1
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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2
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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3
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Situ AJ, Ulmer TS. Comparison of Integrin αIIbβ3 Transmembrane Association in Vesicles and Bicelles. Biochemistry 2023. [PMID: 37279176 DOI: 10.1021/acs.biochem.3c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane proteins are commonly reconstituted in membrane mimics exhibiting discontinuous lipid bilayers. In contrast, the continuous membranes of cells are conceptually best represented by large unilamellar vesicles (LUVs). Here, we compared the thermodynamic stability of the integrin αIIbβ3 transmembrane (TM) complex between vesicles and bicelles to assess the consequence of this simplification. In LUVs, we further evaluated the strength of the αIIb(G972S)-β3(V700T) interaction that corresponds to the hydrogen bond interaction postulated for β2 integrins. An upper limit of 0.9 kcal/mol was estimated for superior TM complex stabilization in LUVs relative to bicelles. Compared to the αIIbβ3 TM complex stability in LUVs of 5.6 ± 0.2 kcal/mol, this limit is modest, indicating that bicelles performed well relative to LUVs. The implementation of β3(V700T) alleviated αIIb(G972S) destabilization by 0.4 ± 0.2 kcal/mol in confirmation of relatively weak hydrogen bonding. Interestingly, the hydrogen bond adjusts the TM complex stability to a level that is not achievable by merely varying the residue corresponding to αIIb(Gly972).
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Affiliation(s)
- Alan J Situ
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Tobias S Ulmer
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
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4
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Lenz J, Larsen AH, Keller S, Luchini A. Effect of Cholesterol on the Structure and Composition of Glyco-DIBMA Lipid Particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3569-3579. [PMID: 36854196 PMCID: PMC10018766 DOI: 10.1021/acs.langmuir.2c03019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Different amphiphilic co-polymers have been introduced to produce polymer-lipid particles with nanodisc structure composed of an inner lipid bilayer and polymer chains self-assembled as an outer belt. These particles can be used to stabilize membrane proteins in solution and enable their characterization by means of biophysical methods, including small-angle X-ray scattering (SAXS). Some of these co-polymers have also been used to directly extract membrane proteins together with their associated lipids from native membranes. Styrene/maleic acid and diisobutylene/maleic acid are among the most commonly used co-polymers for producing polymer-lipid particles, named SMALPs and DIBMALPs, respectively. Recently, a new co-polymer, named Glyco-DIBMA, was produced by partial amidation of DIBMA with the amino sugar N-methyl-d-glucosamine. Polymer-lipid particles produced with Glyco-DIBMA, named Glyco-DIBMALPs, exhibit improved structural properties and stability compared to those of SMALPs and DIBMALPs while retaining the capability of directly extracting membrane proteins from native membranes. Here, we characterize the structure and lipid composition of Glyco-DIBMALPs produced with either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Glyco-DIBMALPs were also prepared with mixtures of either POPC or DMPC and cholesterol at different mole fractions. We estimated the lipid content in the Glyco-DIBMALPs and determined the particle structure and morphology by SAXS. We show that the Glyco-DIBMALPs are nanodisc-like particles whose size and shape depend on the polymer/lipid ratio. This is relevant for designing nanodisc particles with a tunable diameter according to the size of the membrane protein to be incorporated. We also report that the addition of >20 mol % cholesterol strongly perturbed the formation of Glyco-DIBMALPs. Altogether, we describe a detailed characterization of the Glyco-DIBMALPs, which provides relevant inputs for future application of these particles in the biophysical investigation of membrane proteins.
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Affiliation(s)
- Julia Lenz
- Molecular
Biophysics, Technische Universität
Kaiserslautern, Erwin-Schrödinger-Strasse
13, 67663 Kaiserslautern, Germany
| | | | - Sandro Keller
- Biophysics,
Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
- Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Alessandra Luchini
- European
Spallation Source - ERIC, Partikel Gatan, Lund 224
84, Sweden
- Department
of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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5
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Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
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6
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Ehsan M, Wang H, Cecchetti C, Mortensen JS, Du Y, Hariharan P, Nygaard A, Lee HJ, Ghani L, Guan L, Loland CJ, Byrne B, Kobilka BK, Chae PS. Maltose-bis(hydroxymethyl)phenol (MBPs) and Maltose-tris(hydroxymethyl)phenol (MTPs) Amphiphiles for Membrane Protein Stability. ACS Chem Biol 2021; 16:1779-1790. [PMID: 34445864 DOI: 10.1021/acschembio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Membrane protein structures provide a fundamental understanding of their molecular actions and are of importance for drug development. Detergents are widely used to solubilize, stabilize, and crystallize membrane proteins, but membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation. Thus, developing novel detergents with enhanced efficacy for protein stabilization remains important. We report herein the design and synthesis of a class of phenol-derived maltoside detergents. Using two different linkers, we prepared two sets of new detergents, designated maltose-bis(hydroxymethyl)phenol (MBPs) and maltose-tris(hydroxymethyl)phenol (MTPs). The evaluation of these detergents with three transporters and two G-protein coupled receptors allowed us to identify a couple of new detergents (MBP-C9 and MTP-C12) that consistently conferred enhanced stability to all tested proteins compared to a gold standard detergent (DDM). Furthermore, the data analysis based on the detergent structures provides key detergent features responsible for membrane protein stabilization that together will facilitate the future design of novel detergents.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ho Jin Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
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7
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Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021; 22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Affiliation(s)
- Amita R. Sahoo
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
- Department of Neurosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence:
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8
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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9
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Chorev DS, Robinson CV. The importance of the membrane for biophysical measurements. Nat Chem Biol 2020; 16:1285-1292. [PMID: 33199903 PMCID: PMC7116504 DOI: 10.1038/s41589-020-0574-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/22/2020] [Indexed: 11/09/2022]
Abstract
Within cell membranes numerous protein assemblies reside. Among their many functions, these assemblies regulate the movement of molecules between membranes, facilitate signaling into and out of cells, allow movement of cells by cell-matrix attachment, and regulate the electric potential of the membrane. With such critical roles, membrane protein complexes are of considerable interest for human health, yet they pose an enduring challenge for structural biologists because it is difficult to study these protein structures at atomic resolution in in situ environments. To advance structural and functional insights for these protein assemblies, membrane mimetics are typically employed to recapitulate some of the physical and chemical properties of the lipid bilayer membrane. However, extraction from native membranes can sometimes change the structure and lipid-binding properties of these complexes, leading to conflicting results and fueling a drive to study complexes directly from native membranes. Here we consider the co-development of membrane mimetics with technological breakthroughs in both cryo-electron microscopy (cryo-EM) and native mass spectrometry (nMS). Together, these developments are leading to a plethora of high-resolution protein structures, as well as new knowledge of their lipid interactions, from different membrane-like environments.
