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Löwe M, Hänsch S, Hachani E, Schmitt L, Weidtkamp-Peters S, Kedrov A. Probing macromolecular crowding at the lipid membrane interface with genetically-encoded sensors. Protein Sci 2023; 32:e4797. [PMID: 37779215 PMCID: PMC10578116 DOI: 10.1002/pro.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein-packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non-invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically-encoded fluorescence-based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane-tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding-dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis.
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Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Hänsch
- Center for Advanced imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eymen Hachani
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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2
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Exogenous loading of extracellular vesicles, virus-like particles, and lentiviral vectors with supercharged proteins. Commun Biol 2022; 5:485. [PMID: 35590035 PMCID: PMC9120435 DOI: 10.1038/s42003-022-03440-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/03/2022] [Indexed: 12/19/2022] Open
Abstract
Cell membrane-based biovesicles (BVs) are important candidate drug delivery vehicles and comprise extracellular vesicles, virus-like particles, and lentiviral vectors. Here, we introduce a non-enzymatic assembly of purified BVs, supercharged proteins, and plasmid DNA called pDNA-scBVs. This multicomponent vehicle results from the interaction of negative sugar moieties on BVs and supercharged proteins that contain positively charged amino acids on their surface to enhance their affinity for pDNA. pDNA-scBVs were demonstrated to mediate floxed reporter activation in culture by delivering a Cre transgene. We introduced pDNA-scBVs containing both a CRE-encoding plasmid and a BV-packaged floxed reporter into the brains of Ai9 mice. Successful delivery of both payloads by pDNA-scBVs was confirmed with reporter signal in the striatal brain region. Overall, we developed a more efficient method to load isolated BVs with cargo that functionally modified recipient cells. Augmenting the natural properties of BVs opens avenues for adoptive extracellular interventions using therapeutic loaded cargo.
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3
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Tivony R, Fletcher M, Al Nahas K, Keyser UF. A Microfluidic Platform for Sequential Assembly and Separation of Synthetic Cell Models. ACS Synth Biol 2021; 10:3105-3116. [PMID: 34761904 PMCID: PMC8609574 DOI: 10.1021/acssynbio.1c00371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Cell-sized vesicles
like giant unilamellar vesicles (GUVs) are
established as a promising biomimetic model for studying cellular
phenomena in isolation. However, the presence of residual components
and byproducts, generated during vesicles preparation and manipulation,
severely limits the utility of GUVs in applications like synthetic
cells. Therefore, with the rapidly growing field of synthetic biology,
there is an emergent demand for techniques that can continuously purify
cell-like vesicles from diverse residues, while GUVs are being simultaneously
synthesized and manipulated. We have developed a microfluidic platform
capable of purifying GUVs through stream bifurcation, where a vesicles
suspension is partitioned into three fractions: purified GUVs, residual
components, and a washing solution. Using our purification approach,
we show that giant vesicles can be separated from various residues—which
range in size and chemical composition—with a very high efficiency
(e = 0.99), based on size and deformability of the
filtered objects. In addition, by incorporating the purification module
with a microfluidic-based GUV-formation method, octanol-assisted liposome
assembly (OLA), we established an integrated production-purification
microfluidic unit that sequentially produces, manipulates, and purifies
GUVs. We demonstrate the applicability of the integrated device to
synthetic biology through sequentially fusing SUVs with freshly prepared
GUVs and separating the fused GUVs from extraneous SUVs and oil droplets
at the same time.
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Affiliation(s)
- Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Marcus Fletcher
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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5
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Chip-Based Sensing of the Intercellular Transfer of Cell Surface Proteins: Regulation by the Metabolic State. Biomedicines 2021; 9:biomedicines9101452. [PMID: 34680568 PMCID: PMC8533487 DOI: 10.3390/biomedicines9101452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are anchored at the surface of mammalian blood and tissue cells through a carboxy-terminal GPI glycolipid. Eventually, they are released into incubation medium in vitro and blood in vivo and subsequently inserted into neighboring cells, potentially leading to inappropriate surface expression or lysis. To obtain first insight into the potential (patho)physiological relevance of intercellular GPI-AP transfer and its biochemical characterization, a cell-free chip- and microfluidic channel-based sensing system was introduced. For this, rat or human adipocyte or erythrocyte plasma membranes (PM) were covalently captured by the TiO2 chip surface operating as the acceptor PM. To measure transfer between PM, donor erythrocyte or adipocyte PM were injected into the channels of a flow chamber, incubated, and washed out, and the type and amount of proteins which had been transferred to acceptor PM evaluated with specific antibodies. Antibody binding was detected as phase shift of horizontal surface acoustic waves propagating over the chip surface. Time- and temperature-dependent transfer, which did not rely on fusion of donor and acceptor PM, was detected for GPI-APs, but not typical transmembrane proteins. Transfer of GPI-APs was found to be prevented by α-toxin, which binds to the glycan core of GPI anchors, and serum proteins in concentration-dependent fashion. Blockade of transfer, which was restored by synthetic phosphoinositolglycans mimicking the glycan core of GPI anchors, led to accumulation in the chip channels of full-length GPI-APs in association with phospholipids and cholesterol in non-membrane structures. Strikingly, efficacy of transfer between adipocytes and erythrocytes was determined by the metabolic state (genotype and feeding state) of the rats, which were used as source for the PM and sera, with upregulation in obese and diabetic rats and counterbalance by serum proteins. The novel chip-based sensing system for GPI-AP transfer may be useful for the prediction and stratification of metabolic diseases as well as elucidation of the putative role of intercellular transfer of cell surface proteins, such as GPI-APs, in (patho)physiological mechanisms.
