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Meikle T, Drummond C, Separovic F, Conn C. Membrane-Mimetic Inverse Bicontinuous Cubic Phase Systems for Encapsulation of Peptides and Proteins. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/bs.abl.2017.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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van 't Hag L, Knoblich K, Seabrook SA, Kirby NM, Mudie ST, Lau D, Li X, Gras SL, Mulet X, Call ME, Call MJ, Drummond CJ, Conn CE. Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0125. [PMID: 27298442 PMCID: PMC4920275 DOI: 10.1098/rsta.2015.0125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 05/19/2023]
Abstract
The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.
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Affiliation(s)
- Leonie van 't Hag
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Konstantin Knoblich
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A Seabrook
- CSIRO Manufacturing Flagship, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Deborah Lau
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Xu Li
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia
| | - Sally L Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xavier Mulet
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Matthew E Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Melissa J Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Calum J Drummond
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E Conn
- School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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Tse N, Morsch M, Ghazanfari N, Cole L, Visvanathan A, Leamey C, Phillips WD. The neuromuscular junction: measuring synapse size, fragmentation and changes in synaptic protein density using confocal fluorescence microscopy. J Vis Exp 2014:52220. [PMID: 25590231 PMCID: PMC4354481 DOI: 10.3791/52220] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The neuromuscular junction (NMJ) is the large, cholinergic relay synapse through which mammalian motor neurons control voluntary muscle contraction. Structural changes at the NMJ can result in neurotransmission failure, resulting in weakness, atrophy and even death of the muscle fiber. Many studies have investigated how genetic modifications or disease can alter the structure of the mouse NMJ. Unfortunately, it can be difficult to directly compare findings from these studies because they often employed different parameters and analytical methods. Three protocols are described here. The first uses maximum intensity projection confocal images to measure the area of acetylcholine receptor (AChR)-rich postsynaptic membrane domains at the endplate and the area of synaptic vesicle staining in the overlying presynaptic nerve terminal. The second protocol compares the relative intensities of immunostaining for synaptic proteins in the postsynaptic membrane. The third protocol uses Fluorescence Resonance Energy Transfer (FRET) to detect changes in the packing of postsynaptic AChRs at the endplate. The protocols have been developed and refined over a series of studies. Factors that influence the quality and consistency of results are discussed and normative data are provided for NMJs in healthy young adult mice.
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Affiliation(s)
- Nigel Tse
- Physiology and Bosch Institute, University of Sydney
| | - Marco Morsch
- Motor Neuron Disease Research Group, Australian School of Advanced Medicine, Macquarie University
| | | | - Louise Cole
- Advanced Microscopy Facility, Bosch Institute, University of Sydney
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daCosta CJB, Baenziger JE. Gating of pentameric ligand-gated ion channels: structural insights and ambiguities. Structure 2014; 21:1271-83. [PMID: 23931140 DOI: 10.1016/j.str.2013.06.019] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 05/31/2013] [Accepted: 06/26/2013] [Indexed: 01/09/2023]
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast synaptic communication by converting chemical signals into an electrical response. Recently solved agonist-bound and agonist-free structures greatly extend our understanding of these complex molecular machines. A key challenge to a full description of function, however, is the ability to unequivocally relate determined structures to the canonical resting, open, and desensitized states. Here, we review current understanding of pLGIC structure, with a focus on the conformational changes underlying channel gating. We compare available structural information and review the evidence supporting the assignment of each structure to a particular conformational state. We discuss multiple factors that may complicate the interpretation of crystal structures, highlighting the potential influence of lipids and detergents. We contend that further advances in the structural biology of pLGICs will require deeper insight into the nature of pLGIC-lipid interactions.