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Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
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10
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Sharma G, Deuis JR, Jia X, Mueller A, Vetter I, Mobli M. Recombinant production, bioconjugation and membrane binding studies ofPn3a, a selective Na V1.7 inhibitor. Biochem Pharmacol 2020; 181:114148. [PMID: 32663452 DOI: 10.1016/j.bcp.2020.114148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/19/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
Chronic pain is a common and often debilitating condition. Existing treatments are either inefficacious or associated with a wide range of side effects. The progress on developing safer and more effective analgesics has been slow, in large part due to our limited understanding of the physiological mechanisms underlying pain in different diseases. Generation and propagation of action potentials is a central component of pain sensation and voltage-gated sodium channels (NaVs) play a critical role in this process. In particular, the NaV subtype 1.7, has emerged as a promising universal target for the treatment of pain. Recently, a spider venom peptide, μ-TRTX-Pn3a, was found to be a highly selective inhibitor of NaV1.7. Here, we report the first recombinant expression method for Pn3a in a bacterial host, which provides an inexpensive route to production. Furthermore, we have developed a method for bio-conjugation of our recombinantly produced Pn3a via sortase A-mediated ligation, providing avenues for further pre-clinical development. We demonstrate how heterologous expression in bacteria enables facile isotope labelling of Pn3a, which allowed us to study the membrane binding properties of the peptide by high-resolution solution-state nuclear magnetic resonance (NMR) spectroscopy using a recently developed lipid nanodisc system. The heteronuclear NMR data indicate that the C-terminal region of the peptide undergoes a conformational change upon lipid binding. The membrane binding properties of Pn3a are further validated using isothermal titration calorimetry (ITC), which revealed that Pn3a binds to zwitterionic planar lipid bilayers with thermodynamics that are largely driven by enthalpic contributions.
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Affiliation(s)
- Gagan Sharma
- Centre for Advanced Imaging, The University of Queensland, Australia.
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, Australia.
| | - Xinying Jia
- Centre for Advanced Imaging, The University of Queensland, Australia.
| | - Alexander Mueller
- Institute for Molecular Bioscience, The University of Queensland, Australia.
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Australia; School of Pharmacy, The University of Queensland, Australia.
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Australia.
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11
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Sahu ID, Dixit G, Reynolds WD, Kaplevatsky R, Harding BD, Jaycox CK, McCarrick RM, Lorigan GA. Characterization of the Human KCNQ1 Voltage Sensing Domain (VSD) in Lipodisq Nanoparticles for Electron Paramagnetic Resonance (EPR) Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2020; 124:2331-2342. [PMID: 32130007 DOI: 10.1021/acs.jpcb.9b11506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins are responsible for conducting essential biological functions that are necessary for the survival of living organisms. In spite of their physiological importance, limited structural information is currently available as a result of challenges in applying biophysical techniques for studying these protein systems. Electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study the structural and dynamic properties of membrane proteins. However, the application of EPR spectroscopy to membrane proteins in a native membrane-bound state is extremely challenging due to the complexity observed in inhomogeneity sample preparation and the dynamic motion of the spin label. Detergent micelles are very popular membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is important to test whether the protein structure in a micelle environment is the same as that of its membrane-bound state. Lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have been introduced as a potentially good membrane-mimetic system for structural studies of membrane proteins. Recently, we reported on the EPR characterization of the KCNE1 membrane protein having a single transmembrane incorporated into lipodisq nanoparticles. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the more complicated membrane protein system human KCNQ1 voltage sensing domain (Q1-VSD) having four transmembrane helices using site-directed spin-labeling EPR spectroscopy. Characterization of spin-labeled Q1-VSD incorporated into lipodisq nanoparticles was carried out using CW-EPR spectral line shape analysis and pulsed EPR double-electron electron resonance (DEER) measurements. The CW-EPR spectra indicate an increase in spectral line broadening with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated a superior quality of distance measurement with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles when compared to proteoliposomes. These results are consistent with the solution NMR structural studies on the Q1-VSD. This study will be beneficial for researchers working on investigating the structural and dynamic properties of more complicated membrane protein systems using lipodisq nanoparticles.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Warren D Reynolds
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ryan Kaplevatsky
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Colleen K Jaycox
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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12
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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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13
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Burridge KM, Harding BD, Sahu ID, Kearns MM, Stowe RB, Dolan MT, Edelmann RE, Dabney-Smith C, Page RC, Konkolewicz D, Lorigan GA. Simple Derivatization of RAFT-Synthesized Styrene-Maleic Anhydride Copolymers for Lipid Disk Formulations. Biomacromolecules 2020; 21:1274-1284. [PMID: 31961664 DOI: 10.1021/acs.biomac.0c00041] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Styrene-maleic acid copolymers have received significant attention because of their ability to interact with lipid bilayers and form styrene-maleic acid copolymer lipid nanoparticles (SMALPs). However, these SMALPs are limited in their chemical diversity, with only phenyl and carboxylic acid functional groups, resulting in limitations because of sensitivity to low pH and high concentrations of divalent metals. To address this limitation, various nucleophiles were reacted with the anhydride unit of well-defined styrene-maleic anhydride copolymers in order to assess the potential for a new lipid disk nanoparticle-forming species. These styrene-maleic anhydride copolymer derivatives (SMADs) can form styrene-maleic acid derivative lipid nanoparticles (SMADLPs) when they interact with lipid molecules. Polymers were synthesized, purified, characterized by Fourier-transform infrared spectroscopy, gel permeation chromatography, and nuclear magnetic resonance and then used to make disk-like SMADLPs, whose sizes were measured by dynamic light scattering (DLS). The SMADs form lipid nanoparticles, observable by DLS and transmission electron microscopy, and were used to reconstitute a spin-labeled transmembrane protein, KCNE1. The polymer method reported here is facile and scalable and results in functional and robust polymers capable of forming lipid nanodisks that are stable against a wide pH range and 100 mM magnesium.
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Affiliation(s)
- Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, KY 42718, United States
| | - Madison M Kearns
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Rebecca B Stowe
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Madison T Dolan
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Richard E Edelmann
- Center for Advanced Microscopy & Imaging, Miami University, Oxford, Ohio 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
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14
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Schmidpeter PAM, Sukomon N, Nimigean CM. Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses. Methods Mol Biol 2020; 2127:191-205. [PMID: 32112324 PMCID: PMC9288841 DOI: 10.1007/978-1-0716-0373-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.