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Reconstitution of Detergent-Solubilized Membrane Proteins into Proteoliposomes and Nanodiscs for Functional and Structural Studies. Methods Mol Biol 2021; 2302:21-35. [PMID: 33877620 DOI: 10.1007/978-1-0716-1394-8_2] [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: 02/05/2023]
Abstract
Reconstitution of detergent-solubilized membrane proteins into phospholipid bilayers allows for functional and structural studies under close-to-native conditions that greatly support protein stability and function. Here we outline the detailed steps for membrane protein reconstitution to result in proteoliposomes and nanodiscs. Reconstitution can be achieved via a number of different strategies. The protocols for preparation of proteoliposomes use detergent removal via dialysis or via nonpolar polystyrene beads, or a mixture of the two methods. In this chapter, the protocols for nanodiscs apply polystyrene beads only. Proteoliposome preparation methods allow for substantial control of the lipid-to-protein ratio, from minimal amounts of phospholipid to high concentrations, type of phospholipid, and mixtures of phospholipids. In addition, dialysis affords a fairly large degree of control and variation of parameters such as rate of reconstitution, temperature, buffer conditions, and proteoliposome size. For the nanodisc approach, which is highly advantageous for ensuring equal access to both membrane sides of the protein as well as fast reconstitution of only a single membrane protein into a well-defined bilayer environment in each nanodisc, the protocols outline how a number of these parameters are more restricted in comparison to the proteoliposome protocols.
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Damian M, Louet M, Gomes AAS, M'Kadmi C, Denoyelle S, Cantel S, Mary S, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Allosteric modulation of ghrelin receptor signaling by lipids. Nat Commun 2021; 12:3938. [PMID: 34168117 PMCID: PMC8225672 DOI: 10.1038/s41467-021-23756-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
The membrane is an integral component of the G protein-coupled receptor signaling machinery. Here we demonstrate that lipids regulate the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific interactions and bulk effects. We find that PIP2 shifts the conformational equilibrium of GHSR away from its inactive state, favoring basal and agonist-induced G protein activation. This occurs because of a preferential binding of PIP2 to specific intracellular sites in the receptor active state. Another lipid, GM3, also binds GHSR and favors G protein activation, but mostly in a ghrelin-dependent manner. Finally, we find that not only selective interactions but also the thickness of the bilayer reshapes the conformational repertoire of GHSR, with direct consequences on G protein selectivity. Taken together, this data illuminates the multifaceted role of the membrane components as allosteric modulators of how ghrelin signal could be propagated.
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Affiliation(s)
- Marjorie Damian
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Maxime Louet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Antoniel Augusto Severo Gomes
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Céline M'Kadmi
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Séverine Denoyelle
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sonia Cantel
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sophie Mary
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), Paris, France
| | - Nicolas Floquet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Jean-Louis Banères
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
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8
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Membrane Env Liposomes Facilitate Immunization with Multivalent Full-Length HIV Spikes. J Virol 2021; 95:e0000521. [PMID: 33883221 DOI: 10.1128/jvi.00005-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A major goal of HIV vaccine design is to elicit broadly neutralizing antibodies (bNAbs). Such bNAbs target HIV's trimeric, membrane-embedded envelope glycoprotein spikes (mEnv). Soluble Env (sEnv) trimers have been used as vaccines, but engineering sEnvs for stability, multivalency, and desired antigenicity is problematic and deletes key neutralizing epitopes on glycoprotein 41 (gp41) while creating neoepitopes that elicit unwanted antibodies. Meanwhile, multivalent mEnv vaccines are challenging to develop due to trimer instability and low mEnv copy number amid other extraneous proteins on virus-like particles. Here, we describe a multivalent mEnv vaccine platform that does not require protein engineering or extraneous proteins. mEnv trimers were fixed, purified, and combined with naked liposomes in mild detergent. On removal of detergent, mEnv spikes were observed embedded in liposome particles (mean diameter, 133 nm) in correct orientation. These particles were recognized by HIV bNAbs and not non-NAbs and are designated mEnv liposomes (MELs). Following a sequential immunization scheme in rabbits, MELs elicited antibodies that neutralized tier 2 HIV isolates. Analysis of serum antibody specificities, including those to epitopes involving a missing conserved N-glycosylation site at position 197 near the CD4 binding site on two of the immunogens, provides clues on how NAb responses can be improved with modified immunogens. In sum, MELs are a biochemically defined platform that enables rational immunization strategies to elicit HIV bNAbs using multimerized mEnv. IMPORTANCE A vaccine that induced broadly neutralizing antibodies against HIV would likely end the AIDS pandemic. Such antibodies target membrane-embedded envelope glycoprotein spikes (mEnv) that HIV uses to enter cells. Due to HIV Env's low expression and instability, soluble stabilized Env trimers have been used as vaccine candidates, but these have an altered base that disrupts targets of HIV broadly neutralizing antibodies that bind near the membrane and are not available for all HIV isolates. Here, we describe membrane Env liposomes (MELs) that display a multivalent array of stable mEnvs on liposome particles. MELs showed the expected antibody recognition properties, including targeting parts of mEnv missing on soluble Envs. Immunization with MELs elicited antibodies that neutralized diverse HIV isolates. The MEL platform facilitates vaccine development with potentially any HIV Env at high valency, and a similar approach may be useful for eliciting antibodies to membrane-embedded targets of therapeutic interest.
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9
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de la Mora E, Dezi M, Di Cicco A, Bigay J, Gautier R, Manzi J, Polidori J, Castaño-Díez D, Mesmin B, Antonny B, Lévy D. Nanoscale architecture of a VAP-A-OSBP tethering complex at membrane contact sites. Nat Commun 2021; 12:3459. [PMID: 34103503 PMCID: PMC8187361 DOI: 10.1038/s41467-021-23799-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
Membrane contact sites (MCS) are subcellular regions where two organelles appose their membranes to exchange small molecules, including lipids. Structural information on how proteins form MCS is scarce. We designed an in vitro MCS with two membranes and a pair of tethering proteins suitable for cryo-tomography analysis. It includes VAP-A, an ER transmembrane protein interacting with a myriad of cytosolic proteins, and oxysterol-binding protein (OSBP), a lipid transfer protein that transports cholesterol from the ER to the trans Golgi network. We show that VAP-A is a highly flexible protein, allowing formation of MCS of variable intermembrane distance. The tethering part of OSBP contains a central, dimeric, and helical T-shape region. We propose that the molecular flexibility of VAP-A enables the recruitment of partners of different sizes within MCS of adjustable thickness, whereas the T geometry of the OSBP dimer facilitates the movement of the two lipid-transfer domains between membranes.
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Affiliation(s)
- Eugenio de la Mora
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, Paris, France
| | - Manuela Dezi
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.
