
Phospholipid bicelles are valuable membrane model systems to study membrane proteins by NMR and other physicochemical techniques. The range of bicelle compositions that are compatible with uniaxial alignment of the lipid bilayers in a magnetic field is still limited with regard to the addition of large amounts (>20%) of cholesterol and/or sphingolipids. Here, we demonstrate that n-dodecyl-β-D-melibioside (DDMB), which was recently introduced as a detergent to produce sphingolipid-cholesterol-rich isotropic bicelles for solution NMR studies, can also be used to produce magnetically alignable lipid bilayers with high cholesterol content that are well suited for solid-state NMR of membrane proteins. Remarkably, DDMB enables the preparation of high q bicelles that contain 50% mol cholesterol while retaining their ability to form a stable, well-aligned liquid crystalline bilayer phase in a magnetic field. We show that the intact 46-residue membrane-bound form of Pf1 bacteriophage coat protein and a truncated construct of the membrane protein Vpu from HIV-1 (residues 2-30) in DDMB bicelles are well aligned and undergo fast and uniaxial rotational diffusion about the bilayer normal, similarly to what is observed in other bicelle and macrodisc systems. We also demonstrate a spectroscopic method that measures the increase in the thickness of DMPC bilayers that results from the addition of cholesterol, using the PISA-wheel spectral patterns of trans-membrane helices as a molecular goniometer. For example, we find that the hydrophobic thickness of DMPC bilayers is increased by approximately 2.5 Å in the presence of 35% mol cholesterol.
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Affiliation(s)
- Anna De Angelis
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
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3
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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4
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Yang L. Scattering measurements on lipid membrane structures. Methods Enzymol 2022; 677:385-415. [DOI: 10.1016/bs.mie.2022.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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6
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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7
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Long Z, Ruthford J, Opella SJ. 3D printed sample tubes for solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106957. [PMID: 33798799 PMCID: PMC8141027 DOI: 10.1016/j.jmr.2021.106957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The availability of 3D printers and an assortment of polymers that can be fashioned into a wide variety of shapes provides opportunities to rethink the design and construction of probes for NMR spectroscopy. The direct interfacing of computer aided design (CAD) with precise 3D printing enables the simplification and optimization of probes through the rapid production of components. Here we demonstrate the use of 3D printing to fully integrate a permanent former for the radiofrequency (RF) coil with the sample chamber (equivalent to the sample tube). This simultaneously increases the sample volume and improves the filling factor within a fixed outer diameter (OD). It also reduces the space lost in dual coil arrangements where a high frequency resonator is positioned outside a solenoid coil tuned to one or more lower frequencies, making multiple-resonance experiments more efficient. The initial applications demonstrate the possibilities for future designs that reimagine the interface between resonators and the liquid, solid, and heterogeneous samples encountered in NMR studies of biomolecules, polymers, surfaces, and spectroscopy (MRS) and imaging (MRI) of biological organs and intact organisms.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Jamie Ruthford
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States.
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8
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Versatile formation of supported lipid bilayers from bicellar mixtures of phospholipids and capric acid. Sci Rep 2020; 10:13849. [PMID: 32796898 PMCID: PMC7427796 DOI: 10.1038/s41598-020-70872-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/29/2020] [Indexed: 01/07/2023] Open
Abstract
Originally developed for the structural biology field, lipid bicelle nanostructures composed of long- and short-chain phospholipid molecules have emerged as a useful interfacial science tool to fabricate two-dimensional supported lipid bilayers (SLBs) on hydrophilic surfaces due to ease of sample preparation, scalability, and versatility. To improve SLB fabrication prospects, there has been recent interest in replacing the synthetic, short-chain phospholipid component of bicellar mixtures with naturally abundant fatty acids and monoglycerides, i.e., lauric acid and monocaprin. Such options have proven successful under specific conditions, however, there is room for devising more versatile fabrication options, especially in terms of overcoming lipid concentration-dependent SLB formation limitations. Herein, we investigated SLB fabrication by using bicellar mixtures consisting of long-chain phospholipid and capric acid, the latter of which has similar headgroup and chain length properties to lauric acid and monocaprin, respectively. Quartz crystal microbalance-dissipation, epifluorescence microscopy, and fluorescence recovery after photobleaching experiments were conducted to characterize lipid concentration-dependent bicelle adsorption onto silicon dioxide surfaces. We identified that uniform-phase SLB formation occurred independently of total lipid concentration when the ratio of long-chain phospholipid to capric acid molecules ("q-ratio") was 0.25 or 2.5, which is superior to past results with lauric acid- and monocaprin-containing bicelles in which cases lipid concentration-dependent behavior was observed. Together, these findings demonstrate that capric acid-containing bicelles are versatile tools for SLB fabrication and highlight how the molecular structure of bicelle components can be rationally finetuned to modulate self-assembly processes at solid-liquid interfaces.
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9
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Optimal formation of uniform-phase supported lipid bilayers from phospholipid–monoglyceride bicellar mixtures. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.04.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Sut TN, Park S, Yoon BK, Jackman JA, Cho NJ. Supported Lipid Bilayer Formation from Phospholipid-Fatty Acid Bicellar Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5021-5029. [PMID: 32308002 DOI: 10.1021/acs.langmuir.0c00675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Supported lipid bilayers (SLBs) are versatile cell membrane-mimicking biointerfaces for various applications such as biosensors and drug delivery systems, and there is broad interest in developing simple, cost-effective methods to achieve SLB fabrication. One promising approach involves the deposition of quasi-two-dimensional bicelle nanostructures that are composed of long-chain phospholipids and either short-chain phospholipids or detergent molecules. While a variety of long-chain phospholipids have been used to prepare bicelles for SLB fabrication applications, only two short-chain phospholipids, 1,2-dihexanoyl-sn-glycero-3-phosphocholine and 1,2-diheptanoyl-sn-glycero-3-phosphocholine (collectively referred to as DHPC), have been investigated. There remains an outstanding need to identify natural alternatives to DHPC, especially ones that are more affordable, to improve fabrication prospects and application opportunities. Herein, we explored the potential to fabricate SLBs from bicellar mixtures composed of long-chain phospholipids and lauric acid (LA), which is a low-cost, naturally abundant fatty acid that is widely used in soapmaking and various industrial applications. Quartz crystal microbalance-dissipation (QCM-D) experiments were conducted to track bicelle adsorption onto silica surfaces as a function of bicelle composition and lipid concentration, along with time-lapse fluorescence microscopy imaging and fluorescence recovery after photobleaching (FRAP) experiments to further characterize lipid adlayer properties. The results identified optimal conditions where it is possible to efficiently form SLBs from LA-containing bicelles at low lipid concentrations while also unraveling mechanistic insights into the bicelle-mediated SLB formation process and verifying that LA-containing bicelles are biocompatible with human cells for surface coating applications.