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Affiliation(s)
- Corrie J B daCosta
- Receptor Biology Laboratory, Departments of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Caffrey M, Li D, Dukkipati A. Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes. Biochemistry 2012; 51:6266-88. [PMID: 22783824 DOI: 10.1021/bi300010w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been determined. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of 13 distinct receptor types have been determined in the past 5 years. In addition to receptors, the method has proven to be useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, light-harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen, however, the reluctance to adopt it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals are also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nanoliter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional activity of membrane proteins reconstituted into the bilayer of the cubic phase as a prelude to crystallogenesis. Glass crystallization plates that provide unparalleled optical quality and sensitivity to nascent crystals have been built. Lipid and precipitant screens have been designed for a more rational approach to crystallogenesis such that the method can now be applied to an even wider variety of membrane protein types. In this work, these assorted advances are outlined along with a summary of the membrane proteins that have yielded to the method. The prospects for and the challenges that must be overcome to further develop the method are described.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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Effects of lipid-analog detergent solubilization on the functionality and lipidic cubic phase mobility of the Torpedo californica nicotinic acetylcholine receptor. J Membr Biol 2011; 243:47-58. [PMID: 21922299 DOI: 10.1007/s00232-011-9392-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/26/2011] [Indexed: 01/08/2023]
Abstract
Over the past three decades, the Torpedo californica nicotinic acetylcholine receptor (nAChR) has been one of the most extensively studied membrane protein systems. However, the effects of detergent solubilization on nAChR stability and function are poorly understood. The use of lipid-analog detergents for nAChR solubilization has been shown to preserve receptor stability and functionality. The present study used lipid-analog detergents from phospholipid-analog and cholesterol-analog detergent families for solubilization and affinity purification of the receptor and probed nAChR ion channel function using planar lipid bilayers (PLBs) and stability using analytical size exclusion chromatography (A-SEC) in the detergent-solubilized state. We also examined receptor mobility on the lipidic cubic phase (LCP) by measuring the nAChR mobile fraction and diffusion coefficient through fluorescence recovery after photobleaching (FRAP) experiments using lipid-analog and non-lipid-analog detergents. Our results show that it is possible to isolate stable and functional nAChRs using lipid-analog detergents, with characteristic ion channel currents in PLBs and minimal aggregation as observed in A-SEC. Furthermore, fractional mobility and diffusion coefficient values observed in FRAP experiments were similar to the values observed for these parameters in the recently LCP-crystallized β(2)-adrenergic receptor. The overall results show that phospholipid-analog detergents with 16 carbon acyl-chains support nAChR stability, functionality and LCP mobility.
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Shubina VS, Abramova MB, Lavrovskaya VP, Pavlik LL, Lezhnev EI, Moshkov DA. Ultrastructure of BHK-21 cells treated with dopamine. ACTA ACUST UNITED AC 2010. [DOI: 10.1134/s1990519x10010104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rucktooa P, Smit AB, Sixma TK. Insight in nAChR subtype selectivity from AChBP crystal structures. Biochem Pharmacol 2009; 78:777-87. [DOI: 10.1016/j.bcp.2009.06.098] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 06/19/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
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Abstract
The principal route to determine the structure and the function and interactions of membrane proteins is via macromolecular crystallography. For macromolecular crystallography to be successful, structure-quality crystals of the target protein must be forthcoming, and crystallogenesis represents a major challenge. Several techniques are employed to crystallize membrane proteins, and the bulk of these techniques make direct use of solubilized protein-surfactant complexes by the more traditional, so-called in surfo methods. An alternative in meso approach, which employs a bicontinuous lipidic mesophase, has emerged as a method with considerable promise in part because it involves reconstitution of the solubilized protein back into a stabilizing and organizing lipid bilayer reservoir as a prelude to crystallogenesis. A hypothesis for how the method works at the molecular level and experimental evidence in support of the proposal are reviewed here. The latest advances, successes, and challenges associated with the method are described.