- Sorbonne Université, Paris, France.
| | - Aurélie Di Cicco
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, Paris, France
| | - Joëlle Bigay
- CNRS UMR 7275, Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Romain Gautier
- CNRS UMR 7275, Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - John Manzi
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, Paris, France
| | - Joël Polidori
- CNRS UMR 7275, Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | | | - Bruno Mesmin
- CNRS UMR 7275, Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Bruno Antonny
- CNRS UMR 7275, Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
| | - Daniel Lévy
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.
- Sorbonne Université, Paris, France.
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Ribeiro Morais G, Falconer RA. Glycosyl disulfides: importance, synthesis and application to chemical and biological systems. Org Biomol Chem 2021; 19:82-100. [DOI: 10.1039/d0ob02079f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This review explores methodologies for the preparation of glycosyl disulfides, their utility as intermediates in carbohydrate synthesis, and evaluates their biological impact in glycoscience and beyond.
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Affiliation(s)
- Goreti Ribeiro Morais
- Institute of Cancer Therapeutics
- Faculty of Life Sciences
- University of Bradford
- Bradford BD7 1DP
- UK
| | - Robert A. Falconer
- Institute of Cancer Therapeutics
- Faculty of Life Sciences
- University of Bradford
- Bradford BD7 1DP
- UK
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Study of membrane deformations induced by Hepatitis C protein NS4B and its terminal amphipathic peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183537. [PMID: 33383025 DOI: 10.1016/j.bbamem.2020.183537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 11/27/2020] [Accepted: 12/13/2020] [Indexed: 11/21/2022]
Abstract
Many viruses destabilize cellular membranous compartments to form their replication complexes, but the mechanism(s) underlying membrane perturbation remains unknown. Expression in eukaryotic cells of NS4B, a protein of the hepatitis C virus (HCV), alters membranous complexes and induces structures similar to the so-called membranous web that appears crucial to the formation of the HCV replication complex. As over-expression of the protein is lethal to both prokaryotic and eukaryotic cells, NS4B was produced in large quantities in a "cell-free" system in the presence of detergent, after which it was inserted into lipid membranes. X-ray diffraction revealed that NS4B modifies the phase diagram of synthetic lipid aqueous phases considerably, perturbing the transition temperature and cooperativity. Cryo-electron microscopy demonstrated that NS4B introduces significant disorder in the synthetic membrane as well as discontinuities that could be interpreted as due to the formation of pores and membrane merging events. C- and N-terminal fragments of NS4B are both able to destabilize liposomes. While most NS4B amphipathic peptides perforate membranes, one NS4B peptide induces membrane fusion. Cryo-electron microscopy reveals a particular structure that can be interpreted as arising from hemi-fusion-like events. Amphipathic domains are present in many proteins, and if exposed to the aqueous cytoplasmic medium are sufficient to destabilize membranes in order to form viral replication complexes. These domains have important functions in the viral replication cycle, and thus represent potential targets for the development of anti-viral molecules.
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12
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Nicklisch SC, Hamdoun A. Disruption of small molecule transporter systems by Transporter-Interfering Chemicals (TICs). FEBS Lett 2020; 594:4158-4185. [PMID: 33222203 PMCID: PMC8112642 DOI: 10.1002/1873-3468.14005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022]
Abstract
Small molecule transporters (SMTs) in the ABC and SLC families are important players in disposition of diverse endo- and xenobiotics. Interactions of environmental chemicals with these transporters were first postulated in the 1990s, and since validated in numerous in vitro and in vivo scenarios. Recent results on the co-crystal structure of ABCB1 with the flame-retardant BDE-100 demonstrate that a diverse range of man-made and natural toxic molecules, hereafter termed transporter-interfering chemicals (TICs), can directly bind to SMTs and interfere with their function. TIC-binding modes mimic those of substrates, inhibitors, modulators, inducers, and possibly stimulants through direct and allosteric mechanisms. Similarly, the effects could directly or indirectly agonize, antagonize or perhaps even prime the SMT system to alter transport function. Importantly, TICs are distinguished from drugs and pharmaceuticals that interact with transporters in that exposure is unintended and inherently variant. Here, we review the molecular mechanisms of environmental chemical interaction with SMTs, the methodological considerations for their evaluation, and the future directions for TIC discovery.
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Affiliation(s)
- Sascha C.T. Nicklisch
- Department of Environmental Toxicology, University of California, Davis, Davis, CA 95616
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202
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Polystyrene adsorbents: rapid and efficient surrogate for dialysis in membrane protein purification. Sci Rep 2020; 10:16334. [PMID: 33005012 PMCID: PMC7529760 DOI: 10.1038/s41598-020-73522-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022] Open
Abstract
Membrane protein purification is a laborious, expensive, and protracted process involving detergents for its extraction. Purifying functionally active form of membrane protein in sufficient quantity is a major bottleneck in establishing its structure and understanding the functional mechanism. Although overexpression of the membrane proteins has been achieved by recombinant DNA technology, a majority of the protein remains insoluble as inclusion bodies, which is extracted by detergents. Detergent removal is essential for retaining protein structure, function, and subsequent purification techniques. In this study, we have proposed a new approach for detergent removal from the solubilized extract of a recombinant membrane protein: human phospholipid scramblase 3 (hPLSCR3). N-lauryl sarcosine (NLS) has been established as an effective detergent to extract the functionally active recombinant 6X-his- hPLSCR3 from the inclusion bodies. NLS removal before affinity-based purification is essential as the detergent interferes with the matrix binding. Detergent removal by adsorption onto hydrophobic polystyrene beads has been methodically studied and established that the current approach was 10 times faster than the conventional dialysis method. The study established the potency of polystyrene-based beads as a convenient, efficient, and alternate tool to dialysis in detergent removal without significantly altering the structure and function of the membrane protein.