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Affiliation(s)
- Tun Naw Sut
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Bo Kyeong Yoon
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Joshua A Jackman
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
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11
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Sut TN, Park S, Choe Y, Cho NJ. Characterizing the Supported Lipid Membrane Formation from Cholesterol-Rich Bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:15063-15070. [PMID: 31670521 DOI: 10.1021/acs.langmuir.9b02851] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Supported lipid bilayers (SLBs) are simplified model membrane systems that mimic the fundamental properties of biological cell membranes and allow the surface-sensitive tools to be used in numerous sensing applications. SLBs can be prepared by various methods including vesicle fusion, solvent-assisted lipid bilayer (SALB), and bicelle adsorption and are generally composed of phospholipids. Incorporating other biologically relevant molecules, such as cholesterol (Chol), into SLBs has been reported with the vesicle fusion and SALB methods, whereas it remains unexplored with the bicelle absorption method. Herein, using the quartz crystal microbalance-dissipation (QCM-D) and fluorescence microscopy techniques, we explored the possibility of forming SLBs from Chol-containing bicelles and discovered that Chol-enriched SLBs can be fabricated with bicelles. We also compared the Chol-enriched SLB formation of the bicelle method to that of vesicle fusion and SALB and discussed how the differences in lipid assembly properties can cause the differences in the adsorption kinetics and final results of SLB formation. Collectively, our findings demonstrate that the vesicle fusion method is least favorable for forming Chol-enriched SLBs, whereas the SALB and bicelle methods are more favorable, highlighting the need to consider the application requirements when choosing a suitable method for the formation of Chol-enriched SLBs.
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Affiliation(s)
- Tun Naw Sut
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
| | - Soohyun Park
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
| | - Younghwan Choe
- Department of Chemistry , Columbia University , 3000 Broadway , New York 10027 , United States
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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13
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Puthenveetil R, Vinogradova O. Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments. J Biol Chem 2019; 294:15914-15931. [PMID: 31551353 DOI: 10.1074/jbc.rev119.009178] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.
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Affiliation(s)
- Robbins Puthenveetil
- Department of Molecular and Cell Biology, college of liberal arts and sciences, University of Connecticut at Storrs, Storrs, Connecticut 06269
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, Connecticut 06269
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14
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Sanders CR. Life During Wartime: A Personal Recollection of the Circa 1990 Prestegard Lab and Its Contributions to Membrane Biophysics. J Membr Biol 2019; 252:541-548. [PMID: 31471644 DOI: 10.1007/s00232-019-00090-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/16/2019] [Indexed: 12/14/2022]
Abstract
A subjective account is presented of challenges and excitement of being a postdoctoral trainee in the lab of James H. Prestegard at Yale University in New Haven, Connecticut from 1989 to 1991. This includes accounts of the early development of bicelles and of oriented sample NMR results that contributed to our modern understanding of the properties of the water-lipid interface of disordered phase biological membranes.
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Affiliation(s)
- Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, 37240-7917, USA.
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15
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Sut TN, Jackman JA, Cho NJ. Understanding How Membrane Surface Charge Influences Lipid Bicelle Adsorption onto Oxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8436-8444. [PMID: 31141663 DOI: 10.1021/acs.langmuir.9b00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The adsorption of two-dimensional bicellar disks onto solid supports is an emerging fabrication technique to form supported lipid bilayers (SLBs) that is efficient and requires minimal sample preparation. To date, nearly all relevant studies have focused on zwitterionic lipid compositions and silica-based surfaces, and extending the scope of investigation to other lipid compositions and surfaces would improve our understanding of application possibilities and underpinning formation processes. Herein, using the quartz crystal microbalance-dissipation technique, we systematically investigated the adsorption of charged lipid bicelles onto silicon dioxide, titanium oxide, and aluminum oxide surfaces. Depending on the lipid composition and substrate, we observed different adsorption pathways, including (i) SLB formation via one- or two-step adsorption kinetics, (ii) monotonic adsorption without SLB formation, and (iii) negligible adsorption. On each substrate, SLB formation could be achieved with particular lipid compositions, whereas the trend in adsorption pathways varied according to the substrate and could be controlled by adjusting the bicelle?substrate interaction strength. To rationalize these findings, we discuss how electrostatic and hydration forces affect bicelle?substrate interactions on different oxide surfaces. Collectively, our findings demonstrate the broad utility of lipid bicelles for SLB formation while revealing physicochemical insights into the role of interfacial forces in controlling bicelle adsorption pathways.
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Affiliation(s)
- Tun Naw Sut
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
| | - Joshua A Jackman
- School of Chemical Engineering , Sungkyunkwan University , Suwon 16419 , Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive 637459 , Singapore
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Miranda C, Booth VK, Morrow MR. Effects of Amphipathic Polypeptides on Membrane Organization Inferred from Studies Using Bicellar Lipid Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11759-11771. [PMID: 30196696 DOI: 10.1021/acs.langmuir.8b02257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
SP-B63-78, a lung surfactant protein fragment, and magainin 2, an antimicrobial peptide, are amphipathic peptides with the same overall charge but different biological functions. Deuterium nuclear magnetic resonance has been used to compare the interactions of these peptides with dispersions of 1,2-dimyristoyl- sn-glycero-3-phophocholine (DMPC)/1,2-dihexanoyl- sn-glycero-3-phophocholine (DHPC) (4:1) and DMPC/1,2-dimyristoyl- sn-glycero-3-phopho-(1'-rac-glycerol) (DMPG)/DHPC (3:1:1), two mixtures of long-chain and short-chain lipids that display bicellar behavior. This study exploited the sensitivity of a bicellar system structural organization to factors that modify partitioning of their lipid components between different environments. In small bicelle particles formed at low temperatures, short-chain components preferentially occupy curved rim environments around bilayer disks of the long-chain components. Changes in chain order and lipid mixing, on heating, can drive transitions to more extended assemblies including a magnetically orientable phase at intermediate temperature. In this work, neither peptide had a substantial effect on the behavior of the zwitterionic DMPC/DHPC mixture. For bicellar mixtures containing the anionic lipid DMPG, the peptide SP-B63-78 lowered the temperature at which magnetically orientable particles coalesced into more extended lamellar structures. SP-B63-78 did not promote partitioning of the zwitterionic and anionic long-chain lipid components into different environments. Magainin 2, on the other hand, was found to promote separation of the anionic lipid, DMPG, and the zwitterionic lipid, DMPC, into different environments for temperatures above 34 °C. The contrast between the effects of these two peptides on the lipid mixtures studied appears to be consistent with their functional roles in biological systems.