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Affiliation(s)
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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15
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Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
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Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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16
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Bali AP, Sahu ID, Craig AF, Clark EE, Burridge KM, Dolan MT, Dabney-Smith C, Konkolewicz D, Lorigan GA. Structural characterization of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using EPR spectroscopy. Chem Phys Lipids 2019; 220:6-13. [PMID: 30796886 DOI: 10.1016/j.chemphyslip.2019.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/29/2019] [Accepted: 02/18/2019] [Indexed: 12/31/2022]
Abstract
Spectroscopic studies of membrane proteins (MPs) are challenging due to difficulties in preparing homogenous and functional lipid membrane mimetic systems into which membrane proteins can properly fold and function. It has recently been shown that styrene-maleic acid (SMA) copolymers act as a macromolecular surfactant and therefore facilitate the formation of disk-shaped lipid bilayer nanoparticles (styrene-maleic acid copolymer-lipid nanoparticles (SMALPs)) that retain structural characteristics of native lipid membranes. We have previously reported controlled synthesis of SMA block copolymers using reversible addition-fragmentation chain transfer (RAFT) polymerization, and that alteration of the weight ratio of styrene to maleic acid affects nanoparticle size. RAFT-synthesis offers superior control over SMA polymer architecture compared to conventional radical polymerization techniques used for commercially available SMA. However, the interactions between the lipid bilayer and the solubilized RAFT-synthesized SMA polymer are currently not fully understood. In this study, EPR spectroscopy was used to detect the perturbation on the acyl chain upon introduction of the RAFT-synthesized SMA polymer by attaching PC-based nitroxide spin labels to the 5th, 12th, and 16th positions along the acyl chain of the lipid bilayer. EPR spectra showed high rigidity at the 12th position compared to the other two regions, displaying similar qualities to commercially available polymers synthesized via conventional methods. In addition, central EPR linewidths and correlation time data were obtained that are consistent with previous findings.
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Affiliation(s)
- Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Madison T Dolan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
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17
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Keener JE, Zambrano DE, Zhang G, Zak CK, Reid DJ, Deodhar BS, Pemberton JE, Prell JS, Marty MT. Chemical Additives Enable Native Mass Spectrometry Measurement of Membrane Protein Oligomeric State within Intact Nanodiscs. J Am Chem Soc 2019; 141:1054-1061. [PMID: 30586296 DOI: 10.1021/jacs.8b11529] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Membrane proteins play critical biochemical roles but remain challenging to study. Recently, native or nondenaturing mass spectrometry (MS) has made great strides in characterizing membrane protein interactions. However, conventional native MS relies on detergent micelles, which may disrupt natural interactions. Lipoprotein nanodiscs provide a platform to present membrane proteins for native MS within a lipid bilayer environment, but previous native MS of membrane proteins in nanodiscs has been limited by the intermediate stability of nanodiscs. It is difficult to eject membrane proteins from nanodiscs for native MS but also difficult to retain intact nanodisc complexes with membrane proteins inside. Here, we employed chemical reagents that modulate the charge acquired during electrospray ionization (ESI). By modulating ESI conditions, we could either eject the membrane protein complex with few bound lipids or capture the intact membrane protein nanodisc complex-allowing measurement of the membrane protein oligomeric state within an intact lipid bilayer environment. The dramatic differences in the stability of nanodiscs under different ESI conditions opens new applications for native MS of nanodiscs.
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Affiliation(s)
- James E Keener
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Dane Evan Zambrano
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Deseree J Reid
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Bhushan S Deodhar
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Jeanne E Pemberton
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - James S Prell
- Department of Chemistry and Biochemistry , University of Oregon , Eugene , Oregon 97403 , United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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18
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Harding BD, Dixit G, Burridge KM, Sahu ID, Dabney-Smith C, Edelmann RE, Konkolewicz D, Lorigan GA. Characterizing the structure of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for membrane protein spectroscopic studies. Chem Phys Lipids 2018; 218:65-72. [PMID: 30528635 DOI: 10.1016/j.chemphyslip.2018.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/25/2022]
Abstract
Membrane proteins play an important role in maintaining the structure and physiology of an organism. Despite their significance, spectroscopic studies involving membrane proteins remain challenging due to the difficulties in mimicking their native lipid bilayer environment. Membrane mimetic systems such as detergent micelles, liposomes, bicelles, nanodiscs, lipodisqs have improved the solubility and folding properties of the membrane proteins for structural studies, however, each mimetic system suffers from its own limitations. In this study, using three different lipid environments, vesicles were titrated with styrene-maleic acid (StMA) copolymer leading to a homogeneous SMALP system (∼10 nm) at a weight ratio of 1:1.5 (vesicle: StMA solution). A combination of Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM) was used to characterize these SMALPs. We used a controlled synthesis mechanism to synthesize StMA based block copolymers called reversible addition-fragmentation chain transfer polymerization (RAFT) SMALPs. Incorporation of the Voltage Sensor Domain of KCNQ1 (Q1-VSD) into RAFT SMALPs indicates that this is a promising application of this system to study membrane proteins using different biophysical techniques. V165C in Q1-VSD corresponding to the hydrophobic region was incorporated into the SMALP system. Continuous Wave-Electron Paramagnetic Resonance (CW-EPR) line shape analysis showed line shape broadening, exposing a lower rigid component and a faster component of the spin label.
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Affiliation(s)
- Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Richard E Edelmann
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States.
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH, 45056, United States.
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19
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Bibow S, Hiller S. A guide to quantifying membrane protein dynamics in lipids and other native-like environments by solution-state NMR spectroscopy. FEBS J 2018; 286:1610-1623. [PMID: 30133960 DOI: 10.1111/febs.14639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/04/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
Recent biochemical and technical developments permit residue-specific solution NMR measurements of membrane protein (MP) dynamics in lipidic and chaperone-bound environments. This is possible by combinations of improved sample preparations with suitable NMR relaxation experiments to correlate protein function to backbone dynamics on timescales from picoseconds to seconds, even for large MP-lipid assemblies above 100 kDa in molecular mass. Here, we introduce the basic concepts of different NMR relaxation experiments, individually sensitive to specific timescales. We discuss the general limitations of detergent environments and highlight the importance for native-like environments when studying MPs. We then review three practical studies of fast- and slow-timescale MP dynamics in lipid environments, as well as in a natively unfolded, chaperone-bound state. These examples illustrate the new avenues solution NMR spectroscopy is taking to investigate MP dynamics in native-like environments with atomic resolution.