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Caffrey M, Lyons J, Smyth T, Hart D. Chapter 4 Monoacylglycerols. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63004-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Taly A, Changeux JP. Functional Organization and Conformational Dynamics of the Nicotinic Receptor. Ann N Y Acad Sci 2008; 1132:42-52. [DOI: 10.1196/annals.1405.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Wells GB. Structural answers and persistent questions about how nicotinic receptors work. FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2008; 13:5479-510. [PMID: 18508600 PMCID: PMC2430769 DOI: 10.2741/3094] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The electron diffraction structure of nicotinic acetylcholine receptor (nAChR) from Torpedo marmorata and the X-ray crystallographic structure of acetylcholine binding protein (AChBP) are providing new answers to persistent questions about how nAChRs function as biophysical machines and as participants in cellular and systems physiology. New high-resolution information about nAChR structures might come from advances in crystallography and NMR, from extracellular domain nAChRs as high fidelity models, and from prokaryotic nicotinoid proteins. At the level of biophysics, structures of different nAChRs with different pharmacological profiles and kinetics will help describe how agonists and antagonists bind to orthosteric binding sites, how allosteric modulators affect function by binding outside these sites, how nAChRs control ion flow, and how large cytoplasmic domains affect function. At the level of cellular and systems physiology, structures of nAChRs will help characterize interactions with other cellular components, including lipids and trafficking and signaling proteins, and contribute to understanding the roles of nAChRs in addiction, neurodegeneration, and mental illness. Understanding nAChRs at an atomic level will be important for designing interventions for these pathologies.
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Affiliation(s)
- Gregg B Wells
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA.
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Cherezov V, Caffrey M. Membrane protein crystallization in lipidic mesophases. A mechanism study using X-ray microdiffraction. Faraday Discuss 2007; 136:195-212; discussion 213-29. [PMID: 17955811 DOI: 10.1039/b618173b] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The membrane structural biologist seeks to understand how membrane proteins function at a molecular level. One of the most direct ways of accomplishing this requires knowing the structure of the protein, ideally at atomic resolution. To date, this can only be done by the method of macromolecular crystallography. Integral to the method is the need for three-dimensional crystals of diffraction quality and their production represents a major rate-limiting step in the overall process of structure determination. The in meso method is a novel approach for crystallizing membrane proteins. It makes use of lipidic mesophases, the cubic phase in particular. A mechanism for how the method works has been proposed. In this study, we set out to test one aspect of the hypothesis which posits that the protein migrates from the bulk mesophase reservoir to the face of the crystal by way of a lamellar conduit. Using a sub-micrometer-sized X-ray beam the interface between a growing membrane protein crystal and the bulk cubic phase was interrogated with micrometer spatial resolution. Characteristic diffraction from the lamellar phase was observed at the interface as expected. This result supports the proposal that the protein uses a lamellar portal on its way from the bulk mesophase up and into the face of the crystal.
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Affiliation(s)
- Vadim Cherezov
- Department of Molecular Biology, The Scripps Research Institute, La Jolla CA 92037, USA
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Kalamida D, Poulas K, Avramopoulou V, Fostieri E, Lagoumintzis G, Lazaridis K, Sideri A, Zouridakis M, Tzartos SJ. Muscle and neuronal nicotinic acetylcholine receptors. FEBS J 2007; 274:3799-845. [PMID: 17651090 DOI: 10.1111/j.1742-4658.2007.05935.x] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are integral membrane proteins and prototypic members of the ligand-gated ion-channel superfamily, which has precursors in the prokaryotic world. They are formed by the assembly of five transmembrane subunits, selected from a pool of 17 homologous polypeptides (alpha1-10, beta1-4, gamma, delta, and epsilon). There are many nAChR subtypes, each consisting of a specific combination of subunits, which mediate diverse physiological functions. They are widely expressed in the central nervous system, while, in the periphery, they mediate synaptic transmission at the neuromuscular junction and ganglia. nAChRs are also found in non-neuronal/nonmuscle cells (keratinocytes, epithelia, macrophages, etc.). Extensive research has determined the specific function of several nAChR subtypes. nAChRs are now important therapeutic targets for various diseases, including myasthenia gravis, Alzheimer's and Parkinson's diseases, and schizophrenia, as well as for the cessation of smoking. However, knowledge is still incomplete, largely because of a lack of high-resolution X-ray structures for these molecules. Nevertheless, electron microscopy studies on 2D crystals of nAChR from fish electric organs and the determination of the high-resolution X-ray structure of the acetylcholine binding protein (AChBP) from snails, a homolog of the extracellular domain of the nAChR, have been major steps forward and the data obtained have important implications for the design of subtype-specific drugs. Here, we review some of the latest advances in our understanding of nAChRs and their involvement in physiology and pathology.