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14
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Müller GA, Tschöp MH, Müller TD. Upregulated phospholipase D activity toward glycosylphosphatidylinositol-anchored proteins in micelle-like serum complexes in metabolically deranged rats and humans. Am J Physiol Endocrinol Metab 2020; 318:E462-E479. [PMID: 31961708 DOI: 10.1152/ajpendo.00504.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-AP) with the complete glycolipid anchor attached have previously been shown to be released from the outer plasma membrane leaflet of rat adipocytes in positive correlation to cell size and blood glucose/insulin levels of the donor rats. Furthermore, they are present in rat and human serum, however, at amounts that are lower in insulin-resistant/obese rats compared with normal ones. These findings prompted further evaluation of the potential of full-length GPI-AP for the prediction and stratification of metabolically deranged states. A comparison of the signatures of horizontal surface acoustic waves that were generated by full-length GPI-AP in the course of their specific capture by and subsequent dissociation from a chip-based sensor between those from rat serum and those reconstituted into lipidic structures strongly argues for expression of full-length GPI-AP in serum in micelle-like complexes in concert with phospholipids, lysophospholipids, and cholesterol. Both the reconstituted and the rat serum complexes were highly sensitive toward mechanical forces, such as vibration. Furthermore, full-length GPI-AP reconstituted into micelle-like complexes represented efficient substrates for cleavage by serum glycosylphosphatidylinositol-specific phospholipase D (GPI-PLD). These findings raised the possibility that the upregulated release of full-length GPI-AP into micelle-like serum complexes from metabolically deranged cells is compensated by elevated GPI-PLD activity. In fact, serum GPI-PLD activity toward full-length GPI-AP in micelle-like complexes, but not in detergent micelles, was positively correlated to early states of insulin resistance and obesity in genetic and diet-induced rat models as well as to the body weight in humans. Moreover, the differences in the degradation of GPI-AP in micelle-like complexes were found to rely in part on the interaction of serum GPI-PLD with an activating serum factor. These data suggest that serum GPI-PLD activity measured with GPI-AP in micelle-like complexes is indicative of enhanced release of full-length GPI-AP from relevant tissues into the circulation as a consequence of early metabolic derangement in rats and humans.
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Affiliation(s)
- Günter A Müller
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
- Department Biology I, Genetics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
- Division of Metabolic Diseases, Department of Medicine, Technische Universität München, München, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Eberhard Karls University Hospitals and Clinics, Tübingen, Germany
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15
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Baba T, Takagi T, Sumaru K, Kanamori T. Effect of the fluorination degree of partially fluorinated octyl-phosphocholine surfactants on their interfacial properties and interactions with purple membrane as a membrane protein model. Chem Phys Lipids 2020; 227:104870. [DOI: 10.1016/j.chemphyslip.2020.104870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/02/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022]
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16
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Elbahnasawy MA, Farag MMS, Mansour MT, El-Ghamery AA. Cloning, expression and nanodiscs assemble of recombinant HIV-1 gp41. Microb Pathog 2019; 138:103824. [PMID: 31669502 DOI: 10.1016/j.micpath.2019.103824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023]
Abstract
Structural studies of membrane proteins have been hurdled by their difficulty for expression in heterogeneous expression systems due to their intrinsically strong hydrophobicity and requirements for association with other cellular membranes. This study aims to design a construct for expression of membrane proteins. Because of its outstanding interest in HIV-1 vaccine design, transmembrane gp41 amino acid residue 662-723 was chosen as a representative membrane protein. Therefore, we constructed expression vectors for expression of gp41(662-723) alone (pET28a-gp41(662-723)) or coupled with a fusion partner: GB1 (pET30a-GB1-gp41(662-723)) and Trx (pET32a-Trx-gp41(662-723)). For enhancing protein expression, the expression plasmids were transformed into E. coli BL-21 (DE3), E. coli T7 Express lysY/Iq and E. coli Lemo21 (DE3). Interestingly, HIV-1 gp41(662-723) was expressed as a C-terminus fusion to the fusion partner Trx (Trx-gp41(662-723)) with an apparent molecular mass of 21.8 kDa. Trx-gp41(662-723) was overexpressed into E. coli T7 Express lysY/Iq by early induction as OD600 ~0.5 followed by incubation at 20 °C/overnight. Our data demonstrated that almost all recombinant Trx-gp41(662-723) was incorporated into lipid nanodiscs by slowing down the nanodiscs assembly process. Negative-stained electron micrographs revealed homogenous 10 nm Trx-gp41(662-723)-nanodiscs. While the neutralizing epitopes in the purified Trx-gp41(662-723) were accessible and recognizable by anti-MPER bNAbs, these epitopes became less accessibly exposed, particularly in the C-terminal region of MPER, after incorporation of Trx-gp41(662-723) into nanodiscs.
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Affiliation(s)
- Mostafa A Elbahnasawy
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA; Immunology Lab, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
| | - Mohamed M S Farag
- Immunology Lab, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
| | - Mohamed T Mansour
- Molecular Virology Lab, Children's Cancer Hospital Egypt-57357, NCI, Cairo university, Cairo, 11562, Egypt
| | - Abbas A El-Ghamery
- Cytology Lab, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
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17
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Kwon OS, Song HS, Park TH, Jang J. Conducting Nanomaterial Sensor Using Natural Receptors. Chem Rev 2018; 119:36-93. [DOI: 10.1021/acs.chemrev.8b00159] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oh Seok Kwon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Nanobiotechnology and Bioinformatics (Major), University of Science & Technology (UST), Daejon 34141, Republic of Korea
| | - Hyun Seok Song
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Cheongju 28119, Republic of Korea
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jyongsik Jang
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
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18
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Carvalho V, Pronk JW, Engel AH. Characterization of Membrane Proteins Using Cryo-Electron Microscopy. ACTA ACUST UNITED AC 2018; 94:e72. [PMID: 30199146 DOI: 10.1002/cpps.72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The steep increase of atomic scale structures determined by 3D cryo-electron microscopy (EM) deposited in the EMDataBank documents progress of a methodology that was frustratingly slow ten years ago. While sample vitrification on grids has been successfully used in all EM laboratories for decades, beam damage remains a road block. Developments in instrumentation and software to exploit the information carried by elastically scattered electrons made the task to achieve atomic scale resolution easier. This together with the development of fast single electron detecting cameras has resulted in unprecedented possibilities for structure determination by 3D cryo-EM. With such technologies in place, the purification of membrane protein complexes in a functional state is key to collecting atomic scale structural information and insight into the chemistry of physiological processes. Therefore, we focus here on the preparation of membrane proteins for structural analyses by 3D cryo-EM and the data acquisition of such vitrified samples. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Vanessa Carvalho
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Joachim W Pronk
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Andreas H Engel
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
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19
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Schmidt P, Bender BJ, Kaiser A, Gulati K, Scheidt HA, Hamm HE, Meiler J, Beck-Sickinger AG, Huster D. Improved in Vitro Folding of the Y 2 G Protein-Coupled Receptor into Bicelles. Front Mol Biosci 2018; 4:100. [PMID: 29387686 PMCID: PMC5776092 DOI: 10.3389/fmolb.2017.00100] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/28/2017] [Indexed: 12/26/2022] Open
Abstract
Prerequisite for structural studies on G protein-coupled receptors is the preparation of highly concentrated, stable, and biologically active receptor samples in milligram amounts of protein. Here, we present an improved protocol for Escherichia coli expression, functional refolding, and reconstitution into bicelles of the human neuropeptide Y receptor type 2 (Y2R) for solution and solid-state NMR experiments. The isotopically labeled receptor is expressed in inclusion bodies and purified using SDS. We studied the details of an improved preparation protocol including the in vitro folding of the receptor, e.g., the native disulfide bridge formation, the exchange of the denaturating detergent SDS, and the functional reconstitution into bicelle environments of varying size. Full pharmacological functionality of the Y2R preparation was shown by a ligand affinity of 4 nM and G-protein activation. Further, simple NMR experiments are used to test sample quality in high micromolar concentration.