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20
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Mhurchú NN, Zoubak L, McGauran G, Linse S, Yeliseev A, O’Connell DJ. Simplifying G Protein-Coupled Receptor Isolation with a Calcium-Dependent Fragment Complementation Affinity System. Biochemistry 2018; 57:4383-4390. [DOI: 10.1021/acs.biochem.8b00469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niamh Ní Mhurchú
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| | - Lioudmila Zoubak
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Bethesda, Maryland 20892, United States
| | - Gavin McGauran
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Box 118, Lund 221 00, Sweden
| | - Alexei Yeliseev
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Bethesda, Maryland 20892, United States
| | - David J. O’Connell
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
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21
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Molecular dynamics simulations of lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2094-2107. [PMID: 29729280 DOI: 10.1016/j.bbamem.2018.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 01/02/2023]
Abstract
A lipid nanodisc is a discoidal lipid bilayer stabilized by proteins, peptides, or polymers on its edge. Nanodiscs have two important connections to structural biology. The first is associated with high-density lipoprotein (HDL), a particle with a variety of functionalities including lipid transport. Nascent HDL (nHDL) is a nanodisc stabilized by Apolipoprotein A-I (APOA1). Determining the structure of APOA1 and its mimetic peptides in nanodiscs is crucial to understanding pathologies related to HDL maturation and designing effective therapies. Secondly, nanodiscs offer non-detergent membrane-mimicking environments and greatly facilitate structural studies of membrane proteins. Although seemingly similar, natural and synthetic nanodiscs are different in that nHDL is heterogeneous in size, due to APOA1 elasticity, and gradually matures to become spherical. Synthetic nanodiscs, in contrast, should be homogenous, stable, and size-tunable. This report reviews previous molecular dynamics (MD) simulation studies of nanodiscs and illustrates convergence and accuracy issues using results from new multi-microsecond atomistic MD simulations. These new simulations reveal that APOA1 helices take 10-20 μs to rearrange on the nanodisc, while peptides take 2 μs to migrate from the disc surfaces to the edge. These systems can also become kinetically trapped depending on the initial conditions. For example, APOA1 was trapped in a biologically irrelevant conformation for the duration of a 10 μs trajectory; the peptides were similarly trapped for 5 μs. It therefore remains essential to validate MD simulations of these systems with experiments due to convergence and accuracy issues. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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22
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Le Bon C, Marconnet A, Masscheleyn S, Popot JL, Zoonens M. Folding and stabilizing membrane proteins in amphipol A8-35. Methods 2018; 147:95-105. [PMID: 29678587 DOI: 10.1016/j.ymeth.2018.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 01/07/2023] Open
Abstract
Membrane proteins (MPs) are important pharmacological targets because of their involvement in many essential cellular processes whose dysfunction can lead to a large variety of diseases. A detailed knowledge of the structure of MPs and the molecular mechanisms of their activity is essential to the design of new therapeutic agents. However, studying MPs in vitro is challenging, because it generally implies their overexpression under a functional form, followed by their extraction from membranes and purification. Targeting an overexpressed MP to a membrane is often toxic and expression yields tend to be limited. One alternative is the formation of inclusion bodies (IBs) in the cytosol of the cell, from which MPs need then to be folded to their native conformation before structural and functional analysis can be contemplated. Folding MPs targeted to IBs is a difficult task. Specially designed amphipathic polymers called 'amphipols' (APols), which have been initially developed with the view of improving the stability of MPs in aqueous solutions compared to detergents, can be used to fold both α-helical and β-barrel MPs. APols represent an interesting novel amphipathic medium, in which high folding yields can be achieved. In this review, the properties of APol A8-35 and of the complexes they form with MPs are summarized. An overview of the most important studies reported so far using A8-35 to fold MPs is presented. Finally, from a practical point of view, a detailed description of the folding and trapping methods is given.
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Affiliation(s)
- Christel Le Bon
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Anaïs Marconnet
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Sandrine Masscheleyn
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Jean-Luc Popot
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Manuela Zoonens
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France.
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23
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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24
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Galiakhmetov AR, Kovrigina EA, Xia C, Kim JJP, Kovrigin EL. Application of methyl-TROSY to a large paramagnetic membrane protein without perdeuteration: 13C-MMTS-labeled NADPH-cytochrome P450 oxidoreductase. JOURNAL OF BIOMOLECULAR NMR 2018; 70:21-31. [PMID: 29168021 PMCID: PMC5820150 DOI: 10.1007/s10858-017-0152-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/11/2017] [Indexed: 05/03/2023]
Abstract
NMR spectroscopy of membrane proteins involved in electron transport is difficult due to the presence of both the lipids and paramagnetic centers. Here we report the solution NMR study of the NADPH-cytochrome P450 oxidoreductase (POR) in its reduced and oxidized states. We interrogate POR, first, in its truncated soluble form (70 kDa), which is followed by experiments with the full-length protein incorporated in a lipid nanodisc (240 kDa). To overcome paramagnetic relaxation in the reduced state of POR as well as the signal broadening due to its high molecular weight, we utilized the methyl-TROSY approach. Extrinsic 13C-methyl groups were introduced by modifying the engineered surface-exposed cysteines with methyl-methanethiosulfonate. Chemical shift dispersion of the resonances from different sites in POR was sufficient to monitor differential effects of the reduction-oxidation process and conformation changes in the POR structure related to its function. Despite the high molecular weight of the POR-nanodisc complex, the surface-localized 13C-methyl probes were sufficiently mobile to allow for signal detection at 600 MHz without perdeuteration. This work demonstrates a potential of the solution methyl-TROSY in analysis of structure, dynamics, and function of POR, which may also be applicable to similar paramagnetic and flexible membrane proteins.
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Affiliation(s)
| | | | - Chuanwu Xia
- Biochemistry Department, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jung-Ja P Kim
- Biochemistry Department, Medical College of Wisconsin, Milwaukee, WI, USA.
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25
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Hutchison JM, Lu Z, Li G, Travis B, Mittal R, Deatherage CL, Sanders CR. Dodecyl-β-melibioside Detergent Micelles as a Medium for Membrane Proteins. Biochemistry 2017; 56:5481-5484. [PMID: 28980804 PMCID: PMC5685800 DOI: 10.1021/acs.biochem.7b00810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There remains a need for new non-ionic detergents that are suitable for use in biochemical and biophysical studies of membrane proteins. Here we explore the properties of n-dodecyl-β-melibioside (β-DDMB) micelles as a medium for membrane proteins. Melibiose is d-galactose-α(1→6)-d-glucose. Light scattering showed the β-DDMB micelle to be roughly 30 kDa smaller than micelles formed by the commonly used n-dodecyl-β-maltoside (β-DDM). β-DDMB stabilized diacylglycerol kinase (DAGK) against thermal inactivation. Moreover, activity assays conducted using aliquots of DAGK purified into β-DDMB yielded activities that were 40% higher than those of DAGK purified into β-DDM. β-DDMB yielded similar or better TROSY-HSQC NMR spectra for two single-pass membrane proteins and the tetraspan membrane protein peripheral myelin protein 22. β-DDMB appears be a useful addition to the toolbox of non-ionic detergents available for membrane protein research.