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Affiliation(s)
- Dimitra Kalamida
- Department of Pharmacy, University of Patras, Rio Patras, Greece
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Taly A. Opened by a twist: a gating mechanism for the nicotinic acetylcholine receptor. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:911-8. [PMID: 17609938 DOI: 10.1007/s00249-007-0189-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/27/2007] [Accepted: 05/07/2007] [Indexed: 12/25/2022]
Affiliation(s)
- Antoine Taly
- Unité de Recherche Associée Centre National de la Recherche Scientifique 2182 "Récepteurs et Cognition", Département de Neuroscience, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France.
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Gervásio OL, Armson PF, Phillips WD. Developmental increase in the amount of rapsyn per acetylcholine receptor promotes postsynaptic receptor packing and stability. Dev Biol 2007; 305:262-75. [PMID: 17362913 DOI: 10.1016/j.ydbio.2007.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 02/06/2007] [Accepted: 02/09/2007] [Indexed: 02/07/2023]
Abstract
Neuromuscular synaptic transmission depends upon tight packing of acetylcholine receptors (AChRs) into postsynaptic AChR aggregates, but not all postsynaptic AChRs are aggregated. Here we describe a new confocal Fluorescence Resonance Energy Transfer (FRET) assay for semi-quantitative comparison of the degree to which AChRs are aggregated at synapses. During the first month of postnatal life the mouse tibialis anterior muscle showed increases both in the number of postsynaptic AChRs and the efficiency with which AChR was aggregated (by FRET). There was a concurrent two-fold increase in immunofluorescent labeling for the AChR-associated cytoplasmic protein, rapsyn. When 1-month old muscle was denervated, postsynaptic rapsyn immunostaining was reduced, as was the efficiency of AChR aggregation. In vivo electroporation of rapsyn-EGFP into muscle fibers increased postsynaptic rapsyn levels. Those synapses with higher ratios of rapsyn-EGFP to AChR displayed a slower metabolic turnover of AChR. Conversely, the reduction of postsynaptic rapsyn after denervation was accompanied by an acceleration of AChR turnover. Thus, a developmental increase in the amount of rapsyn targeted to the postsynaptic membrane may drive enhanced postsynaptic AChRs aggregation and AChR stability within the postsynaptic membrane.
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Affiliation(s)
- Othon L Gervásio
- School of Medical Sciences (Physiology), Bosch Institute, University of Sydney, Sydney, Australia
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Taly A, Corringer PJ, Grutter T, de Carvalho LP, Karplus M, Changeux JP. Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proc Natl Acad Sci U S A 2006; 103:16965-70. [PMID: 17077146 PMCID: PMC1629088 DOI: 10.1073/pnas.0607477103] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChR) are pentameric ligand-gated ion channels composed of subunits that consist of an extracellular domain that carries the ligand-binding site and a distinct ion-pore domain. Signal transduction results from the allosteric coupling between the two domains: the distance from the binding site to the gate of the pore domain is 50 A. Normal mode analysis with a C(alpha) Gaussian network of a new structural model of the neuronal alpha7 nAChR showed that the lowest mode involves a global quaternary twist motion that opens the ion pore. A molecular probe analysis, in which the network is modified at each individual amino acid residue, demonstrated that the major effect is to change the frequency, but not the form, of the twist mode. The largest effects were observed for the ligand-binding site and the Cys-loop. Most (24/27) of spontaneous mutations known to cause congenital myasthenia and autosomal dominant nocturnal frontal lobe epilepsy are located either at the interface between subunits or, within a given subunit, at the interface between rigid blocks. These interfaces are modified significantly by the twist mode. The present analysis, thus, supports the quaternary twist model of the nAChR allosteric transition and provides a qualitative interpretation of the effect of the mutations responsible for several receptor pathologies.