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Affiliation(s)
- Chris Miranda
- Department of Physics and Physical Oceanography , Memorial University of Newfoundland , St. John's , Newfoundland and Labrador , Canada A1B 3X7
| | - Valerie K Booth
- Department of Biochemistry , Memorial University of Newfoundland , St. John's , Newfoundland and Labrador , Canada A1B 3X9
| | - Michael R Morrow
- Department of Physics and Physical Oceanography , Memorial University of Newfoundland , St. John's , Newfoundland and Labrador , Canada A1B 3X7
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Caldwell TA, Baoukina S, Brock AT, Oliver RC, Root KT, Krueger JK, Glover KJ, Tieleman DP, Columbus L. Low- q Bicelles Are Mixed Micelles. J Phys Chem Lett 2018; 9:4469-4473. [PMID: 30024762 PMCID: PMC6353637 DOI: 10.1021/acs.jpclett.8b02079] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bicelles are used in many membrane protein studies because they are thought to be more bilayer-like than micelles. We investigated the properties of "isotropic" bicelles by small-angle neutron scattering, small-angle X-ray scattering, fluorescence anisotropy, and molecular dynamics. All data suggest that bicelles with a q value below 1 deviate from the classic bicelle that contains lipids in the core and detergent in the rim. Thus not all isotropic bicelles are bilayer-like.
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Affiliation(s)
- Tracy A. Caldwell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Svetlana Baoukina
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ashton T. Brock
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ryan C. Oliver
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kyle T. Root
- Department of Chemistry, Lock Haven University, Lock Haven, Pennsylvania 17745, United States
| | - Joanna K. Krueger
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - D. Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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18
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Isabettini S, Liebi M, Kohlbrecher J, Ishikawa T, Fischer P, Windhab EJ, Walde P, Kuster S. Mastering the magnetic susceptibility of magnetically responsive bicelles with 3β-amino-5-cholestene and complexed lanthanide ions. Phys Chem Chem Phys 2018; 19:10820-10824. [PMID: 28401210 DOI: 10.1039/c7cp01025g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The magnetic susceptibility of lanthanide-chelating bicelles was selectively enhanced by introducing 3β-amino-5-cholestene (aminocholesterol, Chol-NH2) in the bilayer. Unprecedented magnetic alignment of the bicelles was achieved without altering their size. An aminocholesterol conjugate (Chol-C2OC2-NH2), in combination with different lanthanide ions, offers the possibility of fine-tuning the bicelle's magnetic susceptibility.
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Affiliation(s)
- Stéphane Isabettini
- Laboratory of Food Process Engineering, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland.
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19
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Liebau J, Mäler L. Immersion Depths of Lipid Carbons in Bicelles Measured by Paramagnetic Relaxation Enhancement. J Phys Chem B 2017; 121:7660-7670. [DOI: 10.1021/acs.jpcb.7b05822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jobst Liebau
- 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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20
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Isabettini S, Baumgartner ME, Reckey PQ, Kohlbrecher J, Ishikawa T, Fischer P, Windhab EJ, Kuster S. Methods for Generating Highly Magnetically Responsive Lanthanide-Chelating Phospholipid Polymolecular Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6363-6371. [PMID: 28594186 DOI: 10.1021/acs.langmuir.7b00725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and its lanthanide ion (Ln3+) chelating phospholipid conjugate, 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA), assemble into highly magnetically responsive polymolecular assemblies such as DMPC/DMPE-DTPA/Ln3+ (molar ratio 4:1:1) bicelles. Their geometry and magnetic alignability is enhanced by introducing cholesterol into the bilayer in DMPC/Cholesterol/DMPE-DTPA/Ln3+ (molar ratio 16:4:5:5). However, the reported fabrication procedures remain tedious and limit the generation of highly magnetically alignable species. Herein, a simplified procedure where freeze thawing cycles and extrusion are replaced by gentle heating and cooling cycles for the hydration of the dry lipid film was developed. Heating above the phase transition temperature Tm of the lipids composing the bilayer before cooling back below the Tm was essential to guarantee successful formation of the polymolecular assemblies composed of DMPC/DMPE-DTPA/Ln3+ (molar ratio 4:1:1). Planar polymolecular assemblies in the size range of hundreds of nanometers are achieved and deliver unprecedented gains in magnetic response. The proposed heating and cooling procedure further allowed to regenerate the highly magnetically alignable DMPC/Cholesterol/DMPE-DTPA/Ln3+ (molar ratio 16:4:5:5) species after storage for one month frozen at -18 °C. The simplicity and viability of the proposed fabrication procedure offers a new set of highly magnetically responsive lanthanide ion chelating phospholipid polymolecular assemblies as building blocks for the smart soft materials of tomorrow.