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Affiliation(s)
- James M. Hutchison
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Geoffrey Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Ben Travis
- Anatrace, 434 W. Dussel Dr., Maumee, OH 43537
| | | | - Catherine L. Deatherage
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
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26
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Braun L, Uhlig M, von Klitzing R, Campbell RA. Polymers and surfactants at fluid interfaces studied with specular neutron reflectometry. Adv Colloid Interface Sci 2017; 247:130-148. [PMID: 28822539 DOI: 10.1016/j.cis.2017.07.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/08/2017] [Indexed: 01/18/2023]
Abstract
This review addresses the advances made with specular neutron reflectometry in studies of aqueous mixtures of polymers and surfactants at fluid interfaces during the last decade (or so). The increase in neutron flux due to improvements in instrumentation has led to routine measurements at the air/water interface that are faster and involve samples with lower isotopic contrast than in previous experiments. One can now resolve the surface excess of a single deuterated component on the second time scale and the composition of a mixture on the minute time scale, and information about adsorption processes and dynamic rheology can also be accessed. Research areas addressed include the types of formed equilibrium surface structures, the link to foam film stability and the range of non-equilibrium effects that dominate the behavior of oppositely charged polyelectrolyte/surfactant mixtures, macroscopic film formation in like-charged polymer/surfactant mixtures, and the properties of mixtures of bio-polymers with surfactants and lipids.
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27
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Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37204, USA.
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Seu-Na Lee
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Min-Duk Seo
- Department of Molecular Science and Technology & College of Pharmacy, Ajou University, Suwon 16499, Korea.
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea.
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea.
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28
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Sahu ID, Zhang R, Dunagan MM, Craig AF, Lorigan GA. Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2017; 121:5312-5321. [DOI: 10.1021/acs.jpcb.7b01705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Megan M. Dunagan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Andrew F. Craig
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A. Lorigan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
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29
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Daniels JL, Crawford TM, Andreev OA, Reshetnyak YK. Synthesis and characterization of pHLIP ® coated gold nanoparticles. Biochem Biophys Rep 2017; 10:62-69. [PMID: 28955736 PMCID: PMC5614664 DOI: 10.1016/j.bbrep.2017.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/19/2017] [Accepted: 02/26/2017] [Indexed: 11/04/2022] Open
Abstract
Novel approaches in synthesis of spherical and multispiked gold nanoparticles coated with polyethylene glycol (PEG) and pH Low Insertion Peptide (pHLIP®) were introduced. The presence of a tumor-targeting pHLIP® peptide in the nanoparticle coating enhances the stability of particles in solution and promotes a pH-dependent cellular uptake. The spherical particles were prepared with sodium citrate as a gold reducing agent to form particles of 7.0±2.5 nm in mean metallic core diameter and ∼43 nm in mean hydrodynamic diameter. The particles that were injected into tumors in mice (21 µg of gold) were homogeneously distributed within a tumor mass with no staining of the muscle tissue adjacent to the tumor. Up to 30% of the injected gold dose remained within the tumor one hour post-injection. The multispiked gold nanoparticles with a mean metallic core diameter of 146.0±50.4 nm and a mean hydrodynamic size of ~161 nm were prepared using ascorbic acid as a reducing agent and disk-like bicelles as a template. Only the presence of a soft template, like bicelles, ensured the appearance of spiked nanoparticles with resonance in the near infrared region. The irradiation of spiked gold nanoparticles by an 805 nm laser led to the time- and concentration-dependent increase of temperature. Both pHLIP® and PEG coated gold spherical and multispiked nanoparticles might find application in radiation and thermal therapies of tumors. pHLIP®-PEG coated pH-sensitive gold spherical nanoparticles were synthesized. 30% of the injected gold dose remained within the tumor one hour post-injection. pHLIP®-PEG coated pH-sensitive gold multispiked nanoparticles were synthesized. Bicelles were used as a soft template to obtain multispiked nanoparticles. Temperature increases after 805 nm irradiation of spiked gold nanoparticles.
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Affiliation(s)
- Jennifer L Daniels
- Physics Department, University of Rhode Island, 2 Lippitt Rd., Kingston, RI 02881, USA
| | - Troy M Crawford
- Physics Department, University of Rhode Island, 2 Lippitt Rd., Kingston, RI 02881, USA
| | - Oleg A Andreev
- Physics Department, University of Rhode Island, 2 Lippitt Rd., Kingston, RI 02881, USA
| | - Yana K Reshetnyak
- Physics Department, University of Rhode Island, 2 Lippitt Rd., Kingston, RI 02881, USA
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30
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Wimmer R, Uggerhøj LE. Determination of Structure and Micellar Interactions of Small Antimicrobial Peptides by Solution-State NMR. Methods Mol Biol 2017; 1548:73-88. [PMID: 28013498 DOI: 10.1007/978-1-4939-6737-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
NMR spectroscopy is a well-established technique to determine the structure of peptides and small proteins in solution, also when bound to detergent micelles or phospholipid bicelles. The structure of the peptide alone is, however, not conveying the full picture, if the peptide is bound to a micelle, since it does not tell anything about the orientation of the peptide in the micelle. This article describes how to obtain that information together with information on peptide structure.
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Affiliation(s)
- Reinhard Wimmer
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark.
| | - Lars Erik Uggerhøj
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark
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31
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Beaugrand M, Arnold AA, Juneau A, Gambaro AB, Warschawski DE, Williamson PTF, Marcotte I. Magnetically Oriented Bicelles with Monoalkylphosphocholines: Versatile Membrane Mimetics for Nuclear Magnetic Resonance Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:13244-13251. [PMID: 27951690 DOI: 10.1021/acs.langmuir.6b03099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bicelles (bilayered micelles) are model membranes used in the study of peptide structure and membrane interactions. They are traditionally made of long- and short-chain phospholipids, usually dimyristoylphosphatidylcholine (D14PC) and dihexanoyl-PC (D6PC). They are attractive membrane mimetics because their composition and planar surface are similar to the native membrane environment. In this work, to improve the solubilization of membrane proteins and allow their study in bicellar systems, D6PC was replaced by detergents from the monoalkylphosphocholine (MAPCHO) family, of which dodecylphosphocholine (12PC) is known for its ability to solubilize membrane proteins. More specifically 12PC, tetradecyl- (14PC), and hexadecyl-PC (16PC) have been employed. To verify the possibility of making bicelles with different hydrophobic thicknesses to better accommodate membrane proteins, D14PC was also replaced by phospholipids with different alkyl chain lengths: dilauroyl-PC (D12PC), dipalmitoyl-PC (D16PC), distearoyl-PC (D18PC), and diarachidoyl-PC (D20PC). Results obtained by 31P solid-state nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) at several lipid-to-detergent molar ratios (q) and temperatures indicate that these new MAPCHO bicelles can be formed under a variety of conditions. The quality of their alignment is similar to that of classical bicelles, and the low critical micelle concentration (CMC) of the surfactants and their miscibility with phospholipids are likely to be advantageous for the reconstitution of membrane proteins.