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MESH Headings
- Allosteric Regulation
- Animals
- Epilepsy, Frontal Lobe/genetics
- Epilepsy, Frontal Lobe/physiopathology
- Genes, Dominant
- Humans
- Models, Molecular
- Models, Neurological
- Mutation
- Myasthenic Syndromes, Congenital/genetics
- Myasthenic Syndromes, Congenital/physiopathology
- Protein Structure, Quaternary
- Protein Subunits
- Receptors, Nicotinic/chemistry
- Receptors, Nicotinic/physiology
- Torpedo
- alpha7 Nicotinic Acetylcholine Receptor
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Affiliation(s)
- Antoine Taly
- *Recepteurs et Cognition, Unité de Recherche Associée Centre National de la Recherche Scientifique 2182, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
- To whom correspondence may be sent at the present address:
Laboratoire de Chimie Biophysique, Université Louis Pasteur, 8, Allée Gaspard Monge, B.P. 70028, F-67083 Strasbourg Cedex, France. E-mail:
| | - Pierre-Jean Corringer
- *Recepteurs et Cognition, Unité de Recherche Associée Centre National de la Recherche Scientifique 2182, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Thomas Grutter
- *Recepteurs et Cognition, Unité de Recherche Associée Centre National de la Recherche Scientifique 2182, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Lia Prado de Carvalho
- *Recepteurs et Cognition, Unité de Recherche Associée Centre National de la Recherche Scientifique 2182, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Martin Karplus
- Laboratoire de Chimie Biophysique, Institut de Science et d'Ingénierie Supramoléculaire, Université Louis Pasteur, 8, Allée Gaspard Monge, B.P. 70028, F-67083 Strasbourg Cedex, France; and
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Jean-Pierre Changeux
- *Recepteurs et Cognition, Unité de Recherche Associée Centre National de la Recherche Scientifique 2182, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
- To whom correspondence may be addressed. E-mail:
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Cherezov V, Clogston J, Papiz MZ, Caffrey M. Room to move: crystallizing membrane proteins in swollen lipidic mesophases. J Mol Biol 2006; 357:1605-18. [PMID: 16490208 DOI: 10.1016/j.jmb.2006.01.049] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/30/2022]
Abstract
The cubic phase or in meso crystallization method is responsible for almost 40 solved integral membrane protein structures. Most of these are small and compact proteins. A model for how crystals form by the in meso method has been proposed that invokes a transition between mesophases. In light of this model, we speculated that a more hydrated and open mesophase, of reduced interfacial curvature, would support facile crystallization of bigger and bulkier proteins. The proposal was explored here by performing crystallization in the presence of additives that swell the cubic phase. The additive concentration inducing swelling, as quantified by small-angle X-ray diffraction, coincided with a "crystallization window" in which two, very different transmembranal proteins produced crystals. That the swollen mesophase can grow structure-grade crystals was proven with one of these, the light-harvesting II complex. In most regards, the structural details of the corresponding complex resembled those of crystals grown by the conventional vapour diffusion method, with some important differences. In particular, packing density in the in meso-grown crystals was dramatically higher, more akin to that seen with water-soluble proteins, which accounts for their enhanced diffracting power. The layered and close in-plane packing observed has been rationalized in a model for nucleation and crystal growth by the in meso method that involves swollen mesophases. These results present a rational case for including mesophase-swelling additives in screens for in meso crystallogenesis. Their use will contribute to broadening the range of membrane proteins that yield to structure determination.