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Affiliation(s)
- Peter Schmidt
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Brian J Bender
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Holger A Scheidt
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | | | - Daniel Huster
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
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20
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Lacabanne D, Lends A, Danis C, Kunert B, Fogeron ML, Jirasko V, Chuilon C, Lecoq L, Orelle C, Chaptal V, Falson P, Jault JM, Meier BH, Böckmann A. Gradient reconstitution of membrane proteins for solid-state NMR studies. JOURNAL OF BIOMOLECULAR NMR 2017; 69:81-91. [PMID: 28900789 DOI: 10.1007/s10858-017-0135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR. NMR spectra recorded on a sample produced by GRecon showed a highly similar fingerprint as those recorded previously on samples reconstituted by dialysis. GRecon sample preparation presents a gain in time of nearly an order of magnitude for reconstitution, and shall represent a valuable alternative in solid-state NMR membrane protein sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Alons Lends
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Clément Danis
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vlastimil Jirasko
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France.
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21
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Rosier P, Gélébart F, Dumesnil N, Esnot G, Dezi M, Morand M, Vénien-Bryan C. The CRACAM Robot: Two-Dimensional Crystallization of Membrane Protein. Methods Mol Biol 2017; 1635:303-316. [PMID: 28755376 DOI: 10.1007/978-1-4939-7151-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Membrane proteins are key cellular components that perform essential functions. They are major therapeutic targets. Electron crystallography can provide structural experimental information at atomic scale for membrane proteins forming two-dimensional (2D) crystals. There are two different methods to produce 2D crystals of membrane proteins. (1) either directly in the bulk of the solution (2) or under a lipid monolayer at the air-water interface. This extra lipid monolayer helps to pre-orient the proteins in order to facilitate the growth of 2D crystals. We present here these two methods for 2D crystallization of membrane proteins implemented in a fully automated robot called CRACAM. These methods require small volume of low concentration of proteins, making it possible to explore more conditions with the same amount of protein. These automated methods outperform traditional 2D crystallization approaches in terms of accuracy, flexibility, and throughput.
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Affiliation(s)
- Philippe Rosier
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Frédéric Gélébart
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Nicolas Dumesnil
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Gauthier Esnot
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Manuela Dezi
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Marc Morand
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France
| | - Catherine Vénien-Bryan
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, UMR 7590 CNRS-UPMC-MNHN-IRD Case Courrier 115, 4 Place Jussieu, 75252, Paris, Cédex 05, France.
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22
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Assay of Flippase Activity in Proteoliposomes Using Fluorescent Lipid Derivatives. Methods Mol Biol 2016; 1377:181-91. [PMID: 26695033 DOI: 10.1007/978-1-4939-3179-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Specific membrane proteins, termed lipid flippases, play a central role in facilitating the movement of lipids across cellular membranes. In this protocol, we describe the reconstitution of ATP-driven lipid flippases in liposomes and the analysis of their in vitro flippase activity based on the use of fluorescent lipid derivatives. Working with purified and reconstituted systems provides a well-defined experimental setup and allows to directly characterize these membrane proteins at the molecular level.
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23
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Goparaju G, Fry BA, Chobot SE, Wiedman G, Moser CC, Leslie Dutton P, Discher BM. First principles design of a core bioenergetic transmembrane electron-transfer protein. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:503-512. [PMID: 26672896 PMCID: PMC4846532 DOI: 10.1016/j.bbabio.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 11/14/2015] [Accepted: 12/01/2015] [Indexed: 12/26/2022]
Abstract
Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Geetha Goparaju
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Chobot
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory Wiedman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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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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25
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Textor M, Keller S. Calorimetric Quantification of Cyclodextrin-Mediated Detergent Extraction for Membrane-Protein Reconstitution. Methods Enzymol 2016; 567:129-56. [DOI: 10.1016/bs.mie.2015.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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26
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Logez C, Damian M, Legros C, Dupré C, Guéry M, Mary S, Wagner R, M’Kadmi C, Nosjean O, Fould B, Marie J, Fehrentz JA, Martinez J, Ferry G, Boutin JA, Banères JL. Detergent-free Isolation of Functional G Protein-Coupled Receptors into Nanometric Lipid Particles. Biochemistry 2015; 55:38-48. [DOI: 10.1021/acs.biochem.5b01040] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christel Logez
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Marjorie Damian
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Céline Legros
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Clémence Dupré
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Mélody Guéry
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Sophie Mary
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Renaud Wagner
- CNRS
UMR7242, Institut de Recherche de l’ESBS, Biotechnologie et
Signalisation Cellulaire, Université de Strasbourg, 300 Boulevard
Sébastien Brant, 67412 Ilkirch cedex, France
| | - Céline M’Kadmi
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Olivier Nosjean
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jacky Marie
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean-Alain Fehrentz
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean Martinez
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Gilles Ferry
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean A. Boutin
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean-Louis Banères
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
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27
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Cole CM, Brea RJ, Kim YH, Hardy MD, Yang J, Devaraj NK. Spontaneous Reconstitution of Functional Transmembrane Proteins During Bioorthogonal Phospholipid Membrane Synthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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28
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Cole CM, Brea RJ, Kim YH, Hardy MD, Yang J, Devaraj NK. Spontaneous Reconstitution of Functional Transmembrane Proteins During Bioorthogonal Phospholipid Membrane Synthesis. Angew Chem Int Ed Engl 2015; 54:12738-42. [PMID: 26316292 DOI: 10.1002/anie.201504339] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/02/2015] [Indexed: 11/11/2022]
Abstract
Transmembrane proteins are critical for signaling, transport, and metabolism, yet their reconstitution in synthetic membranes is often challenging. Non-enzymatic and chemoselective methods to generate phospholipid membranes in situ would be powerful tools for the incorporation of membrane proteins. Herein, the spontaneous reconstitution of functional integral membrane proteins during the de novo synthesis of biomimetic phospholipid bilayers is described. The approach takes advantage of bioorthogonal coupling reactions to generate proteoliposomes from micelle-solubilized proteins. This method was successfully used to reconstitute three different transmembrane proteins into synthetic membranes. This is the first example of the use of non-enzymatic chemical synthesis of phospholipids to prepare proteoliposomes.