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Affiliation(s)
- Maïwenn Beaugrand
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Alexandre A Arnold
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Antoine Juneau
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Aline Balieiro Gambaro
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Dror E Warschawski
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
- UMR 7099, CNRS - Université Paris Diderot, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Philip T F Williamson
- Centre for Biological Sciences/Institute of Life Sciences, Highfield Campus, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Isabelle Marcotte
- Département de Chimie, Université du Québec à Montréal , P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
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32
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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33
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Nasr ML, Baptista D, Strauss M, Sun ZYJ, Grigoriu S, Huser S, Plückthun A, Hagn F, Walz T, Hogle JM, Wagner G. Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nat Methods 2016; 14:49-52. [PMID: 27869813 DOI: 10.1038/nmeth.4079] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 10/19/2016] [Indexed: 12/22/2022]
Abstract
We engineered covalently circularized nanodiscs (cNDs) which, compared with standard nanodiscs, exhibit enhanced stability, defined diameter sizes and tunable shapes. Reconstitution into cNDs enhanced the quality of nuclear magnetic resonance spectra for both VDAC-1, a β-barrel membrane protein, and the G-protein-coupled receptor NTR1, an α-helical membrane protein. In addition, we used cNDs to visualize how simple, nonenveloped viruses translocate their genomes across membranes to initiate infection.
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Affiliation(s)
- Mahmoud L Nasr
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Diego Baptista
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mike Strauss
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zhen-Yu J Sun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Simina Grigoriu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sonja Huser
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Franz Hagn
- Department of Chemistry and Institute for Advanced Study, Technische Universität München and Helmholtz Centre Munich, Munich, Germany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - James M Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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34
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From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins. Structure 2016; 24:1830-1841. [PMID: 27618661 DOI: 10.1016/j.str.2016.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/25/2016] [Accepted: 07/25/2016] [Indexed: 01/04/2023]
Abstract
Nanodiscs and isotropic bicelles are promising membrane mimetics in the field of solution nuclear magnetic resonance (NMR) spectroscopy of integral membrane proteins (IMPs). Despite varied challenges to solution NMR studies of IMPs, we attribute the paucity of solution NMR structures in these environments to the inability of diverse IMPs to withstand detergent treatment during standard nanodisc and bicelle preparations. Here, we present a strategy that creates small isotropic bicelles from IMPs co-translationally embedded in large nanodiscs using cell-free expression. Our results demonstrate appreciable gains in NMR spectral quality while preserving lipid-IMP contacts. We validate the approach on the detergent-sensitive LspA, which finally allowed us to perform high-quality triple-resonance NMR experiments for structural studies. Our strategy of producing bicelles from nanodiscs comprehensively avoids detergent during expression and preparation and is suitable for solution NMR spectroscopy of lipid-IMP complexes.
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35
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Craig AF, Clark EE, Sahu ID, Zhang R, Frantz ND, Al-Abdul-Wahid MS, Dabney-Smith C, Konkolewicz D, Lorigan GA. Tuning the size of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for biophysical studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2931-2939. [PMID: 27539205 DOI: 10.1016/j.bbamem.2016.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 08/07/2016] [Indexed: 11/29/2022]
Abstract
Characterization of membrane proteins is challenging due to the difficulty in mimicking the native lipid bilayer with properly folded and functional membrane proteins. Recently, styrene-maleic acid (StMA) copolymers have been shown to facilitate the formation of disc-like lipid bilayer mimetics that maintain the structural and dynamic integrity of membrane proteins. Here we report the controlled synthesis and characterization of StMA containing block copolymers. StMA polymers with different compositions and molecular weights were synthesized and characterized by size exclusion chromatography (SEC). These polymers act as macromolecular surfactants for 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol (POPG) lipids, forming disc like structures of the lipids with the polymer wrapping around the hydrophobic lipid edge. A combination of dynamic light scattering (DLS), solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and transmission electron microscopy (TEM) was used to characterize the size of the nanoparticles created using these StMA polymers. At a weight ratio of 1.25:1 StMA to lipid, the nanoparticle size created is 28+1nm for a 2:1 ratio, 10+1nm for a 3:1 StMA ratio and 32+1nm for a 4:1 StMA ratio independent of the molecular weight of the polymer. Due to the polymer acting as a surfactant that forms disc like nanoparticles, we term these StMA based block copolymers "RAFT SMALPs". RAFT SMALPs show promise as a new membrane mimetic with different nanoscale sizes, which can be used for a wide variety of biophysical studies of membrane proteins.
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Affiliation(s)
- Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Nick D Frantz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - M Sameer Al-Abdul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States.
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36
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Kaur H, Lakatos A, Spadaccini R, Vogel R, Hoffmann C, Becker-Baldus J, Ouari O, Tordo P, Mchaourab H, Glaubitz C. The ABC exporter MsbA probed by solid state NMR – challenges and opportunities. Biol Chem 2016; 396:1135-49. [PMID: 25849794 DOI: 10.1515/hsz-2015-0119] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/26/2015] [Indexed: 01/20/2023]
Abstract
ATP binding cassette (ABC) transporters form a superfamily of integral membrane proteins involved in translocation of substrates across the membrane driven by ATP hydrolysis. Despite available crystal structures and extensive biochemical data, many open questions regarding their transport mechanisms remain. Therefore, there is a need to explore spectroscopic techniques such as solid state NMR in order to bridge the gap between structural and mechanistic data. In this study, we investigate the feasibility of using Escherichia coli MsbA as a model ABC transporter for solid state NMR studies. We show that optimised solubilisation and reconstitution procedures enable preparing stable and homogenous protein samples. Depending on the duration of solubilisation, MsbA can be obtained in either an apo- or in a native lipid A bound form. Building onto these optimisations, the first promising MAS-NMR spectra with narrow lines have been recorded. However, further sensitivity improvements are required so that complex NMR experiments can be recorded within a reasonable amount of time. We therefore demonstrate the usability of paramagnetic doping for rapid data acquisition and explore dynamic nuclear polarisation as a method for general signal enhancement. Our results demonstrate that solid state NMR provides an opportunity to address important biological questions related to complex mechanisms of ABC transporters.