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Affiliation(s)
- Vadim Cherezov
- College of Science and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
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Mordvintsev DY, Polyak YL, Levtsova OV, Tourleigh YV, Kasheverov IE, Shaitan KV, Utkin YN, Tsetlin VI. A model for short α-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: Comparison with long-chain α-neurotoxins and α-conotoxins. Comput Biol Chem 2005; 29:398-411. [PMID: 16290328 DOI: 10.1016/j.compbiolchem.2005.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2005] [Revised: 08/14/2005] [Accepted: 09/15/2005] [Indexed: 01/09/2023]
Abstract
Short-chain alpha-neurotoxins from snakes are highly selective antagonists of the muscle-type nicotinic acetylcholine receptors (nAChR). Although their spatial structures are known and abundant information on topology of binding to nAChR is obtained by labeling and mutagenesis studies, the accurate structure of the complex is not yet known. Here, we present a model for a short alpha-neurotoxin, neurotoxin II from Naja oxiana (NTII), bound to Torpedo californica nAChR. It was built by comparative modeling, docking and molecular dynamics using 1H NMR structure of NTII, cross-linking and mutagenesis data, cryoelectron microscopy structure of Torpedo marmorata nAChR [Unwin, N., 2005. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J. Mol. Biol. 346, 967-989] and X-ray structures of acetylcholine-binding protein (AChBP) with agonists [Celie, P.H., van Rossum-Fikkert, S.E., van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K., 2004. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures. Neuron 41 (6), 907-914] and antagonists: alpha-cobratoxin, a long-chain alpha-neurotoxin [Bourne, Y., Talley, T.T., Hansen, S.B., Taylor, P., Marchot, P., 2005. Crystal structure of Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors. EMBO J. 24 (8), 1512-1522] and alpha-conotoxin [Celie, P.H., Kasheverov, I.E., Mordvintsev, D.Y., Hogg, R.C., van Nierop, P., van Elk, R., van Rossum-Fikkert, S.E., Zhmak, M.N., Bertrand, D., Tsetlin, V., Sixma, T.K., Smit, A.B., 2005. Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant. Nat. Struct. Mol. Biol. 12 (7), 582-588]. In complex with the receptor, NTII was located at about 30 A from the membrane surface, the tip of its loop II plunges into the ligand-binding pocket between the alpha/gamma or alpha/delta nAChR subunits, while the loops I and III contact nAChR by their tips only in a 'surface-touch' manner. The toxin structure undergoes some changes during the final complex formation (for 1.45 rmsd in 15-25 ps according to AMBER'99 molecular dynamics simulation), which correlates with NMR data. The data on the mobility and accessibility of spin- and fluorescence labels in free and bound NTII were used in MD simulations. The binding process is dependent on spontaneous outward movement of the C-loop earlier found in the AChBP complexes with alpha-cobratoxin and alpha-conotoxin. Among common features in binding of short- and long alpha-neurotoxins is the rearrangement of aromatic residues in the binding pocket not observed for alpha-conotoxin binding. Being in general very similar, the binding modes of short- and long alpha-neurotoxins differ in the ways of loop II entry into nAChR.
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Affiliation(s)
- D Yu Mordvintsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Miklukho-Maklaya str., 16/10, GSP-7, Moscow, Russia.
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20
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Misquitta LV, Misquitta Y, Cherezov V, Slattery O, Mohan JM, Hart D, Zhalnina M, Cramer WA, Caffrey M. Membrane protein crystallization in lipidic mesophases with tailored bilayers. Structure 2005; 12:2113-24. [PMID: 15576026 DOI: 10.1016/j.str.2004.09.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 09/24/2004] [Accepted: 09/24/2004] [Indexed: 11/18/2022]
Abstract
Monoacylglycerols have been used as bilayered hosts for growing crystals of membrane proteins. To date, the lipids used have had chains 16 and 18 carbon atoms long. We hypothesized that a shorter-chained lipid producing a thinner bilayer would facilitate the so-called in meso crystallization process. A 14 carbon monoacylglycerol was chosen as the lipid with which to test the proposal. To be compatible with the in meso method, a cis olefinic bond was placed in its acyl chain at a location arrived at by rational design. The target lipid was synthesized and was shown to form the requisite mesophase at room temperature. In support of the hypothesis, it produced crystals of bacteriorhodopsin and the outer membrane transporter, BtuB. The latter is the first beta barrel protein to be crystallized by the in meso method. Protein stability in the short-chain lipid and how this relates to crystallogenesis are discussed.
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Affiliation(s)
- Lisa V Misquitta
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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21
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Taly A, Delarue M, Grutter T, Nilges M, Le Novère N, Corringer PJ, Changeux JP. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys J 2005; 88:3954-65. [PMID: 15805177 PMCID: PMC1305627 DOI: 10.1529/biophysj.104.050229] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a three-dimensional model of the homopentameric alpha7 nicotinic acetylcholine receptor (nAChR), that includes the extracellular and membrane domains, developed by comparative modeling on the basis of: 1), the x-ray crystal structure of the snail acetylcholine binding protein, an homolog of the extracellular domain of nAChRs; and 2), cryo-electron microscopy data of the membrane domain collected on Torpedo marmorata nAChRs. We performed normal mode analysis on the complete three-dimensional model to explore protein flexibility. Among the first 10 lowest frequency modes, only the first mode produces a structural reorganization compatible with channel gating: a wide opening of the channel pore caused by a concerted symmetrical quaternary twist motion of the protein with opposing rotations of the upper (extracellular) and lower (transmembrane) domains. Still, significant reorganizations are observed within each subunit, that involve their bending at the domain interface, an increase of angle between the two beta-sheets composing the extracellular domain, the internal beta-sheet being significantly correlated to the movement of the M2 alpha-helical segment. This global symmetrical twist motion of the pentameric protein complex, which resembles the opening transition of other multimeric ion channels, reasonably accounts for the available experimental data and thus likely describes the nAChR gating process.