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Affiliation(s)
- Stéphane Isabettini
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Mirjam E Baumgartner
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Pernille Q Reckey
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | | | | | - Peter Fischer
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Erich J Windhab
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Simon Kuster
- Laboratory of Food Process Engineering, ETH Zurich , Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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21
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Kolahdouzan K, Jackman JA, Yoon BK, Kim MC, Johal MS, Cho NJ. Optimizing the Formation of Supported Lipid Bilayers from Bicellar Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5052-5064. [PMID: 28457139 DOI: 10.1021/acs.langmuir.7b00210] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Supported lipid bilayers (SLBs) are widely studied model membrane platforms that are compatible with various surface-sensitive measurement techniques. SLBs are typically formed on silica-based materials, and there are numerous possible fabrication routes involving either bottom-up molecular self-assembly or vesicle adsorption and rupture. In between these two classes of fabrication strategies lies an emerging approach based on depositing quasi-two-dimensional lamellar, bicellar disks composed of a mixture of long-chain and short-chain phospholipids to promote the formation of SLBs. This approach takes advantage of the thermodynamic preference of long-chain phospholipids to form planar SLBs, whereas short-chain phospholipids have brief residence times. Although a few studies have shown that SLBs can be formed on silica-based materials from bicellar mixtures, outstanding questions remain about the self-assembly mechanism as well as the influence of the total phospholipid concentration, ratio of the two phospholipids (termed the "q-ratio"), and process of sample preparation. Herein, we address these questions through comprehensive quartz crystal microbalance-dissipation, fluorescence microscopy, and fluorescence recovery after photobleaching experiments. Our findings identify that optimal SLB formation occurs at lower total concentrations of phospholipids than previously used as short-chain phospholipids behave like membrane-destabilizing detergents at higher concentrations. Using lower phospholipid concentrations, we also discovered that the formation of SLBs proceeds through a two-step mechanism involving a critical coverage of bicellar disks akin to vesicle fusion. In addition, the results indicate that at least one cycle of freeze-thaw-vortexing is useful during the sample preparation process to produce SLBs. Taken together, the findings in this work identify optimal routes for fabricating SLBs from bicellar mixtures and reveal mechanistic details about the bicelle-mediated SLB formation process, which will aid further exploration of bicellar mixtures as tools for model membrane fabrication.
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Affiliation(s)
- Kavoos Kolahdouzan
- Department of Chemistry, Pomona College , 645 North College Avenue, Claremont, California 91711, United States
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Min Chul Kim
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
| | - Malkiat S Johal
- Department of Chemistry, Pomona College , 645 North College Avenue, Claremont, California 91711, United States
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive, 637459, Singapore
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22
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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: 1.6] [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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23
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Affiliation(s)
- M. J. Greenall
- Institute of Mathematics,
Physics and Computer Science, Physical Sciences Building, Aberystwyth University, Aberystwyth SY23 3BZ, United Kingdom
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24
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Xia Y, Li M, Charubin K, Liu Y, Heberle FA, Katsaras J, Jing B, Zhu Y, Nieh MP. Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12920-8. [PMID: 26540211 DOI: 10.1021/acs.langmuir.5b03291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C14, DMPC) in discoidal "bicelles" (0.156 h(-1)) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10(-3) h(-1)). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C14 DMPC to di-C16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and fluorescence correlation spectroscopy (FCS) are in good agreement. The present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.
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Affiliation(s)
- Yan Xia
- Department of Chemical and Biomolecular Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Ming Li
- Polymer Program, Institute of Materials Science, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Ying Liu
- Department of Chemical and Biomolecular Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Frederick A Heberle
- Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831 United States
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831 United States
- Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Benxin Jing
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Yingxi Zhu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
- Department of Chemical Engineering and Materials Science, Wayne State University , Detroit, Michigan 48202 United States
| | - Mu-Ping Nieh
- Department of Chemical and Biomolecular Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
- Polymer Program, Institute of Materials Science, University of Connecticut , Storrs, Connecticut 06269, United States
- Department of Biomedical Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
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25
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Martin RW, Kelly JE, Collier KA. Spatial reorientation experiments for NMR of solids and partially oriented liquids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:92-122. [PMID: 26592947 PMCID: PMC6936739 DOI: 10.1016/j.pnmrs.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Motional reorientation experiments are extensions of Magic Angle Spinning (MAS) where the rotor axis is changed in order to average out, reintroduce, or scale anisotropic interactions (e.g. dipolar couplings, quadrupolar interactions or chemical shift anisotropies). This review focuses on Variable Angle Spinning (VAS), Switched Angle Spinning (SAS), and Dynamic Angle Spinning (DAS), all of which involve spinning at two or more different angles sequentially, either in successive experiments or during a multidimensional experiment. In all of these experiments, anisotropic terms in the Hamiltonian are scaled by changing the orientation of the spinning sample relative to the static magnetic field. These experiments vary in experimental complexity and instrumentation requirements. In VAS, many one-dimensional spectra are collected as a function of spinning angle. In SAS, dipolar couplings and/or chemical shift anisotropies are reintroduced by switching the sample between two different angles, often 0° or 90° and the magic angle, yielding a two-dimensional isotropic-anisotropic correlation spectrum. Dynamic Angle Spinning (DAS) is a related experiment that is used to simultaneously average out the first- and second-order quadrupolar interactions, which cannot be accomplished by spinning at any unique rotor angle in physical space. Although motional reorientation experiments generally require specialized instrumentation and data analysis schemes, some are accessible with only minor modification of standard MAS probes. In this review, the mechanics of each type of experiment are described, with representative examples. Current and historical probe and coil designs are discussed from the standpoint of how each one accomplishes the particular objectives of the experiment(s) it was designed to perform. Finally, applications to inorganic materials and liquid crystals, which present very different experimental challenges, are discussed. The review concludes with perspectives on how motional reorientation experiments can be applied to current problems in chemistry, molecular biology, and materials science, given the many advances in high-field NMR magnets, fast spinning, and sample preparation realized in recent years.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Kelsey A Collier
- Department of Physics and Astronomy, University of California, Irvine 92697-4575, United States
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26
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Analysing DHPC/DMPC bicelles by diffusion NMR and multivariate decomposition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2910-7. [DOI: 10.1016/j.bbamem.2015.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/16/2022]
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Tang J, Alsop RJ, Schmalzl K, Epand RM, Rheinstädter MC. Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes. MEMBRANES 2015; 5:532-52. [PMID: 26426063 PMCID: PMC4703998 DOI: 10.3390/membranes5040532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/17/2015] [Indexed: 11/16/2022]
Abstract
It was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains’ electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state.
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Affiliation(s)
- Jennifer Tang
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Richard J Alsop
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Karin Schmalzl
- JCNS, Forschungszentrum Jülich, Outstation at ILL, 38042 Grenoble, France.