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37
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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38
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Orwick‐Rydmark M, Arnold T, Linke D. The Use of Detergents to Purify Membrane Proteins. ACTA ACUST UNITED AC 2016; 84:4.8.1-4.8.35. [DOI: 10.1002/0471140864.ps0408s84] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Thomas Arnold
- Boehringer‐Ingelheim Veterinary Research Center Hannover Germany
| | - Dirk Linke
- University of Oslo, Department of Biosciences Oslo Norway
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39
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Frauenfeld J, Löving R, Armache JP, Sonnen AFP, Guettou F, Moberg P, Zhu L, Jegerschöld C, Flayhan A, Briggs JAG, Garoff H, Löw C, Cheng Y, Nordlund P. A saposin-lipoprotein nanoparticle system for membrane proteins. Nat Methods 2016; 13:345-51. [PMID: 26950744 PMCID: PMC4894539 DOI: 10.1038/nmeth.3801] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated with protein instability and poor compatibility with structural and biophysical studies. Here we present a saposin-lipoprotein nanoparticle system, Salipro, which allows for the reconstitution of membrane proteins in a lipid environment that is stabilized by a scaffold of saposin proteins. We demonstrate the applicability of the method on two purified membrane protein complexes as well as by the direct solubilization and nanoparticle incorporation of a viral membrane protein complex from the virus membrane. Our approach facilitated high-resolution structural studies of the bacterial peptide transporter PeptTSo2 by single-particle cryo-electron microscopy (cryo-EM) and allowed us to stabilize the HIV envelope glycoprotein in a functional state.
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Affiliation(s)
- Jens Frauenfeld
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robin Löving
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jean-Paul Armache
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Andreas F-P Sonnen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Fatma Guettou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lin Zhu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Technology and Health, Royal Institute of Technology, Novum, Huddinge, Sweden
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Technology and Health, Royal Institute of Technology, Novum, Huddinge, Sweden
| | | | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Henrik Garoff
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,EMBL Hamburg, Hamburg, Germany
| | - Yifan Cheng
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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40
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Li D, Li J, Zhuang Y, Zhang L, Xiong Y, Shi P, Tian C. Nano-size uni-lamellar lipodisq improved in situ auto-phosphorylation analysis of E. coli tyrosine kinase using (19)F nuclear magnetic resonance. Protein Cell 2015; 6:229-33. [PMID: 25564343 PMCID: PMC4348245 DOI: 10.1007/s13238-014-0129-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Dong Li
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026 China
| | - Juan Li
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026 China
| | - Yonglong Zhuang
- Department of Chemistry, Anhui University, Hefei, 230027 China
| | - Longhua Zhang
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026 China
| | - Ying Xiong
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026 China
| | - Pan Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031 China
| | - Changlin Tian
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026 China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031 China
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41
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Real-time and label-free analysis of binding thermodynamics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a QCM biosensor. Sci Rep 2015; 5:14066. [PMID: 26369583 PMCID: PMC4570189 DOI: 10.1038/srep14066] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/17/2015] [Indexed: 11/08/2022] Open
Abstract
A novel approach to the study of binding thermodynamics and kinetics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a quartz crystal microbalance (QCM) biosensor was developed, in which binding events take place at the cell surface, more closely mimicking a biologically relevant environment. In this study, colon adenocarcinoma cells (KM-12) and ovary adenocarcinoma cells (SKOV-3) grew on the optimized polystyrene-coated biosensor chip without fixation. The association and dissociation between the cell surface carbohydrates and a range of lectins, including WGA, Con A, UEA-I, GS-II, PNA and SBA, were monitored in real time and without label for evaluation of cell surface glycosylation. Furthermore, the thermodynamic and kinetic parameters of the interaction between lectins and cell surface glycan were studied, providing detailed information about the interactions, such as the association rate constant, dissociation rate constant, affinity constant, as well as the changes of entropy, enthalpy and Gibbs free energy. This application provides an insight into the cell surface glycosylation and the complex molecular recognition on the intact cell surface, which may have impacts on disease diagnosis and drug discovery.
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42
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Ambroso MR, Haworth IS, Langen R. Structural Characterization of Membrane-Curving Proteins: Site-Directed Spin Labeling, EPR, and Computational Refinement. Methods Enzymol 2015; 564:259-88. [PMID: 26477254 DOI: 10.1016/bs.mie.2015.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Endocytosis and other membrane remodeling processes require the coordinated generation of different membrane shapes. Proteins capable of manipulating lipid bilayers mediate these events using mechanisms that are not fully understood. Progress is limited by the small number of structures solved for proteins bound to different membrane shapes and tools capable of resolving such information. However, recent studies have shown site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) to be capable of obtaining high-resolution structural information for proteins bound to different membrane shapes. This technique can be applied to proteins with no known structure or proteins with structures known in solution. By refining the data obtained by EPR with computational modeling, 3D structures or structural models of membrane-bound proteins can be generated. In this chapter, we highlight the basic considerations and steps required to investigate the structures of membrane-bound proteins using SDSL, EPR, and computational refinement.
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Affiliation(s)
- Mark R Ambroso
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Ralf Langen
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA.
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43
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Bell AJ, Frankel LK, Bricker TM. High Yield Non-detergent Isolation of Photosystem I-Light-harvesting Chlorophyll II Membranes from Spinach Thylakoids: IMPLICATIONS FOR THE ORGANIZATION OF THE PS I ANTENNAE IN HIGHER PLANTS. J Biol Chem 2015; 290:18429-37. [PMID: 26055710 DOI: 10.1074/jbc.m115.663872] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 11/06/2022] Open
Abstract
Styrene-maleic acid copolymer was used to effect a non-detergent partial solubilization of thylakoids from spinach. A high density membrane fraction, which was not solubilized by the copolymer, was isolated and was highly enriched in the Photosystem (PS) I-light-harvesting chlorophyll (LHC) II supercomplex and depleted of PS II, the cytochrome b6/f complex, and ATP synthase. The LHC II associated with the supercomplex appeared to be energetically coupled to PS I based on 77 K fluorescence, P700 photooxidation, and PS I electron transport light saturation experiments. The chlorophyll (Chl) a/b ratio of the PS I-LHC II membranes was 3.2 ± 0.9, indicating that on average, three LHC II trimers may associate with each PS I. The implication of these findings within the context of higher plant PS I antenna organization is discussed.