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Affiliation(s)
- Christian M Cole
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Young Hun Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Pacific Hall 6160, La Jolla, CA 92093 (USA)
| | - Michael D Hardy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Pacific Hall 6160, La Jolla, CA 92093 (USA)
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Building: Urey Hall 4120, La Jolla, CA 92093 (USA) http://devarajgroup.ucsd.edu.
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Rupprecht KR, Lang EZ, Gregory SD, Bergsma JM, Rae TD, Fishpaugh JR. A precise spectrophotometric method for measuring sodium dodecyl sulfate concentration. Anal Biochem 2015; 486:78-80. [PMID: 26150094 DOI: 10.1016/j.ab.2015.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/15/2015] [Accepted: 06/06/2015] [Indexed: 10/23/2022]
Abstract
Sodium dodecyl sulfate (SDS) is used to denature and solubilize proteins, especially membrane and other hydrophobic proteins. A quantitative method to determine the concentration of SDS using the dye Stains-All is known. However, this method lacks the accuracy and reproducibility necessary for use with protein solutions where SDS concentration is a critical factor, so we modified this method after examining multiple parameters (solvent, pH, buffers, and light exposure). The improved method is simple to implement, robust, accurate, and (most important) precise.
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Affiliation(s)
- Kevin R Rupprecht
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA.
| | - Ewa Z Lang
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA
| | - Svetoslava D Gregory
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA
| | - Janet M Bergsma
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA
| | - Tracey D Rae
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA
| | - Jeffrey R Fishpaugh
- Diagnostics Analytical Chemistry Research, Abbott Laboratories, Abbott Park, IL 60049, USA
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Stahlberg H, Biyani N, Engel A. 3D reconstruction of two-dimensional crystals. Arch Biochem Biophys 2015; 581:68-77. [PMID: 26093179 DOI: 10.1016/j.abb.2015.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 02/02/2023]
Abstract
Electron crystallography of two-dimensional (2D) crystals determines the structure of membrane proteins in the lipid bilayer by imaging with cryo-electron microscopy and image processing. Membrane proteins can be packed in regular 2D arrays by their reconstitution in the presence of lipids at low lipid to protein weight-to-weight ratio. The crystal quality depends on the protein purity and homogeneity, its stability, and on the crystallization conditions. A 2D crystal presents the membrane protein in a functional and fully lipidated state. Electron crystallography determines the 3D structure even of small membrane proteins up to atomic resolution, but 3D density maps have a better resolution in the membrane plane than in the vertical direction. This problem can be partly eliminated by applying an iterative algorithm that exploits additional known constraints about the 2D crystal. 2D electron crystallography is particularly attractive for the structural analysis of membrane proteins that are too small for single particle analyses and too unstable to form 3D crystals. With the recent introduction of direct electron detector cameras, the routine determination of the atomic 3D structure of membrane-embedded membrane proteins is in reach.
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Affiliation(s)
- Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Engel
- Department of BioNanoscience, Delft University of Technology, Van der Waalsweg 8, 2628 CH Delft, The Netherlands; Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Wood Bldg 321D, Cleveland, OH 44106-4965, USA.
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31
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Uddin YM, Schmidt-Krey I. Inducing two-dimensional crystallization of membrane proteins by dialysis for electron crystallography. Methods Enzymol 2015; 557:351-62. [PMID: 25950973 DOI: 10.1016/bs.mie.2014.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron crystallography is an electron cryo-microscopy (cryo-EM) method that is particularly suitable for structure-function studies of small membrane proteins, which are crystallized in two-dimensional (2D) arrays for subsequent cryo-EM data collection and image processing. This approach allows for structural analysis of membrane proteins in a close-to-native, phospholipid bilayer environment. The process of growing 2D crystals from purified membrane proteins by dialysis detergent removal is described in this chapter. A short section covers screening for and identifying 2D crystals by transmission electron microscopy, and in the last section, optimization of the purification to obtain crystals of higher quality is discussed.
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Affiliation(s)
- Yusuf M Uddin
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ingeborg Schmidt-Krey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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Textor M, Vargas C, Keller S. Calorimetric quantification of linked equilibria in cyclodextrin/lipid/detergent mixtures for membrane-protein reconstitution. Methods 2015; 76:183-193. [DOI: 10.1016/j.ymeth.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/30/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022] Open
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Quantification of detergent using colorimetric methods in membrane protein crystallography. Methods Enzymol 2015; 557:95-116. [PMID: 25950961 DOI: 10.1016/bs.mie.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Membrane protein crystallography has the potential to greatly aid our understanding of membrane protein biology. Yet, membrane protein crystals remain challenging to produce. Although robust methods for the expression and purification of membrane proteins continue to be developed, the detergent component of membrane protein samples is equally important to crystallization efforts. This chapter describes the development of three colorimetric assays for the quantitation of detergent in membrane protein samples and provides detailed protocols. All of these techniques use small sample volumes and have potential applications in crystallography. The application of these techniques in crystallization prescreening, detergent concentration modification, and detergent exchange experiments is demonstrated. It has been observed that the concentration of detergent in a membrane protein sample can be just as important as the protein concentration when attempting to reproduce crystallization lead conditions.
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Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai Z, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. J Struct Biol 2014; 189:123-34. [PMID: 25478971 DOI: 10.1016/j.jsb.2014.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023]
Abstract
Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.