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Affiliation(s)
- Antoine Taly
- Récepteurs et Cognition, Unité de Recherche Associeé (URA) Centre National de la Recherche Scientifique 2182, Institut Pasteur, Paris, France
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22
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Bourne Y, Talley TT, Hansen SB, Taylor P, Marchot P. Crystal structure of a Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors. EMBO J 2005; 24:1512-22. [PMID: 15791209 PMCID: PMC1142565 DOI: 10.1038/sj.emboj.7600620] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Accepted: 02/16/2005] [Indexed: 11/09/2022] Open
Abstract
The crystal structure of the snake long alpha-neurotoxin, alpha-cobratoxin, bound to the pentameric acetylcholine-binding protein (AChBP) from Lymnaea stagnalis, was solved from good quality density maps despite a 4.2 A overall resolution. The structure unambiguously reveals the positions and orientations of all five three-fingered toxin molecules inserted at the AChBP subunit interfaces and the conformational changes associated with toxin binding. AChBP loops C and F that border the ligand-binding pocket move markedly from their original positions to wrap around the tips of the toxin first and second fingers and part of its C-terminus, while rearrangements also occur in the toxin fingers. At the interface of the complex, major interactions involve aromatic and aliphatic side chains within the AChBP binding pocket and, at the buried tip of the toxin second finger, conserved Phe and Arg residues that partially mimic a bound agonist molecule. Hence this structure, in revealing a distinctive and unpredicted conformation of the toxin-bound AChBP molecule, provides a lead template resembling a resting state conformation of the nicotinic receptor and for understanding selectivity of curaremimetic alpha-neurotoxins for the various receptor species.
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Affiliation(s)
- Yves Bourne
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. E-mail:
| | - Todd T Talley
- Department of Pharmacology 0636, University of California at San Diego, La Jolla, CA, USA
| | - Scott B Hansen
- Department of Pharmacology 0636, University of California at San Diego, La Jolla, CA, USA
| | - Palmer Taylor
- Department of Pharmacology 0636, University of California at San Diego, La Jolla, CA, USA
| | - Pascale Marchot
- Ingénierie des Protéines, CNRS FRE-2738, Institut Fédératif de Recherche Jean Roche, Université de la Méditerranée, Faculté de Médecine Secteur Nord, Marseille, France
- Université de la Méditerranée, Faculté de Médecine Secteur Nord, Ingénierie des Protéines, Blvd Pierre Dramard, 13916 Marseille Cedex 20, France. Tel.: +33 4 91 69 89 08; Fax: +33 4 91 65 75 95; E-mail:
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daCosta CJB, Kaiser DEE, Baenziger JE. Role of glycosylation and membrane environment in nicotinic acetylcholine receptor stability. Biophys J 2004; 88:1755-64. [PMID: 15626708 PMCID: PMC1305231 DOI: 10.1529/biophysj.104.052944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of glycosylation and membrane environment on the structural stability of the nicotinic acetylcholine receptor (nAChR) from Torpedo have been investigated to improve our understanding of factors that influence eukaryotic membrane protein crystallization. Gel shift assays and carbohydrate-specific staining show that the deglycosylation enzyme, Endo F1, removes at least 50% of membrane-reconstituted nAChR glycosylation. The extent of deglycosylation with Endo F1 increases upon detergent solubilization. Removal of between 60-100% of high mannose moieties from the nAChR has no effect on nAChR secondary structure, stability, or flexibility. Deglycosylation does not influence either agonist binding or the ability of the nAChR to undergo agonist-induced conformational change. In contrast, nAChR structural stability, flexibility, and function are all negatively influenced by simple changes in reconstituted membrane lipid composition. Our results suggest that deglycosylation may represent a feasible approach for enhancing the crystallizability of the nAChR. Our data also demonstrate that the dependence of nAChR structural stability on lipid environment may represent a significant obstacle to nAChR crystallization. Some membrane proteins may have evolved complex interactions with their lipid environments. Understanding the complexity of these interactions may be essential for devising an appropriate strategy for the crystallization of some membrane proteins.