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Maikel C Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
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28
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Fillion M, Auger M. Oriented samples: a tool for determining the membrane topology and the mechanism of action of cationic antimicrobial peptides by solid-state NMR. Biophys Rev 2015; 7:311-320. [PMID: 28510228 PMCID: PMC5425733 DOI: 10.1007/s12551-015-0167-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/05/2015] [Indexed: 01/12/2023] Open
Abstract
Overuse and misuse of antibiotics have led bacteria to acquire several mechanisms of resistance. In response to this, researchers have identified natural antimicrobial peptides as promising candidates to fight against multiresistant bacteria. However, their mode of action is still unclear, and a better understanding of the mode of action of these peptides is of primary importance to develop new peptides displaying high antibacterial activity and low hemolytic activity. One of the main features that defines the mechanism of action is the membrane topology of the peptide. Among the spectroscopic techniques, solid-state NMR is the technique of choice for determining the location of the peptide within the membrane. It can be achieved by performing experiments with oriented samples. In the literature, the two most common types of oriented samples are bicelles and phospholipids mechanically oriented between glass plates. The mode of perturbation of the membrane-active peptide can be studied by phosphorus-31 and deuterium NMR. On the other hand, several experiments such as nitrogen-15 and fluorine solid-state NMR, that require labeled peptides, can give valuable information on the membrane topology of the peptide. The combination of the latter techniques allows the determination of a precise topology, thus a better knowledge of the molecular determinants involved in the membrane interactions of antimicrobial peptides.
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Affiliation(s)
- Matthieu Fillion
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada.
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29
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McCaffrey JE, James ZM, Thomas DD. Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 250:71-75. [PMID: 25514061 PMCID: PMC4286475 DOI: 10.1016/j.jmr.2014.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/24/2014] [Accepted: 09/29/2014] [Indexed: 06/04/2023]
Abstract
We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below.
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Affiliation(s)
- Jesse E McCaffrey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary M James
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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30
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Beaugrand M, Arnold A, Hénin J, Warschawski DE, Williamson PTF, Marcotte I. Lipid concentration and molar ratio boundaries for the use of isotropic bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6162-70. [PMID: 24797658 PMCID: PMC4072726 DOI: 10.1021/la5004353] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/02/2014] [Indexed: 05/27/2023]
Abstract
Bicelles are model membranes generally made of long-chain dimyristoylphosphatidylcholine (DMPC) and short-chain dihexanoyl-PC (DHPC). They are extensively used in the study of membrane interactions and structure determination of membrane-associated peptides, since their composition and morphology mimic the widespread PC-rich natural eukaryotic membranes. At low DMPC/DHPC (q) molar ratios, fast-tumbling bicelles are formed in which the DMPC bilayer is stabilized by DHPC molecules in the high-curvature rim region. Experimental constraints imposed by techniques such as circular dichroism, dynamic light scattering, or microscopy may require the use of bicelles at high dilutions. Studies have shown that such conditions induce the formation of small aggregates and alter the lipid-to-detergent ratio of the bicelle assemblies. The objectives of this work were to determine the exact composition of those DMPC/DHPC isotropic bicelles and study the lipid miscibility. This was done using (31)P nuclear magnetic resonance (NMR) and exploring a wide range of lipid concentrations (2-400 mM) and q ratios (0.15-2). Our data demonstrate how dilution modifies the actual DMPC/DHPC molar ratio in the bicelles. Care must be taken for samples with a total lipid concentration ≤250 mM and especially at q ∼ 1.5-2, since moderate dilutions could lead to the formation of large and slow-tumbling lipid structures that could hinder the use of solution NMR methods, circular dichroism or dynamic light scattering studies. Our results, supported by infrared spectroscopy and molecular dynamics simulations, also show that phospholipids in bicelles are largely segregated only when q > 1. Boundaries are presented within which control of the bicelles' q ratio is possible. This work, thus, intends to guide the choice of q ratio and total phospholipid concentration when using isotropic bicelles.
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Affiliation(s)
- Maïwenn Beaugrand
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
| | - Alexandre
A. Arnold
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique, CNRS, Université
Paris Diderot and Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie-Curie, 75005 Paris, France
| | - Dror E. Warschawski
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Université Paris Diderot and Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie-Curie, 75005 Paris, France
| | - Philip T. F. Williamson
- School
of Biological Sciences, Highfield Campus,
University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Isabelle Marcotte
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
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31
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Ye W, Lind J, Eriksson J, Mäler L. Characterization of the morphology of fast-tumbling bicelles with varying composition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5488-5496. [PMID: 24785902 DOI: 10.1021/la500231z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Small, fast-tumbling bicelles are frequently used in solution NMR studies of protein-lipid interactions. For this purpose it is critical to have information about the organization of the lipids within the bicelle structure. We have studied the morphology of small, fast-tumbling bicelles containing DMPC and DHPC as a function of temperature, lipid concentration, and the relative ratio (q value) of lipid (DMPC) to detergent (DHPC) amounts. Dynamic light scattering and cryo-transmission electron microscopy techniques were used to measure the size of the bicelles and to monitor the shape and dispersity of the particles in the samples. The stability and size of DMPC-containing bicelle mixtures were found to be highly dependent on temperature and the total lipid concentration for mixtures with q = 1 and q = 1.5. Stable DMPC/DHPC bicelles are only formed at low q values (0.5). Bicelle mixtures with q > 0.5 appear to be multidisperse containing more than one component, one with r(H) around 2.5 nm and one with r(H) of 6-8 nm. This is interpreted as a coexistence of small (possibly mixed micelles) bicelles and much larger bicelles. Incubating the sample at 37 °C increases the phase separation. Moreover, low total amphiphile concentrations and low q values lead to the formation of a temperature-independent morphology, interpreted as the formation of small particles in which the DHPC and DMPC are more mixed. On the basis of these results, we propose the existence of a critical bicelle concentration, a parameter that determines the existence of bilayered bicelles, which varies with q value. This polymorphism was not observed at any concentrations for q = 0.5 bicelles, for which a small but detectable temperature dependence was observed at high concentrations. The results demonstrate that q = 0.5 mixtures predominantly form "classical" bicelles, but that caution is needed when using fast-tumbling mixtures with q values higher than 0.5.