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Affiliation(s)
- Adam J Bell
- From the Department of Biological Sciences, Biochemistry and Molecular Biology Section, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Laurie K Frankel
- From the Department of Biological Sciences, Biochemistry and Molecular Biology Section, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Terry M Bricker
- From the Department of Biological Sciences, Biochemistry and Molecular Biology Section, Louisiana State University, Baton Rouge, Louisiana 70803
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44
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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45
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Eichmann C, Orts J, Tzitzilonis C, Vögeli B, Smrt S, Lorieau J, Riek R. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes. J Phys Chem B 2014; 118:14288-301. [PMID: 25419869 DOI: 10.1021/jp509137q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
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Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , CH-8093 Zürich, Switzerland
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How Amphipols Embed Membrane Proteins: Global Solvent Accessibility and Interaction with a Flexible Protein Terminus. J Membr Biol 2014; 247:965-70. [DOI: 10.1007/s00232-014-9657-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
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Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents at the transmembrane surface of membrane proteins (MPs) and, thereby, keep them soluble in detergent free aqueous solutions. APol-trapped MPs are, as a rule, more stable biochemically than their detergent-solubilized counterparts. APols have proven useful to produce MPs, most noticeably by assisting their folding from the denatured state obtained after solubilizing MP inclusion bodies in either SDS or urea. They facilitate the handling in aqueous solution of fragile MPs for the purpose of proteomics, structural and functional studies, and therapeutics. Because APols can be chemically labeled or functionalized, and they form very stable complexes with MPs, they can also be used to functionalize those indirectly, which opens onto many novel applications. Following a brief recall of the properties of APols and MP/APol complexes, an update is provided of recent progress in these various fields.
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Affiliation(s)
- Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
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48
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Long-term stability of a vaccine formulated with the amphipol-trapped major outer membrane protein from Chlamydia trachomatis. J Membr Biol 2014; 247:1053-65. [PMID: 24942817 DOI: 10.1007/s00232-014-9693-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
Chlamydia trachomatis is a major bacterial pathogen throughout the world. Although antibiotic therapy can be implemented in the case of early detection, a majority of the infections are asymptomatic, requiring the development of preventive measures. Efforts have focused on the production of a vaccine using the C. trachomatis major outer membrane protein (MOMP). MOMP is purified in its native (n) trimeric form using the zwitterionic detergent Z3-14, but its stability in detergent solutions is limited. Amphipols (APols) are synthetic polymers that can stabilize membrane proteins (MPs) in detergent-free aqueous solutions. Preservation of protein structure and optimization of exposure of the most effective antigenic regions can avoid vaccination with misfolded, poorly protective protein. Previously, we showed that APols maintain nMOMP secondary structure and that nMOMP/APol vaccine formulations elicit better protection than formulations using either recombinant or nMOMP solubilized in Z3-14. To achieve a greater understanding of the structural behavior and stability of nMOMP in APols, we have used several spectroscopic techniques to characterize its secondary structure (circular dichroism), tertiary and quaternary structures (immunochemistry and gel electrophoresis) and aggregation state (light scattering) as a function of temperature and time. We have also recorded NMR spectra of (15)N-labeled nMOMP and find that the exposed loops are detectable in APols but not in detergent. Our analyses show that APols protect nMOMP much better than Z3-14 against denaturation due to continuous heating, repeated freeze/thaw cycles, or extended storage at room temperature. These results indicate that APols can help improve MP-based vaccine formulations.
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Characterizing the structure of lipodisq nanoparticles for membrane protein spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:329-33. [PMID: 24853657 DOI: 10.1016/j.bbamem.2014.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/28/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
Abstract
Membrane protein spectroscopic studies are challenging due to the difficulty introduced in preparing homogenous and functional hydrophobic proteins incorporated into a lipid bilayer system. Traditional membrane mimics such as micelles or liposomes have proved to be powerful in solubilizing membrane proteins for biophysical studies, however, several drawbacks have limited their applications. Recently, a nanosized complex termed lipodisq nanoparticles was utilized as an alternative membrane mimic to overcome these caveats by providing a homogeneous lipid bilayer environment. Despite all the benefits that lipodisq nanoparticles could provide to enhance the biophysical studies of membrane proteins, structural characterization in different lipid compositions that closely mimic the native membrane environment is still lacking. In this study, the formation of lipodisq nanoparticles using different weight ratios of POPC/POPG lipids to SMA polymers was characterized via solid-state nuclear magnetic resonance (SSNMR) spectroscopy and dynamic light scattering (DLS). A critical weight ratio of (1/1.25) for the complete solubilization of POPC/POPG vesicles has been observed and POPC/POPG vesicles turned clear instantaneously upon the addition of the SMA polymer. The size of lipodisq nanoparticles formed from POPC/POPG lipids at this weight ratio of (1/1.25) was found to be about 30 nm in radius. We also showed that upon the complete solubilization of POPC/POPG vesicles by SMA polymers, the average size of the lipodisq nanoparticles is weight ratio dependent, when more SMA polymers were introduced, smaller lipodisq nanoparticles were obtained. The results of this study will be helpful for a variety of biophysical experiments when specific size of lipid disc is required. Further, this study will provide a proper path for researchers working on membrane proteins to obtain pertinent structure and dynamic information in a physiologically relevant membrane mimetic environment.
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50
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López-Cebral R, Martín-Pastor M, Seijo B, Sanchez A. Progress in the characterization of bio-functionalized nanoparticles using NMR methods and their applications as MRI contrast agents. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 79:1-13. [PMID: 24815362 DOI: 10.1016/j.pnmrs.2014.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 05/22/2023]
Abstract
Significant progress has been made over the last three decades in the field of NMR, a technique which has proven to have a variety of applications in many scientific disciplines, including nanotechnology. Herein we describe how NMR enables the characterization of nanosystems at different stages of their formation and modification (raw materials, bare or functionalized nanosystems), even making it possible to study in vivo nanoparticle interactions, thereby importantly contributing to nanoparticle design and subsequent optimization. Furthermore, the unique characteristics of nanosystems can open up new prospects for site-targeted, more specific contrast agents, contributing to the development of certain nuclear magnetic resonance applications such as MRI.
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Affiliation(s)
- Rita López-Cebral
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Santiago de Compostela (USC), Campus Sur, 15782 Santiago de Compostela, Spain
| | - Manuel Martín-Pastor
- Nuclear Magnetic Resonance Unit, RIADT, University of Santiago de Compostela (USC), Campus Vida, 15706 Santiago de Compostela, Spain
| | - Begoña Seijo
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Santiago de Compostela (USC), Campus Sur, 15782 Santiago de Compostela, Spain; Molecular ImageGroup, IDIS, Santiago de Compostela University Hospital Complex (CHUS), A Choupana, 15706 Santiago de Compostela, Spain
| | - Alejandro Sanchez
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Santiago de Compostela (USC), Campus Sur, 15782 Santiago de Compostela, Spain; Molecular ImageGroup, IDIS, Santiago de Compostela University Hospital Complex (CHUS), A Choupana, 15706 Santiago de Compostela, Spain.
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