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Affiliation(s)
- R Lasala
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - N Coudray
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - A Abdine
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Z Zhang
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - M Lopez-Redondo
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - R Kirshenbaum
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - J Alexopoulos
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Z Zolnai
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - D L Stokes
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - I Ubarretxena-Belandia
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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35
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Jahnke N, Krylova OO, Hoomann T, Vargas C, Fiedler S, Pohl P, Keller S. Real-time monitoring of membrane-protein reconstitution by isothermal titration calorimetry. Anal Chem 2013; 86:920-7. [PMID: 24354292 PMCID: PMC3886389 DOI: 10.1021/ac403723t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
Phase diagrams offer a wealth of
thermodynamic information on aqueous
mixtures of bilayer-forming lipids and micelle-forming detergents,
providing a straightforward means of monitoring and adjusting the
supramolecular state of such systems. However, equilibrium phase diagrams
are of very limited use for the reconstitution of membrane proteins
because of the occurrence of irreversible, unproductive processes
such as aggregation and precipitation that compete with productive
reconstitution. Here, we exemplify this by dissecting the effects
of the K+ channel KcsA on the process of bilayer self-assembly
in a mixture of Escherichia coli polar lipid extract
and the nonionic detergent octyl-β-d-glucopyranoside.
Even at starting concentrations in the low micromolar range, KcsA
has a tremendous impact on the supramolecular organization of the
system, shifting the critical lipid/detergent ratios at the onset
and completion of vesicle formation by more than 2-fold. Thus, equilibrium
phase diagrams obtained for protein-free lipid/detergent mixtures
would be misleading when used to guide the reconstitution process.
To address this issue, we demonstrate that, even under such nonequilibrium
conditions, high-sensitivity isothermal titration calorimetry can
be exploited to monitor the progress of membrane-protein reconstitution
in real time, in a noninvasive manner, and at high resolution to yield
functional proteoliposomes with a narrow size distribution for further
downstream applications.
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Affiliation(s)
- Nadin Jahnke
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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Wang L, Quan C, Liu B, Wang J, Xiong W, Zhao P, Fan S. Functional reconstitution of Staphylococcus aureus truncated AgrC histidine kinase in a model membrane system. PLoS One 2013; 8:e80400. [PMID: 24303011 PMCID: PMC3841183 DOI: 10.1371/journal.pone.0080400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The integral membrane protein AgrC is a histidine kinase whose sensor domains interact with an autoinducing peptide, resulting in a series of downstream responses. In this study, truncated AgrCTM5-6C and AgrCTM5-6C-GFP with GFP as a reporter gene were produced using a bacterial system. Purified AgrCTM5-6C and AgrCTM5-6C-GFP were reconstituted into liposomes by a detergent-mediated method. To achieve high-yield protein incorporation, we investigated the effect of different detergents on protein reconstitution efficiency. The highest incorporation was found with N,N-dimethyldode-cylamine N-oxide during complete liposome solubilization, which resulted in a yield of 85±5%. The COOH-terminus of the protein AgrCTM5-6C was almost exclusively oriented towards the inside of the vesicles. AgrCTM5-6C in proteoliposomes exhibited approximately a 6-fold increase in constitutive activity compared with AgrCTM5-6C in detergent micelles. The reconstitution of AgrCTM5-6C or AgrCTM5-6C-GFP was characterized using dynamic light scattering, fluorescence microscopy, and transmission electron microscopy. Based on the results, the optimal conditions for protein incorporation were defined. These findings contribute to the study of membrane protein structure and function in vitro using a reconstitution system.
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Affiliation(s)
- Lina Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
- * E-mail:
| | - Baoquan Liu
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Jianfeng Wang
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Wen Xiong
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Pengchao Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Shengdi Fan
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
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37
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Soto-Arriaza M, Olivares-Ortega C, Quina F, Aguilar L, Sotomayor C. Effect of cholesterol content on the structural and dynamic membrane properties of DMPC/DSPC large unilamellar bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2763-9. [DOI: 10.1016/j.bbamem.2013.07.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 07/02/2013] [Accepted: 07/31/2013] [Indexed: 12/15/2022]
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38
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Das N, Murray DT, Cross TA. Lipid bilayer preparations of membrane proteins for oriented and magic-angle spinning solid-state NMR samples. Nat Protoc 2013; 8:2256-70. [PMID: 24157546 DOI: 10.1038/nprot.2013.129] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Solid-state NMR spectroscopy has been used successfully for characterizing the structure and dynamics of membrane proteins as well as their interactions with other proteins in lipid bilayers. Such an environment is often necessary for achieving native-like structures. Sample preparation is the key to this success. Here we present a detailed description of a robust protocol that results in high-quality membrane protein samples for both magic-angle spinning and oriented-sample solid-state NMR. The procedure is demonstrated using two proteins: CrgA (two transmembrane helices) and Rv1861 (three transmembrane helices), both from Mycobacterium tuberculosis. The success of this procedure relies on two points. First, for samples for both types of NMR experiment, the reconstitution of the protein from a detergent environment to an environment in which it is incorporated into liposomes results in 'complete' removal of detergent. Second, for the oriented samples, proper dehydration followed by rehydration of the proteoliposomes is essential. By using this protocol, proteoliposome samples for magic-angle spinning NMR and uniformly aligned samples (orientational mosaicity of <1°) for oriented-sample NMR can be obtained within 10 d.
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Affiliation(s)
- Nabanita Das
- 1] Institute of Molecular Biophysics (IMB), Florida State University (FSU), Tallahassee, Florida, USA. [2] National High Magnetic Field Laboratory (NMHFL), FSU, Tallahassee, Florida, USA
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39
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Cord factor (trehalose 6,6′-dimycolate) forms fully stable and non-permeable lipid bilayers required for a functional outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2173-81. [DOI: 10.1016/j.bbamem.2013.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/22/2022]
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40
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Nannenga BL, Iadanza MG, Vollmar BS, Gonen T. Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.15. [PMID: 23546618 PMCID: PMC3850493 DOI: 10.1002/0471140864.ps1715s72] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.
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Affiliation(s)
- Brent L Nannenga
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
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41
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Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents. Proc Natl Acad Sci U S A 2013; 110:7276-81. [PMID: 23589883 DOI: 10.1073/pnas.1303857110] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs.