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Affiliation(s)
- Weihua Ye
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
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32
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Maltsev S, Lorigan GA. Membrane proteins structure and dynamics by nuclear magnetic resonance. Compr Physiol 2013; 1:2175-87. [PMID: 23733702 DOI: 10.1002/cphy.c110022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Membrane proteins represent a challenging class of biological systems to study. They are extremely difficult to crystallize and in most cases they retain their structure and functions only in membrane environments. Therefore, commonly used diffraction methods fail to give detailed molecular structure and other approaches have to be utilized to obtain biologically relevant information. Nuclear magnetic resonance (NMR) spectroscopy, however, can provide powerful structural and dynamical constraints on these complicated systems. Solution- and solid-state NMR are powerful methods for investigating membrane proteins studies. In this work, we briefly review both solution and solid-state NMR techniques for membrane protein studies and illustrate the applications of these methods to elucidate proteins structure, conformation, topology, dynamics, and function. Recent advances in electronics, biological sample preparation, and spectral processing provided opportunities for complex biological systems, such as membrane proteins inside lipid vesicles, to be studied faster and with outstanding quality. New analysis methods therefore have emerged, that benefit from the combination of sample preparation and corresponding specific high-end NMR techniques, which give access to more structural and dynamic information.
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Affiliation(s)
- Sergey Maltsev
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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33
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Song Y, Kenworthy AK, Sanders CR. Cholesterol as a co-solvent and a ligand for membrane proteins. Protein Sci 2013; 23:1-22. [PMID: 24155031 DOI: 10.1002/pro.2385] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 01/23/2023]
Abstract
As of mid 2013 a Medline search on "cholesterol" yielded over 200,000 hits, reflecting the prominence of this lipid in numerous aspects of animal cell biology and physiology under conditions of health and disease. Aberrations in cholesterol homeostasis underlie both a number of rare genetic disorders and contribute to common sporadic and complex disorders including heart disease, stroke, type II diabetes, and Alzheimer's disease. The corresponding author of this review and his lab stumbled only recently into the sprawling area of cholesterol research when they discovered that the amyloid precursor protein (APP) binds cholesterol, a topic covered by the Hans Neurath Award lecture at the 2013 Protein Society Meeting. Here, we first provide a brief overview of cholesterol-protein interactions and then offer our perspective on how and why binding of cholesterol to APP and its C99 domain (β-CTF) promotes the amyloidogenic pathway, which is closely related to the etiology of Alzheimer's disease.
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Affiliation(s)
- Yuanli Song
- Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
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34
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Rahmani A, Knight C, Morrow MR. Response to hydrostatic pressure of bicellar dispersions containing an anionic lipid: pressure-induced interdigitation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13481-13490. [PMID: 24116385 DOI: 10.1021/la4035694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bicellar dispersions of chain perdeuterated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC-d54), 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG), and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), with molar ratios of 3:1:1, were studied using variable-pressure (2)H NMR spectroscopy at hydrostatic pressures up to 125 MPa. Upon warming of the dispersions, spectra at ambient pressure indicated a progressive coalescence from small bilayered disks undergoing isotropic reorientation to more extended micellar structures in which spectra indicated anisotropic reorientation and, under some conditions, magnetic orientation and finally to randomly oriented lamellae or multilamellar vesicles. Temperatures for the onsets of anisotropic reorientation and random lamellar orientation increased with pressure at rates of 0.22 and 0.15 °C/MPa, respectively. In the 3.5-T magnetic field used for this work, magnetic orientation within the intermediate phase was not observed at 83 MPa or higher pressures. Comparison of spectra obtained at fixed pressure showed significant asymmetry between behaviors upon warming and cooling. For samples of DMPC-d54/DMPG/DHPC (3:1:1), but not DMPC-d54/DHPC (4:1), a persistent interdigitated phase was formed after repeated cooling from high temperature at 83 MPa. This is likely a metastable phase and might reflect kinetic trapping of the short-chain lipid component, DHPC, in a nonequilibrium spatial distribution as temperature is lowered at high pressure. Bicellar dispersions typically behave differently upon warming and cooling, and these observations could provide some insight into the observed behaviors in such systems. This work also suggests the possibility of trapping bicellar dispersions in persistent nonequilibrium morphologies.
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Affiliation(s)
- Ashkan Rahmani
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada A1B 3X7
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35
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Mäler L. Solution NMR studies of cell-penetrating peptides in model membrane systems. Adv Drug Deliv Rev 2013; 65:1002-11. [PMID: 23137785 DOI: 10.1016/j.addr.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a class of short, often cationic peptides that have the capability to translocate across cellular membranes, and although the translocation most likely involves several pathways, they interact directly with membranes, as well as with model bilayers. Most CPPs attain a three-dimensional structure when interacting with bilayers, while they are more or less unstructured in aqueous solution. To understand the relationship between structure and the effect that CPPs have on membranes it is of great importance to investigate CPPs at atomic resolution in a suitable membrane model. Moreover, the location in bilayers is likely to be correlated with the translocation mechanism. Solution-state NMR offers a unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating CPP-lipid interactions. Structural propensities and cell-penetrating capabilities can be derived from a combination of CPP solution structures and studies of the effect that the peptides have on bilayers and the localization in a bilayer.
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Affiliation(s)
- Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
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36
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Baek SB, Lee HJ, Lee HC, Kim C. Thermodynamics of Partitioning of Substance P in Isotropic Acidic Bicelles. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.3.743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Liebi M, van Rhee PG, Christianen PCM, Kohlbrecher J, Fischer P, Walde P, Windhab EJ. Alignment of bicelles studied with high-field magnetic birefringence and small-angle neutron scattering measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:3467-3473. [PMID: 23406168 DOI: 10.1021/la3050785] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Birefringence measurements at high magnetic field strength of up to 33 T were used to detect magnetically induced alignment of bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), cholesterol, and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-diethylenetriaminepentaacetate (DMPE-DTPA) with complexed lanthanide ions. These birefringence measurements together with a small-angle neutron scattering (SANS) analysis in a magnetic field showed parallel alignment of the bicelles if the lanthanide was thulium (Tm(3+)), and perpendicular alignment with dysprosium (Dy(3+)). With the birefringence measurements, the order parameter S can be determined as a function of the magnetic field strength, if the magnetic alignment reaches saturation. Additional structural information can be obtained if the maximum induced birefringence is considered. The degree of alignment of the studied bicelles increased with decreasing temperature from 40 to 5 °C and showed a new bicellar structure comprising a transient hole formation at intermediate temperatures (20 °C) during heating from 5 to 40 °C.