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Affiliation(s)
- Corrie J B daCosta
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Rd., Ottawa, Ontario, ON K1H 8M5, Canada
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Abstract
This review provides detailed procedures for the crystallization of membrane proteins via the lipidic cubic phase method. Bacteriorhodopsin-specific, hands-on protocols are given for (i) the preparation of bacteriohordopsin from purple membrane by monomerization in octylglucoside and gel filtration chromatography or by selective extraction after pre-treatment with dodecyl-trimethylammonium bromide, (ii) the incorporation of bacteriorhodopsin into lipidic cubic phases by mixing in vials or within coupled syringes and, (iii) the crystallization of bacteriorhodopsin in the lipidic matrix by adding a solid salt or an overlaying with a solution. References for further useful procedures and materials are listed in order to provide biochemists and crystallographers with all information that is necessary to grow crystals of the membrane protein bacteriorhodopsin.
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Affiliation(s)
- Peter Nollert
- deCODE genetics, BioStructures Group, 7869 NE Day RdW, Bainbridge Island, WA 98110, USA.
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Avramopoulou V, Mamalaki A, Tzartos SJ. Soluble, oligomeric, and ligand-binding extracellular domain of the human alpha7 acetylcholine receptor expressed in yeast: replacement of the hydrophobic cysteine loop by the hydrophilic loop of the ACh-binding protein enhances protein solubility. J Biol Chem 2004; 279:38287-93. [PMID: 15226316 DOI: 10.1074/jbc.m402533200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N-terminal extracellular domain (ECD; amino acids 1-208) of the neuronal nicotinic acetylcholine receptor (AChR) alpha7 subunit, the only human AChR subunit known to assemble as a homopentamer, was expressed as a glycosylated form in the yeast Pichia pastoris in order to obtain a native-like model of the extracellular part of an intact pentameric nicotinic AChR. This molecule, alpha7-ECD, although able to bind the specific ligand alpha-bungarotoxin, existed mainly in the form of microaggregates. Substitution of Cys-116 in the alpha7-ECD with serine led to a decrease in microaggregate size. A second mutant form, alpha7-ECD(C116S,Cys-loop), was generated in which, in addition to the C116S mutation, the hydrophobic Cys-loop (Cys(128)-Cys(142)) was replaced by the corresponding hydrophilic Cys-loop from the snail glial cell acetylcholine-binding protein. This second mutant protein was water-soluble, expressed at a moderate level (0.5 +/- 0.1 mg/liter), and had a size corresponding approximately to a pentamer as judged by gel filtration and electron microscopy studies. It also bound (125)I-alpha-bungarotoxin with relatively high affinity (K(d) = 57 nm), the binding being inhibited by unlabeled alpha-bungarotoxin, d-tubocurarine, or nicotine (K(i) = 0.8 x 10(-7) m, K(i) = 1 x 10(-5) m, and K(i) = 0.9 x 10(-2) m, respectively). All three constructs were expressed as glycosylated forms, but in vitro deglycosylation reduced the heterogeneity without affecting their ligand binding properties. These results show that alpha7-ECD(C116S,Cys-loop) was expressed in P. pastoris as an oligomer (probably a pentamer) with a near native conformation and that its deglycosylated form seems to be suitable starting material for structural studies on the ligand-binding domain of a neurotransmitter receptor.
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Affiliation(s)
- Vassiliki Avramopoulou
- Department of Biochemistry, Hellenic Pasteur Institute, 127 Vassilissis Sofias Avenue, GR11521 Athens, Greece
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