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42
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Johnson MC, Dreaden TM, Kim LY, Rudolph F, Barry BA, Schmidt-Krey I. Two-dimensional crystallization of membrane proteins by reconstitution through dialysis. Methods Mol Biol 2013; 955:31-58. [PMID: 23132054 DOI: 10.1007/978-1-62703-176-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Studies of membrane proteins by two-dimensional (2D) crystallization and electron crystallography have provided crucial information on the structure and function of a rapidly growing number of these intricate proteins within a close-to-native lipid bilayer. Here we provide protocols for planning and executing 2D crystallization trials by detergent removal through dialysis, including the preparation of phospholipids and the dialysis setup. General factors to be considered, such as the protein preparation, solubilizing detergent, lipid for reconstitution, and buffer conditions are discussed. Several 2D crystallization conditions are highlighted that have shown great promise to grow 2D crystals within a surprisingly short amount of time. Finally, conditions for optimizing order and size of 2D crystals are outlined.
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Affiliation(s)
- Matthew C Johnson
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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43
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44
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Abstract
Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.
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45
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Two-dimensional crystalline array formation of glucuronide transporter from Escherichia coli by the use of polystyrene beads for detergent removal. J Membr Biol 2012. [PMID: 23188061 DOI: 10.1007/s00232-012-9521-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
n-Dodecyl-β-D-maltoside solubilized glucuronide transporter (GusB), the product of gusB gene from Escherichia coli, was treated with Bio-Beads as an agent for removing the detergent from a micellar solution under suitable combination with dimyristoylphosphatidylcholine. Optimizing conditions led to a two-dimensional crystalline array formation of GusB. The crystalline arrays appear to have a hexagonal lattice with layer group P6, the unit cell dimensions of a = b = 13.8 nm and γ = 120°. Each stain-protruding periodic unit showed approximately 11.8 ± 0.3 nm in a diameter in the inverse Fourier-filtered image to have formed with pentameric GusB (5 × 49.7 kDa).
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46
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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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Teboul D, Beaufils S, Taveau JC, Iatmanen-Harbi S, Renault A, Venien-Bryan C, Vie V, Lacapere JJ. Mouse TSPO in a lipid environment interacting with a functionalized monolayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2791-800. [PMID: 22771765 DOI: 10.1016/j.bbamem.2012.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/11/2012] [Accepted: 06/26/2012] [Indexed: 12/28/2022]
Abstract
Translocator protein TSPO is a membrane protein highly conserved in evolution which does not belong to any structural known family. TSPO is involved in physiological functions among which transport of molecules such as cholesterol to form steroids and bile salts in mammalian cells. Membrane protein structure determination remains a difficult task and needs concomitant approaches (for instance X-ray- or Electron-crystallography and NMR). Electron microscopy and two-dimensional crystallization under functionalized monolayers have been successfully developed for recombinant tagged proteins. The difficulty comes from the detergent carried by membrane proteins that disrupt the lipid monolayer. We identified the best conditions for injecting the histidine tagged recombinant TSPO in detergent in the subphase and to keep the protein stable. Reconstituted recombinant protein into a lipid bilayer favors its adsorption to functionalized monolayers and limits the disruption of the monolayer by reducing the amount of detergent. Finally, we obtained the first transmission electron microscopy images of recombinant mouse TSPO negatively stained bound to the lipid monolayer after injection into the subphase of pre-reconstituted TSPO in lipids. Image analysis reveals that circular objects could correspond to an association of at least four monomers of mouse TSPO. The different amino acid compositions and the location of the polyhistidine tag between bacterial and mouse TSPO could account for the formation of dimer versus tetramer, respectively. The difference in the loop between the first and second putative transmembrane domain may contribute to distinct monomer interaction, this is supported by differences in ligand binding parameters and biological functions of both proteins.
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Aguilar LF, Pino JA, Soto-Arriaza MA, Cuevas FJ, Sánchez S, Sotomayor CP. Differential dynamic and structural behavior of lipid-cholesterol domains in model membranes. PLoS One 2012; 7:e40254. [PMID: 22768264 PMCID: PMC3386959 DOI: 10.1371/journal.pone.0040254] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 06/04/2012] [Indexed: 12/15/2022] Open
Abstract
Changes in the cholesterol (Chol) content of biological membranes are known to alter the physicochemical properties of the lipid lamella and consequently the function of membrane-associated enzymes. To characterize these changes, we used steady-state and time resolved fluorescence spectroscopy and two photon-excitation microscopy techniques. The membrane systems were chosen according to the techniques that were used: large unilamellar vesicles (LUVs) for cuvette and giant unilamellar vesicles (GUVs) for microscopy measurements; they were prepared from dipalmitoyl phosphatidylcholine (DPPC) and dioctadecyl phosphatidylcholine (DOPC) in mixtures that are well known to form lipid domains. Two fluorescent probes, which insert into different regions of the bilayer, were selected: 1,6-diphenyl-1,3,5-hexatriene (DPH) was located at the deep hydrophobic core of the acyl chain regions and 2-dimethylamino-6-lauroylnaphthalene (Laurdan) at the hydrophilic-hydrophobic membrane interface. Our spectroscopy results show that (i) the changes induced by cholesterol in the deep hydrophobic phospholipid acyl chain domain are different from the ones observed in the superficial region of the hydrophilic-hydrophobic interface, and these changes depend on the state of the lamella and (ii) the incorporation of cholesterol into the lamella induces an increase in the orientation dynamics in the deep region of the phospholipid acyl chains with a corresponding decrease in the orientation at the region close to the polar lipid headgroups. The microscopy data from DOPC/DPPC/Chol GUVs using Laurdan generalized polarization (Laurdan GP) suggest that a high cholesterol content in the bilayer weakens the stability of the water hydrogen bond network and hence the stability of the liquid-ordered phase (Lo).
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Affiliation(s)
- Luis F Aguilar
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: An alternative to gel-based approaches. Anal Biochem 2012; 424:97-107. [DOI: 10.1016/j.ab.2012.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 11/19/2022]
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Wisedchaisri G, Reichow SL, Gonen T. Advances in structural and functional analysis of membrane proteins by electron crystallography. Structure 2012; 19:1381-93. [PMID: 22000511 DOI: 10.1016/j.str.2011.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/01/2011] [Accepted: 09/06/2011] [Indexed: 12/27/2022]
Abstract
Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.
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Affiliation(s)
- Goragot Wisedchaisri
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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