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Affiliation(s)
- Marianne Liebi
- Laboratory of Food Process Engineering, ETH Zurich, Zurich, Switzerland
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38
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Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
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39
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NMR methods for measuring lateral diffusion in membranes. Chem Phys Lipids 2013; 166:31-44. [DOI: 10.1016/j.chemphyslip.2012.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 02/07/2023]
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40
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Lateral diffusion of bilayer lipids measured via 31P CODEX NMR. Chem Phys Lipids 2012; 165:721-30. [DOI: 10.1016/j.chemphyslip.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 11/18/2022]
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41
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Morigaki K, Kimura S, Okada K, Kawasaki T, Kawasaki K. Formation of substrate-supported membranes from mixtures of long- and short-chain phospholipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:9649-9655. [PMID: 22591412 DOI: 10.1021/la300696z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We studied the formation of substrate-supported planar phospholipid bilayers (SPBs) on glass and silica from mixtures of long- and short-chain phospholipids to assess the effects of detergent additives on SPB formation. 1,2-Hexyanoyl-sn-glycero-3-phosphocholine (DHPC-C6) and 1,2-heptanoyl-sn-glycero-3-phosphocholine (DHPC-C7) were chosen as short-chain phospholipids. 1-Palmitoyl-2-oleol-sn-glycero-3-phosphocholine (POPC) was used as a model long-chain phospholipid. Kinetic studies by quartz crystal microbalance with dissipation monitoring (QCM-D) showed that the presence of short-chain phospholipids significantly accelerated the formation of SPBs. Rapid rinsing with a buffer solution did not change the adsorbed mass on the surface if POPC/DHPC-C6 mixtures were used below the critical micelle concentration (cmc) of DHPC-C6, indicating that an SPB composed of POPC molecules remained on the surface. Fluorescence microscopy observation showed homogeneous SPBs, and the fluorescence recovery after photobleaching (FRAP) measurements gave a diffusion coefficient comparable to that for SPBs formed from POPC vesicles. However, mixtures of POPC/DHPC-C7 resulted in a smaller mass of lipid adsorption on the substrate. FRAP measurements also yielded significantly smaller diffusion coefficients, suggesting the presence of defects. The different behaviors for DHPC-C6 and DHPC-C7 point to the dual roles of detergents to enhance the formation of SPBs and to destabilize them, depending on their structures and aggregation properties.
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Affiliation(s)
- Kenichi Morigaki
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan.
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42
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43
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Nolandt OV, Walther TH, Grage SL, Ulrich AS. Magnetically oriented dodecylphosphocholine bicelles for solid-state NMR structure analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1142-7. [PMID: 22274567 DOI: 10.1016/j.bbamem.2012.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 01/05/2012] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
Abstract
A mixture of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with the short-chain detergent n-dodecylphosphocholine (DPC) is introduced here as a new membrane-mimetic bicelle system for solid-state NMR structure analysis of membrane proteins in oriented samples. Magnetically aligned DMPC/DPC bicelles are stable over a range of concentrations, with an optimum lipid ratio of q=3:1, and they can be flipped with lanthanide ions. The advantage of DMPC/DPC over established bicelle systems lies in the possibility to use one and the same detergent for purification and NMR analysis of the membrane protein, without any need for detergent exchange. Furthermore, the same batch of protein can be studied in both micelles and bicelles, using liquid-state and solid-state NMR, respectively. The applicability of the DMPC/DPC bicelles is demonstrated here with the (15)N-labeled transmembrane protein TatA.
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Affiliation(s)
- Olga V Nolandt
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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44
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Abstract
This minireview focuses on diffusion NMR studies in bicelles. Following a discourse on diffusion fundamentals, and a comparative overview of fluorescence and NMR-based techniques for measuring diffusion, the pulsed field gradient (PFG) NMR diffusion method is introduced, emphasizing its specific advantages and limitations when applied to diffusion measurements in macroscopically oriented lamellar systems such as magnetically aligned bicelles. The utility of PFG NMR diffusion measurements in bicellar model membrane systems for examining lateral diffusion of membrane-bound molecular species is demonstrated, along with certain features of lateral diffusion that such studies illuminate. Further, those aspects of bicelle morphology that have been resolved using PFG NMR diffusion studies of various molecular weight soluble polymeric species are reviewed. The discussion concludes with an outline of future prospects for diffusion NMR studies in bicelles.
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Affiliation(s)
- Peter M. Macdonald
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Ronald Soong
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
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45
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Warschawski DE, Arnold AA, Beaugrand M, Gravel A, Chartrand É, Marcotte I. Choosing membrane mimetics for NMR structural studies of transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1957-74. [DOI: 10.1016/j.bbamem.2011.03.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 12/11/2022]
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46
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Unnerståle S, Mäler L, Draheim RR. Structural characterization of AS1-membrane interactions from a subset of HAMP domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2403-12. [PMID: 21763270 DOI: 10.1016/j.bbamem.2011.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 02/07/2023]
Abstract
HAMP domains convert an extracellular sensory input into an intracellular signaling response in a wide variety of membrane-embedded bacterial proteins. These domains are almost invariably found adjacent to the inner leaflet of the cell membrane. We therefore examined the interaction of peptides corresponding to either AS1 or AS2 of four different, well-characterized HAMP domains with several membrane model systems. The proteins included an Archaeoglobus fulgidus protein (Af1503), the Escherichia coli osmosensor EnvZ(Ec), the E. coli nitrate/nitrite sensor NarX(Ec), and the aspartate chemoreceptor of E. coli (Tar(Ec)). Far-UV CD and NMR spectroscopy were used to monitor the induction of secondary structure upon association with neutral or acidic large unilamellar vesicles (LUVs) and bicelles. We observed significant increases in α-helicity within AS1 from NarX(Ec) and Tar(Ec) but not in AS1 from the other proteins. To characterize these interactions further, we determined the solution structure of AS1 from Tar(Ec) associated with acidic bicelles. The bulk of AS1 formed an amphipathic α-helix, whereas the N-terminal control cable, the region between TM2 and AS1, remained unstructured. We observed that the conserved prolyl residue found in AS1 of many membrane-adjacent HAMP domains defined the boundary between the unstructured and helical regions. In addition, two positively charged residues that flank the hydrophobic surface of AS1 are thought to facilitate electrostatic interactions with the membrane. We interpret these results within the context of the helix-interaction model for HAMP signaling and propose roles for AS1-membrane interactions during the membrane assembly and transmembrane communication of HAMP-containing receptors.
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Affiliation(s)
- Sofia Unnerståle
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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47
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Nieh MP, Raghunathan VA, Pabst G, Harroun T, Nagashima K, Morales H, Katsaras J, Macdonald P. Temperature driven annealing of perforations in bicellar model membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4838-4847. [PMID: 21438512 DOI: 10.1021/la104750x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Bicellar model membranes composed of 1,2-dimyristoylphosphatidylcholine (DMPC) and 1,2-dihexanoylphosphatidylcholine (DHPC), with a DMPC/DHPC molar ratio of 5, and doped with the negatively charged lipid 1,2-dimyristoylphosphatidylglycerol (DMPG), at DMPG/DMPC molar ratios of 0.02 or 0.1, were examined using small angle neutron scattering (SANS), (31)P NMR, and (1)H pulsed field gradient (PFG) diffusion NMR with the goal of understanding temperature effects on the DHPC-dependent perforations in these self-assembled membrane mimetics. Over the temperature range studied via SANS (300-330 K), these bicellar lipid mixtures exhibited a well-ordered lamellar phase. The interlamellar spacing d increased with increasing temperature, in direct contrast to the decrease in d observed upon increasing temperature with otherwise identical lipid mixtures lacking DHPC. (31)P NMR measurements on magnetically aligned bicellar mixtures of identical composition indicated a progressive migration of DHPC from regions of high curvature into planar regions with increasing temperature, and in accord with the "mixed bicelle model" (Triba, M. N.; Warschawski, D. E.; Devaux, P. E. Biophys. J.2005, 88, 1887-1901). Parallel PFG diffusion NMR measurements of transbilayer water diffusion, where the observed diffusion is dependent on the fractional surface area of lamellar perforations, showed that transbilayer water diffusion decreased with increasing temperature. A model is proposed consistent with the SANS, (31)P NMR, and PFG diffusion NMR data, wherein increasing temperature drives the progressive migration of DHPC out of high-curvature regions, consequently decreasing the fractional volume of lamellar perforations, so that water occupying these perforations redistributes into the interlamellar volume, thereby increasing the interlamellar spacing.
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Affiliation(s)
- Mu-Ping Nieh
- Chemical, Materials and Biomolecular Engineering Department, Institute of Material Sciences, University of Connecticut, 97 North Eagleville Road, Storrs, Connecticut 06269-3136, USA
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48
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Abstract
The chapter deals with some biophysical methods used for investigating CPP-induced changes in membrane properties by spectroscopy methods such as fluorescence or NMR and methods used for probing CPP-induced leakage in membranes. Some useful model systems for biomembranes are described. These include large unilamellar phospholipid vesicles (LUVs) of well-defined size (diameter typically 100 nm). A protocol for the preparation of such vesicles is included. The leakage studies make use of LUVs with entrapped dye molecules. The NMR studies make use of mixed micelles (bicelles) as a membrane mimetic system, which can be oriented in the magnetic field of the spectrometer.
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Affiliation(s)
- Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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49
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Cook GA, Zhang H, Park SH, Wang Y, Opella SJ. Comparative NMR studies demonstrate profound differences between two viroporins: p7 of HCV and Vpu of HIV-1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:554-60. [PMID: 20727848 DOI: 10.1016/j.bbamem.2010.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 10/19/2022]
Abstract
The p7 protein from hepatitis C virus and the Vpu protein from HIV-1 are members of the viroporin family of small viral membrane proteins. It is essential to determine their structures in order to obtain an understanding of their molecular mechanisms and to develop new classes of anti-viral drugs. Because they are membrane proteins, it is challenging to study them in their native phospholipid bilayer environments by most experimental methods. Here we describe applications of NMR spectroscopy to both p7 and Vpu. Isotopically labeled p7 and Vpu samples were prepared by heterologous expression in bacteria, initial isolation as fusion proteins, and final purification by chromatography. The purified proteins were studied in the model membrane environments of micelles by solution NMR spectroscopy and in aligned phospholipid bilayers by solid-state NMR spectroscopy. The resulting structural findings enable comparisons to be made between the two proteins, demonstrating that they have quite different architectures. Most notably, Vpu has one trans-membrane helix and p7 has two trans-membrane helices; in addition, there are significant differences in the structures and dynamics of their internal loop and terminal regions.
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Affiliation(s)
- Gabriel A Cook
- Department of Chemistry and Biochemistry, University of California, San Diego, Lajolla, CA 92093, USA
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Uddin MN, Morrow MR. Bicellar mixture phase behavior examined by variable-pressure deuterium NMR and ambient pressure DSC. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:12104-12111. [PMID: 20536154 DOI: 10.1021/la1014362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Variable-pressure deuterium nuclear magnetic resonance ((2)H NMR) has been used to study the pressure-temperature phase diagram of bicellar mixtures containing 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC). Spectra were obtained for DMPC-d(54)/DHPC (3:1), DMPC-d(54)/DHPC (4.4:1), DMPC/DHPC-d(22) (3:1), and DMPC/DHPC-d(22) (4.4:1) in the range 10-68 degrees C at ambient pressure, 66 MPa, 102 MPa, and 135 MPa. Isotropic-to-nematic and nematic-to-lamellar transition temperatures were found to rise with pressure at approximately 0.15 and approximately 0.14 degrees C/MPa, respectively, for DMPC-d(54)/DHPC (3:1) and at at approximately 0.19 and approximately 0.18 degrees C/MPa, respectively, for DMPC-d(54)/DHPC (4.4:1). Pressure had little effect on the range of DMPC-d(54) chain orientational order through the nematic phase temperature range, but the behavior of chain orientational order at the nematic-to-lamellar transition was found to vary slightly with pressure. Comparison of differential scanning calorimetry (DSC) observations with ambient-pressure (2)H NMR observations of DMPC-d(54) in the bicellar mixtures suggests that absorption of heat persists for a few degrees above the onset of axially symmetric DMPC-d(54) reorientation.
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Affiliation(s)
- Md Nasir Uddin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3X7
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